pax_global_header00006660000000000000000000000064136077775510014534gustar00rootroot0000000000000052 comment=db4c833f0d1366de1f107af1ec6451c6233d4494 thesias-3.1.1/000077500000000000000000000000001360777755100131765ustar00rootroot00000000000000thesias-3.1.1/.gitignore000066400000000000000000000000361360777755100151650ustar00rootroot00000000000000*.o *.so *.so.* *.jar class/* thesias-3.1.1/.travis.yml000066400000000000000000000010211360777755100153010ustar00rootroot00000000000000language: c jobs: include: - os: linux dist: bionic - os: osx jdk: openjdk11 before_install: - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get update ; fi - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get install -y default-jdk-headless ; fi - if [ "$TRAVIS_OS_NAME" = "osx" ]; then if [[ ! -n $JAVA_HOME ]]; then export JAVA_HOME="/Library/Java/JavaVirtualMachines/openjdk-13.0.1.jdk/Contents/Home" ; fi ; fi install: - echo $JAVA_HOME - java --version script: - make - ls -R thesias-3.1.1/LICENSE000066400000000000000000001045151360777755100142110ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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But first, please read . thesias-3.1.1/Makefile000066400000000000000000000031341360777755100146370ustar00rootroot00000000000000#!/usr/bin/make -f CC ?= gcc CFLAGS ?= -O2 CPPFLAGS ?= LDFLAGS ?= JAVA_HOME ?=/usr/lib/jvm/default-java UNAME_S ?=$(shell uname -s | tr '[:upper:]' '[:lower:]') LIBNAME =libthesiaslib SOVERSION =0 SONAME =${LIBNAME}.so.${SOVERSION} CFLAGS += -fPIC -I${JAVA_HOME}/include -I${JAVA_HOME}/include/${UNAME_S}/ CPPFLAGS += LDFLAGS += -shared -fPIC ifeq ($(UNAME_S), darwin) LDFLAGS += -Wl,-install_name,${SONAME} else LDFLAGS += -Wl,-soname,${SONAME} endif export JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8 PREFIX = /usr all: thesias thesias: libthesiaslib.so thesias.jar libthesiaslib.so: ${CC} ${CPPFLAGS} ${CFLAGS} -c src/*.c ${CC} ${LDFLAGS} *.o -o ${SONAME} thesias.jar: javac -d class java/*.java jar cfe thesias.jar GraficT -C class . -C misc LogoThesias.png .PHONY: clean install uninstall install: install -d $(DESTDIR)$(PREFIX)/lib/jni/ install ${SONAME} $(DESTDIR)$(PREFIX)/lib/jni/ install -d $(DESTDIR)$(PREFIX)/share/java/ install thesias.jar $(DESTDIR)$(PREFIX)/share/java/ install -d $(DESTDIR)$(PREFIX)/bin/ install misc/THESIAS $(DESTDIR)$(PREFIX)/bin/ install -d $(DESTDIR)$(PREFIX)/share/man/man1/ install misc/THESIAS.1 $(DESTDIR)$(PREFIX)/share/man/man1/ ln -s $(DESTDIR)$(PREFIX)/lib/jni/${SONAME} $(DESTDIR)$(PREFIX)/lib/jni/${LIBNAME}.so uninstall: rm -f $(DESTDIR)$(PREFIX)/lib/jni/${SONAME} rm -f $(DESTDIR)$(PREFIX)/lib/jni/${LIBNAME}.so rm -f $(DESTDIR)$(PREFIX)/share/java/thesias.jar rm -f $(DESTDIR)$(PREFIX)/bin/THESIAS rm -f $(DESTDIR)$(PREFIX)/share/man/man1/THESIAS.1 clean: rm -f *.o rm -f *.so rm -f *.so.* rm -f *.jar rm -rf class/ thesias-3.1.1/README.md000066400000000000000000000027611360777755100144630ustar00rootroot00000000000000

THESIAS

**THESIAS** (**Testing Haplotype EffectS In Association Studies**) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. ## Changes - 2020/01/16: **3.1.1** - Clarify license with GPL-3+. - Update contact email address. - New makefile. - 2007: **3.1** - [Download archive](https://github.com/daissi/thesias/releases/download/3.1/ThesiasPackage.zip) ## License THESIAS is licensed under [GPL-3+](LICENSE). ## References - D.A. Trégouët and V. Garelle, *Bioinformatics* (2007), [A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies](https://dx.doi.org/10.1093/bioinformatics/btm058). - D.A. Trégouët and L. Tiret, *European Journal of Human Genetics* (2004), [Cox proportional hazards survival regression in haplotype-based association analysis using the Stochastic-EM algorithm](https://dx.doi.org/10.1038/sj.ejhg.5201238). - D.A. Trégouët et al., *Human Molecular Genetics* (2002), [Specific haplotypes of the P-selectin gene are associated with myocardial infarction](https://doi.org/10.1093/hmg/11.17.2015). thesias-3.1.1/examples/000077500000000000000000000000001360777755100150145ustar00rootroot00000000000000thesias-3.1.1/examples/Readme.txt000066400000000000000000000070321360777755100167540ustar00rootroot00000000000000 The THESIAS program "Testing Haplotype Effects In Association Studies" by Tregouet David-Alexandre (david.tregouet@chups.jussieu.fr) INSERM U525, Genetic Epidemiology and Molecular of Cardiovascular Pathologies Paris, France /*THESIAS program was updated on Tuesday 21st february 2006 : Haplotype analysis of a categorical phenotype is now possible by use of a polytomous formulation. Besides, X-linked SNPs analysis is now available for case-control and quantitative analysis. */ ************************************************************************************************** The objectif of the THESIAS program is to performed haplotype-based association analysis in unrelated individuals. This program is based on the maximum likelihood model described in Tregouet et al. 2002 and is linked to the SEM algorithm (Tregouet et al. 2004). THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, quantitative, qualitative, categorical and survival outcome can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. Every information on how to run THESIAS and on what THESIAS do can be found in the Documentation3.1.htm File. In order to illustrate the use of the THESIAS program, several .txt and .html files are available for download through the example.zip file. ************************************************************************************************** The Data.txt file includes one quantitative phenotype (in position 2),two polymorphisms (in position 3 and 4) and two additional covariates (in position 5 and 6). In the Answer0.txt file are given the appropriate responses to be given to THESIAS in order to get the parameter file (para.txt). The results files should then be similar to para0.txt, result0.txt and result0.htm In the Answer1.txt file are given the appropriate responses to be given to THESIAS in order to get the loglikelihood of a model testing the effect of the two covariates on the phenotype but with no haplotype effects. The results files should then be similar to result1.txt and result1.htm . If one wants to further estimate haplotype effects, para.txt must have to be modified as in para1.txt . Then run the THESIAS program with the responses given in the answer2.txt file. The results files should then be similar to result2.txt and result2.htm . ************************************************************************************************** In order to illustrate the use of the extended THESIAS program for survival outcome analysis, several .txt files are available for download through the example2.zip file. The data.dat file includes one censored phenotype (in position 3) with its associated survival time (in position 4),six polymorphisms (in position 5 to 10) and three additional covariates (in position 11 to 13). In the Answer0.txt file are given the appropriate responses to be given to THESIAS in order to get the parameter file (para.txt). The results files should then be similar to para0.txt, result0.txt In the Answer1.txt file are given the appropriate responses to be given to THESIAS in order to get the loglikelihood of a model testing the effects of the five most frequent haplotypes. The results file should then be similar to result1.txt. ************************************************************************************************** thesias-3.1.1/examples/dataset1/000077500000000000000000000000001360777755100165225ustar00rootroot00000000000000thesias-3.1.1/examples/dataset1/answer0.txt000066400000000000000000000000371360777755100206420ustar00rootroot00000000000000data.txt 6 2 3 4 y n 0 thesias-3.1.1/examples/dataset1/answer1.txt000066400000000000000000000000611360777755100206400ustar00rootroot00000000000000data.txt 6 2 3 4 y n 2 2 y 2 5 6 n thesias-3.1.1/examples/dataset1/answer2.txt000066400000000000000000000000751360777755100206460ustar00rootroot00000000000000data.txt 6 2 3 4 y n 2 2 y 2 5 6 y n n n n thesias-3.1.1/examples/dataset1/data.txt000066400000000000000000000475041360777755100202060ustar00rootroot000000000000001 0.44 0 0 2 0.02978 2 0.64 GG CC 2 0.37342 3 0.51 0 0 2 -1.1157 4 0.56 0 CC 2 0.37342 5 0.555 GG TT 1 0.48797 6 0.495 GG CC 2 1.63345 7 0.45 GG CC 2 0.14433 8 0.575 0 0 1 -.31386 9 0.685 GG CC 1 0.83162 10 0.58 GA CC 1 -.31386 11 0.535 GA 0 1 0.71707 12 0.495 GA CC 2 -.54296 13 0.55 0 0 2 2.09164 14 0.455 GA 0 2 0.14433 15 0.635 GG CC 2 0.94616 16 0.395 GG TT 2 -2.1466 17 0.445 GG CC 1 -1.3448 18 0.605 GA CT 1 0.14433 19 0.46 AA CT 1 -.31386 20 0.5 GA CC 2 0.02978 21 0.515 GA CC 1 0.25888 22 0.685 GA CT 1 1.63345 23 0.515 GG CT 1 0.25888 24 0.575 GG CT 2 0.71707 25 0.645 GA CT 2 1.17526 26 0.42 GA CT 2 -.88660 27 0.5 GG CT 2 0.37342 28 0.51 GG CT 1 -.54296 29 0.44 GG CC 2 -.42841 30 0.45 GA TT 1 -1.6884 31 0.49 GG TT 2 -.88660 32 0.485 AA CC 2 0.25888 33 0.51 GG TT 1 -.54296 34 0.505 GG CC 2 -.77205 35 0.41 GA CT 2 -1.4593 36 0.445 GA CC 2 -.42841 37 0.55 GG TT 2 1.63345 38 0.435 AA CT 1 -1.3448 39 0.485 AA CT 2 -.31386 40 0.44 GA 0 2 0.02978 41 0.685 GG CC 1 2.09164 42 0.42 0 0 2 -.65750 43 0.585 0 0 2 -.65750 44 0.475 GA CT 2 0.37342 45 0.55 GG CC 2 1.40435 46 0.455 GG CT 2 -.88660 47 0.41 GA CT 2 -.54296 48 0.44 GG CT 2 -.31386 49 0.445 GA CC 2 0.25888 50 0.585 0 0 1 0.14433 51 0.785 GG TT 2 1.40435 52 0.52 GG CC 2 -1.0011 53 0.46 GG TT 1 -1.5739 54 0.505 GG CT 2 -.77205 55 0.58 GA CC 2 0.60252 56 0.43 GG CT 1 -.54296 57 0.455 GG CC 2 0.83162 58 0.425 GG CC 2 -.54296 59 0.83 0 CT 1 1.63345 60 0.43 GA TT 1 -.77205 61 0.535 GA CC 1 0.83162 62 0.49 GA CC 1 0.14433 63 0.585 0 0 2 -.54296 64 0.525 GA CC 2 1.63345 65 0.5 GG CT 1 -.19931 66 0.58 GG CT 1 -.42841 67 0.475 GA CC 1 0.02978 68 0.505 0 TT 2 -.77205 69 0.59 GG CT 2 2.09164 70 0.5 GA TT 2 -1.0011 71 0.455 GG CT 1 -1.0011 72 0.465 GA CT 1 -.42841 73 0.605 GG CT 1 0.60252 74 0.575 GA CC 2 1.28981 75 0.525 GG CC 2 0.94616 76 0.53 GG CT 1 0.71707 77 0.59 0 0 2 -.42841 78 0.63 GG CT 1 0.60252 79 0.765 GG CT 1 0.37342 80 0.535 GG CC 2 -.08477 81 0.465 GG TT 1 0.37342 82 0.59 0 CC 2 0.37342 83 0.64 0 CT 1 2.43528 84 0.545 GG CC 2 -.54296 85 0.505 0 CC 2 -.19931 86 0.575 GA CC 1 -.08477 87 0.61 GG CT 2 0.25888 88 0.71 GA CT 1 1.51890 89 0.445 GG TT 1 -.88660 90 0.565 GG 0 1 1.63345 91 0.785 GG TT 1 1.28981 92 0.48 GG CT 1 -.42841 93 0.545 GG CT 1 -1.3448 94 0.67 GG CC 1 1.17526 95 0.415 0 CT 2 -1.1157 96 0.56 GG TT 2 1.51890 97 0.5 GG 0 2 0.02978 98 0.45 GG TT 2 0.71707 99 0.495 GA 0 2 -.54296 100 0.505 GG CC 2 -1.0011 101 0.47 GG CT 1 -.54296 102 0.565 0 CT 1 -1.3448 103 0.51 GG CT 2 0.83162 104 0.54 GG TT 2 -.42841 105 0.45 0 0 2 -1.5739 106 0.475 0 CC 2 0.02978 107 0.62 0 CT 2 1.51890 108 0.45 GG CT 2 -.31386 109 0.485 0 0 1 -1.6884 110 0.57 GA CT 1 -.19931 111 0.68 GG CC 2 0.94616 112 0.565 GG CT 1 0.94616 113 0.55 GG CT 2 1.28981 114 0.465 AA CT 2 -.19931 115 0.585 0 0 2 0.25888 116 0.49 0 0 2 -.19931 117 0.62 0 0 2 0.25888 118 0.555 AA CT 2 1.17526 119 0.65 0 CT 2 1.40435 120 0.495 GG CT 1 0.25888 121 0.55 GA CC 1 1.51890 122 0.505 AA CT 2 0.48797 123 0.555 AA CT 2 1.06071 124 0.53 GA CT 1 0.25888 125 0.67 GG CT 2 1.97709 126 0.42 AA CC 1 -1.0011 127 0.53 GG 0 2 -.77205 128 0.55 GG CT 1 -1.6884 129 0.515 AA CT 2 0.71707 130 0.475 0 0 2 0.71707 131 0.57 GG CT 1 2.20619 132 0.525 AA CT 1 0.37342 133 0.62 GG CT 2 0.37342 134 0.555 GG CT 1 0.37342 135 0.61 GG CT 2 -.42841 136 0.54 GA CT 1 1.86254 137 0.57 GA CT 2 1.63345 138 0.59 GA CT 1 1.86254 139 0.605 GG CC 1 1.17526 140 0.58 GG CC 2 0.83162 141 0.495 AA CT 1 0.14433 142 0.45 GA CT 2 -1.6884 143 0.86 0 CT 1 0.71707 144 0.44 AA CT 2 -.54296 145 0.585 GG CC 1 0.48797 146 0.465 GG CT 2 -.77205 147 0.585 GA CC 2 -.42841 148 0.5 GA CC 2 0.25888 149 0.435 GA CC 1 -1.1157 150 0.545 GG CT 2 1.51890 151 0.425 GG CC 2 -.65750 152 0.705 AA TT 2 1.51890 153 0.755 GA TT 1 1.06071 154 0.595 GA CC 2 1.97709 155 0.54 GA CT 2 0.83162 156 0.6 GG CT 2 0.71707 157 0.525 GG CC 1 -.19931 158 0.48 GG CT 1 -.19931 159 0.555 GG CT 1 -.08477 160 0.465 GA TT 1 -.42841 161 0.455 GA CC 1 1.97709 162 0.565 GA CC 1 0.14433 163 0.675 AA TT 1 1.86254 164 0.58 GG CC 1 0.48797 165 0.51 GA CC 1 -.08477 166 0.61 GG CT 2 0.60252 167 0.54 GG CC 1 -1.3448 168 0.405 GG CT 1 -.19931 169 0.425 GA CT 1 -.77205 170 0.52 GG TT 2 1.74800 171 0.41 GA CC 2 -1.4593 172 0.425 GG CC 1 1.17526 173 0.715 GA CC 1 -.31386 174 0.425 AA CT 1 0.14433 175 0.43 GA CT 1 0.14433 176 0.495 GA CT 2 0.48797 177 0.65 GG TT 1 0.14433 178 0.58 0 0 2 1.28981 179 0.64 GG CT 1 0.48797 180 0.555 GG CT 2 -.54296 181 0.61 GA CC 1 1.28981 182 0.49 AA CT 2 0.94616 183 0.48 GA CC 1 0.60252 184 0.47 GG CC 2 -.54296 185 0.445 GG CC 2 -1.4593 186 0.69 0 CC 1 0.94616 187 0.535 GG CT 2 -.31386 188 0.46 GG CT 1 0.02978 189 0.56 0 TT 1 -.54296 190 0.52 GA CT 2 -.08477 191 0.545 GG TT 1 0.60252 192 0.42 GG CC 2 -.42841 193 0.47 GA CT 1 -1.9175 194 0.54 GG CT 2 -.42841 195 0.47 GA TT 1 -.19931 196 0.44 GA CT 1 -.54296 197 0.48 GG CT 2 0.02978 198 0.67 GG CT 1 0.94616 199 0.565 GA CT 2 -1.5739 200 0.415 GG CT 2 -1.5739 201 0.475 GA CT 2 -.88660 202 0.56 GA CT 2 1.17526 203 0.415 GG CT 1 -2.0321 204 0.53 GG CT 1 -.19931 205 0.43 GA CC 1 -1.1157 206 0.66 GG CC 1 0.71707 207 0.48 GA TT 2 0.14433 208 0.545 GG CC 2 0.60252 209 0.76 GG CT 1 0.25888 210 0.4 GG CC 1 -.88660 211 0.53 GG CT 2 -.31386 212 0.965 GA TT 1 1.63345 213 0.365 GG CC 2 -2.6048 214 0.88 0 CT 1 1.51890 215 0.57 GA CC 2 1.86254 216 0.45 GG CT 1 -1.2302 217 0.44 GA CT 1 -1.0011 218 0.495 GA TT 2 -.88660 219 0.53 GA CT 1 0.14433 220 0.565 GG CT 2 0.48797 221 0.795 GA 0 1 0.83162 222 0.615 GG CT 2 0.60252 223 0.445 GA CT 1 -.54296 224 0.585 GA CC 1 0.60252 225 0.445 GA CC 2 -.42841 226 0.435 AA CT 2 -.31386 227 0.52 GG CC 2 -.54296 228 0.485 GG CC 2 -.08477 229 0.535 GG CT 1 -.77205 230 0.585 GG CT 1 -.77205 231 0.545 GG CT 1 0.37342 232 0.475 GG TT 2 -2.0321 233 0.475 0 0 2 -.42841 234 0.51 GG TT 1 1.51890 235 0.515 GG TT 1 -.31386 236 0.485 GA CT 1 -1.9175 237 0.775 GA TT 1 1.86254 238 0.43 GG TT 1 -.88660 239 0.535 GG CC 2 -.19931 240 0.47 GG CT 2 -.31386 241 0.91 GG TT 1 2.09164 242 0.515 GA CT 1 0.48797 243 0.565 GA CC 1 -.54296 244 0.545 GG CT 1 0.02978 245 0.505 GA CT 2 0.60252 246 0.485 GG TT 1 -.88660 247 0.44 GG CC 2 -1.6884 248 0.49 GG CT 1 -1.5739 249 0.475 GA CC 2 0.60252 250 0.705 GA CC 2 0.83162 251 0.395 GA CC 1 -1.8030 252 0.845 GA CT 2 1.86254 253 0.52 GG TT 1 -1.5739 254 0.68 GG CT 1 0.02978 255 0.415 GA 0 1 -1.3448 256 0.455 GG CC 2 -.77205 257 0.545 GG TT 2 -.19931 258 0.425 0 CT 2 -1.5739 259 0.785 GG CT 1 0.48797 260 0.67 GA TT 2 1.74800 261 0.965 GG CC 1 1.86254 262 0.535 0 CT 2 0.94616 263 0.53 GA CT 1 0.71707 264 0.51 GG CC 1 -1.0011 265 0.385 GG CT 2 -.19931 266 0.485 GA CC 2 0.71707 267 0.545 GG TT 1 0.14433 268 0.45 GG CT 2 -.65750 269 0.685 GG CT 1 1.86254 270 0.48 0 CT 2 0.14433 271 0.56 GG CC 1 -.31386 272 0.555 GA CC 2 0.14433 273 0.535 0 0 2 -.65750 274 0.485 GG TT 1 -.19931 275 0.425 AA 0 2 0.83162 276 0.74 GG CT 1 1.74800 277 0.55 GG 0 2 1.86254 278 0.495 GG TT 2 -1.0011 279 0.49 GG CC 2 -.31386 280 0.755 GG 0 2 1.86254 281 0.435 GA TT 2 -.77205 282 0.45 GA CC 2 0.14433 283 0.455 GA CT 2 -.65750 284 0.63 AA TT 1 -.19931 285 0.42 GA CT 1 -.65750 286 0.46 GA CC 2 1.06071 287 0.465 AA CT 2 0.02978 288 0.43 GA CC 1 -1.1157 289 0.53 GG CC 1 -1.2302 290 0.48 GG 0 1 -1.3448 291 0.52 GG CC 2 0.83162 292 0.495 GG CC 2 0.94616 293 0.45 AA CC 2 -.19931 294 0.515 GG CC 1 -.54296 295 0.465 AA TT 1 0.14433 296 0.65 GG TT 1 1.51890 297 0.69 GG CT 2 1.40435 298 0.48 GA CC 2 0.02978 299 0.52 GA TT 2 0.37342 300 0.425 GG TT 2 -.54296 301 0.44 GG CT 1 -.54296 302 0.465 AA TT 1 -1.2302 303 0.49 GA CT 1 -1.1157 304 0.755 GA CC 1 1.28981 305 0.46 GA CT 2 -.31386 306 0.43 GA CC 2 -.65750 307 0.58 GA CT 1 0.25888 308 0.47 GA CC 1 0.25888 309 0.465 GA CT 1 0.02978 310 0.475 GG CC 2 1.06071 311 0.61 GG CC 1 0.14433 312 0.435 GA CT 2 -.08477 313 0.52 GA CC 1 -1.0011 314 0.46 GG CT 1 -.54296 315 0.405 GG CT 1 -.19931 316 0.485 GG TT 2 -.77205 317 0.485 GG CC 2 0.02978 318 0.5 GG CC 2 -.19931 319 0.44 GG CC 2 -1.2302 320 0.53 GG CT 1 0.48797 321 0.42 GG CC 2 -1.2302 322 0.585 AA CT 2 1.51890 323 0.565 GG CT 1 -1.2302 324 0.545 GA CT 2 0.37342 325 0.45 GG CT 2 -.19931 326 0.475 GG CC 1 0.14433 327 0.545 GG CT 2 -.19931 328 0.515 GA CC 2 0.60252 329 0.455 GA CT 1 -.42841 330 0.595 GA CC 2 -.19931 331 0.555 GA CC 2 -.88660 332 0.485 GG TT 2 -2.0321 333 0.56 0 0 2 0.71707 334 0.495 GG CT 2 0.60252 335 0.575 GA CT 2 0.37342 336 0.49 AA CC 1 -1.4593 337 0.535 GA CC 1 0.94616 338 0.47 GA CT 2 -1.0011 339 0.48 GA CC 2 0.48797 340 0.45 GA CT 2 -1.4593 341 0.45 GA CC 1 0.37342 342 0.45 GA CC 2 -.19931 343 0.47 GA CT 2 -1.4593 344 0.555 GA CC 2 1.06071 345 0.535 GG CT 1 -.08477 346 0.63 GG CT 1 -.31386 347 0.415 GG CT 2 -1.9175 348 0.73 0 0 1 -.31386 349 0.61 GA CT 2 1.17526 350 0.605 GG CT 1 0.02978 351 0.53 GG CT 2 -.31386 352 0.56 GG CT 2 -.42841 353 0.445 AA CC 2 -.54296 354 0.64 GA CC 2 0.37342 355 0.415 GA CT 1 -.77205 356 0.485 GA TT 1 0.25888 357 0.48 GA CT 1 0.25888 358 0.645 AA CT 1 1.86254 359 0.56 GG CC 1 1.97709 360 0.57 AA CT 2 0.02978 361 0.4 GG CC 2 -1.2302 362 0.445 GG CT 2 -1.0011 363 0.945 GG CT 1 1.17526 364 0.63 GA CT 1 1.17526 365 0.47 GA CT 1 0.02978 366 0.575 GA CT 2 1.86254 367 0.425 GA TT 2 0.14433 368 0.63 GG TT 1 0.48797 369 0.625 GG CT 1 0.02978 370 0.515 GG CC 1 -.65750 371 0.61 GA CT 1 0.02978 372 0.48 GG CC 2 0.37342 373 0.635 0 CT 2 0.60252 374 0.495 GA TT 2 0.25888 375 0.435 0 0 1 0.71707 376 0.58 GA CT 2 1.06071 377 0.44 GG CC 2 -.31386 378 0.81 GA CT 1 0.25888 379 0.895 GG CT 1 1.86254 380 0.49 0 0 2 -.65750 381 0.555 0 0 1 0.94616 382 0.66 GG CT 2 0.14433 383 0.565 GG TT 2 1.51890 384 0.435 GA TT 1 -.77205 385 0.455 GG TT 1 -2.0321 386 0.565 GA CT 1 0.83162 387 0.49 GG TT 2 -.19931 388 0.575 GA CT 1 0.37342 389 0.485 GA CC 2 0.37342 390 0.485 GA CT 1 1.40435 391 0.4 AA CT 1 -1.5739 392 0.605 GG CT 1 1.51890 393 0.585 GA CC 2 1.17526 394 0.66 0 0 1 -.19931 395 0.525 GA TT 1 -1.4593 396 0.645 AA CC 1 1.40435 397 0.445 GG CT 1 -1.5739 398 0.4 GG CT 2 -1.8030 399 0.55 GG CC 2 -.31386 400 0.435 GG CC 2 0.25888 401 0.78 GG TT 1 1.28981 402 0.58 GA CC 1 0.37342 403 1.01 GG CT 2 1.17526 404 0.38 GA CT 1 -2.1466 405 0.755 GG CT 1 1.06071 406 0.415 GG CC 2 -1.2302 407 0.425 AA CT 2 -1.0011 408 0.865 GG CT 1 0.48797 409 0.56 GA CT 2 1.17526 410 0.71 GG TT 2 0.94616 411 0.685 GG CT 1 0.71707 412 0.45 AA CC 2 0.25888 413 0.69 GG CC 2 -.42841 414 0.515 GA CC 1 0.83162 415 0.46 GG CT 2 0.25888 416 0.69 GA CT 1 -.42841 417 0.45 GG CC 2 -2.2612 418 0.395 GG CT 2 -1.4593 419 0.42 GG CT 1 -1.3448 420 0.49 GA CC 1 -.42841 421 0.46 GG TT 2 -1.6884 422 0.6 GA CC 1 -.19931 423 0.59 GG CC 1 -1.0011 424 0.43 0 0 2 -1.5739 425 0.48 GA CT 2 1.17526 426 0.425 GG CC 2 0.14433 427 0.47 GG TT 1 -1.0011 428 0.505 GG CT 1 -.42841 429 0.74 GA CT 1 -.19931 430 0.68 GA CT 2 0.94616 431 0.435 GG CT 2 -.65750 432 0.56 GG CC 1 0.25888 433 0.66 GG CC 1 2.20619 434 0.43 GG TT 2 0.25888 435 0.68 GA CT 2 0.83162 436 0.42 GG CT 1 -.65750 437 0.46 GA CT 1 0.25888 438 0.49 GG CC 2 0.02978 439 0.55 GG CT 2 -.08477 440 0.485 GG CT 2 0.25888 441 0.455 0 0 2 -1.4593 442 0.485 GA CT 2 1.28981 443 0.45 GG TT 2 0.14433 444 0.44 GG TT 2 -1.5739 445 0.41 GA CT 2 -.19931 446 0.605 GG CC 1 -.08477 447 0.73 GG CC 1 0.48797 448 0.485 GA CT 2 -1.1157 449 0.445 0 0 2 -.19931 450 0.54 GG CC 1 0.71707 451 0.46 GG CT 1 -1.3448 452 0.72 AA CT 1 1.63345 453 0.44 GG CT 2 0.25888 454 0.44 GG CT 2 -1.2302 455 0.54 GA CT 2 -.42841 456 0.42 GG CC 1 0.14433 457 0.5 GG CT 1 -.42841 458 0.535 GA CT 2 0.25888 459 0.565 GG CT 2 0.25888 460 0.52 GA CC 2 -.54296 461 0.415 GG CT 2 -.31386 462 0.54 GA CT 1 0.14433 463 0.715 GG CT 1 0.25888 464 0.545 GG CT 2 0.02978 465 0.485 GG CC 2 -.77205 466 0.425 GA CT 2 0.48797 467 0.52 0 0 1 0.94616 468 0.54 GG CC 2 1.74800 469 0.425 GA TT 2 -2.1466 470 0.425 GG CC 1 -1.4593 471 0.825 GG CC 1 0.02978 472 0.595 0 CC 2 -.08477 473 0.65 AA CT 1 -1.4593 474 0.445 0 CT 2 -.42841 475 0.605 GG CC 1 1.06071 476 0.44 0 CT 2 -2.1466 477 0.555 GG CT 2 -.08477 478 0.51 GA CC 2 0.02978 479 0.41 GG CT 2 -.65750 480 0.45 0 0 2 0.02978 481 0.57 GA TT 2 1.28981 482 0.45 GA CT 1 0.37342 483 0.56 GG CT 2 -.42841 484 0.45 GG CT 2 -1.1157 485 0.41 0 TT 2 0.14433 486 0.56 0 CT 2 1.51890 487 0.475 GG TT 2 -.77205 488 0.675 0 0 2 1.63345 489 0.615 GG CC 1 -.08477 490 0.485 GG CT 2 0.14433 491 0.73 GA CT 2 1.86254 492 0.435 GA CC 2 -.08477 493 0.535 GG CC 2 0.60252 494 0.5 AA CC 1 -.31386 495 0.655 GG CT 1 0.02978 496 0.44 GG TT 2 -.08477 497 0.595 GG CT 1 1.17526 498 0.46 GA CC 1 -.08477 499 0.565 GG CT 1 1.86254 500 0.465 GG CT 2 -1.4593 501 0.515 GA CC 2 0.94616 502 0.535 GG TT 2 -1.3448 503 0.495 GA CC 1 2.09164 504 0.53 GG TT 2 0.83162 505 0.54 GG CT 2 0.25888 506 0.475 GA CT 2 -.19931 507 0.655 GA CT 1 1.63345 508 0.42 GA CC 2 -.31386 509 0.62 GG CC 1 1.28981 510 0.475 0 0 2 0.14433 511 0.655 0 CT 2 0.94616 512 0.52 GG CT 2 -.77205 513 0.53 GG CT 2 0.71707 514 0.615 GA CC 1 0.14433 515 0.495 GA CT 1 0.02978 516 0.515 GG TT 2 -2.0321 517 0.475 GG CC 2 -1.0011 518 0.695 GG TT 2 1.51890 519 0.55 GG CC 2 -.42841 520 0.55 GG CT 2 -.08477 521 0.475 GG CT 1 1.40435 522 0.48 0 CC 2 -1.3448 523 0.405 0 TT 1 -1.5739 524 0.415 GG CC 2 -1.5739 525 0.475 0 CC 2 -1.0011 526 0.45 GA CC 2 -.65750 527 0.59 GG CC 2 0.71707 528 0.565 GA CT 2 -.08477 529 0.65 GG CT 2 1.40435 530 0.555 GG TT 2 -.77205 531 0.515 GA TT 1 -.54296 532 0.415 0 TT 1 0.48797 533 0.67 GA CC 2 -.54296 534 0.49 0 0 2 -1.3448 535 0.485 GG CC 2 1.28981 536 0.455 GG CC 2 -.31386 537 0.495 GG CC 2 -.31386 538 0.445 0 TT 1 -1.4593 539 0.43 GA CT 1 0.14433 540 0.435 GA CT 2 -1.1157 541 0.435 GG CT 2 -1.1157 542 0.555 GG CC 2 -.19931 543 0.55 GG CT 1 0.94616 544 0.47 GG CT 1 -.08477 545 0.525 GG CT 2 0.37342 546 0.575 0 TT 1 -.31386 547 0.51 0 0 2 0.83162 548 0.455 0 CT 2 0.94616 549 0.455 GG CC 1 -.08477 550 0.43 GG CC 2 -1.4593 551 0.405 GG CT 2 -1.6884 552 0.61 GA CC 1 1.28981 553 0.46 0 CC 1 -.42841 554 0.69 0 0 2 1.74800 555 0.6 GA CC 2 0.94616 556 0.59 GA TT 1 0.37342 557 0.535 GG CC 1 1.40435 558 0.6 GG TT 2 0.02978 559 0.555 GG CC 2 0.02978 560 0.49 GG CT 2 0.14433 561 0.45 AA CC 2 -1.1157 562 0.53 0 CT 1 -1.5739 563 0.48 0 CC 1 1.17526 564 0.625 0 TT 2 -1.0011 565 0.44 0 CT 2 -.31386 566 0.625 0 0 2 0.60252 567 0.65 0 TT 2 0.48797 568 0.555 0 TT 2 0.94616 569 0.67 GG TT 2 -.54296 570 0.51 AA CC 2 0.25888 571 0.555 GA CT 2 0.25888 572 0.42 GA CC 2 -.54296 573 . GG CT 2 -.88660 574 0.595 GG CC 2 0.83162 575 0.58 GG CT 1 0.60252 576 0.58 0 CT 1 0.37342 577 0.59 GG 0 1 0.02978 578 0.45 GA CT 2 -.42841 579 0.495 GA CT 1 -1.1157 580 0.49 GG CT 2 0.14433 581 0.73 0 CT 1 1.51890 582 0.425 GA CT 2 0.60252 583 0.575 GG CT 2 2.20619 584 0.475 GG TT 1 -.54296 585 0.48 GG CC 2 -1.1157 586 0.85 GG CT 1 0.14433 587 0.595 GA CC 2 0.25888 588 0.41 GG CT 2 -.19931 589 0.63 GG CT 2 0.25888 590 0.41 GA CT 1 -.77205 591 0.615 GG CC 1 0.25888 592 0.56 GA CC 2 0.83162 593 0.59 GA CT 2 0.83162 594 0.6 GG 0 2 0.60252 595 0.48 GA CT 2 -1.0011 596 0.475 GG CC 1 0.25888 597 0.505 GG CT 2 0.02978 598 0.465 0 0 2 1.17526 599 0.415 GG CT 2 -1.0011 600 0.54 GG CT 1 -.42841 601 0.465 GG TT 1 -1.0011 602 0.445 GG CT 2 0.02978 603 0.495 GG CT 1 -.19931 604 0.43 GA CC 2 -.54296 605 0.525 GG TT 1 -.31386 606 0.56 GA CT 2 0.48797 607 0.46 0 CC 2 -1.5739 608 0.475 GA CC 2 -.19931 609 0.475 GG TT 2 -1.2302 610 0.45 GA CT 1 -1.4593 611 0.42 0 CC 1 -1.2302 612 0.59 0 TT 1 -.08477 613 0.455 0 0 2 0.02978 614 0.58 GG TT 1 -1.1157 615 0.45 GG CT 2 -.65750 616 0.47 GG CC 2 0.02978 617 0.575 GG CT 1 1.28981 618 0.54 GG TT 1 -.08477 619 0.455 AA TT 2 0.14433 620 0.705 GA TT 1 -.19931 621 0.435 GA CT 2 -2.4903 622 0.485 GG CT 1 -.88660 623 0.455 GG CT 2 -1.2302 624 0.455 AA CC 2 -.19931 625 0.45 AA CT 2 -1.3448 626 0.395 GA CC 2 -1.2302 627 0.545 GA CC 2 0.71707 628 0.535 AA CT 2 0.02978 629 0.39 GA CT 1 -1.8030 630 0.5 GG CT 2 0.14433 631 0.655 GG CT 1 1.51890 632 0.51 GG CT 1 1.86254 633 0.4 GA TT 2 -2.0321 634 0.67 0 CC 1 0.48797 635 0.72 0 CT 2 1.17526 636 0.365 GA CT 2 -1.4593 637 0.535 0 CC 1 0.37342 638 0.43 GG CC 1 -1.8030 639 0.41 GG CC 2 -2.9485 640 0.455 GA CC 2 -1.8030 641 0.465 GG CT 1 -.65750 642 0.51 GA CC 2 0.14433 643 0.5 GG CC 2 0.02978 644 0.51 GG CT 2 -1.2302 645 0.48 GG CT 2 -.42841 646 0.545 GG TT 1 -.19931 647 0.92 GG CT 1 1.74800 648 0.605 GA CT 2 1.74800 649 0.53 GG CT 1 0.02978 650 0.435 GG CT 1 -.42841 651 0.635 GA CC 1 0.60252 652 0.42 GG TT 2 -1.6884 653 0.48 GG TT 2 0.48797 654 0.485 GG CC 2 -.77205 655 0.54 GA CC 2 -.08477 656 0.445 0 CT 2 -1.1157 657 0.685 GG TT 1 1.86254 658 0.565 GG CT 2 0.71707 659 0.425 GG TT 2 -.88660 660 0.79 GG CC 1 -.31386 661 0.555 GG CT 1 0.14433 662 0.505 AA TT 2 0.48797 663 0.405 GA CT 2 -2.0321 664 0.435 GA CT 1 0.02978 665 0.56 GA CT 2 0.14433 666 0.615 GG CT 1 1.40435 667 0.54 GG CT 1 1.86254 668 0.485 GA CT 2 -2.2612 669 0.4 GA CT 2 -1.3448 670 0.4 GG CC 2 -1.5739 671 0.675 GG CT 2 2.32073 672 0.48 GA CC 2 -.08477 673 0.825 GG CC 1 1.63345 674 0.485 GG TT 2 -.31386 675 0.7 GG CT 1 1.86254 676 0.82 GG CT 1 1.86254 677 0.47 GG CT 2 -.31386 678 0.405 GG TT 2 -2.0321 679 0.505 GA CT 2 1.17526 680 0.54 GG CC 1 -.19931 681 0.51 GG CT 2 -.31386 682 0.615 GA CT 2 0.94616 683 0.48 GG CT 2 -.54296 684 0.425 GG CC 2 -1.0011 685 0.555 GG CT 1 0.25888 686 0.475 GG CT 1 0.37342 687 0.41 GA CT 2 -.19931 688 0.54 GG CC 1 -.31386 689 0.545 GA CC 1 -1.4593 690 0.64 GA CT 2 1.86254 691 0.47 GA CC 2 0.83162 692 0.505 GG CT 1 -.54296 693 0.415 GG CT 2 0.02978 694 0.455 GG CT 2 -.77205 695 0.66 GA CC 2 0.94616 696 0.455 AA CT 2 0.14433 697 0.425 GG CC 1 0.25888 698 0.62 GG CT 2 0.14433 699 0.625 GA CT 1 0.48797 700 0.66 GG CC 1 0.37342 701 0.46 GG CT 1 0.37342 702 0.53 GG CT 2 -.42841 703 0.53 GG TT 2 1.17526 704 0.45 GA CC 2 0.37342 705 0.635 GG CT 2 -.08477 706 0.525 GA CT 2 0.14433 707 0.86 GA CT 2 2.20619 708 0.51 GA CC 1 0.14433 709 0.575 GA CT 2 0.14433 710 0.45 0 0 2 -.42841 711 0.495 GG CT 2 -.31386 712 0.56 GG CC 2 -1.0011 713 0.5 GG CC 2 -.54296 714 0.625 GA CC 1 0.14433 715 0.575 0 0 2 -.88660 716 0.525 GG CT 2 0.48797 717 0.52 GG CT 2 0.60252 718 0.43 GG CT 2 0.94616 719 0.645 GA CC 2 1.40435 720 0.64 GG CT 2 0.37342 721 0.68 GA CT 1 2.20619 722 0.43 GG CT 2 -1.3448 723 0.53 AA CT 2 0.25888 724 0.79 GA TT 1 0.25888 725 0.435 GG CC 1 -1.4593 726 0.495 GG CT 2 -.65750 727 0.45 GA CC 1 -.54296 728 0.46 GG CT 1 -1.4593 729 0.555 GG CC 2 -.42841 730 0.38 GG CT 2 -2.1466 731 0.45 0 CT 2 -.08477 732 0.505 GG CC 2 0.14433 733 0.43 GG CT 2 0.14433 734 0.46 GG CT 2 -.19931 735 0.425 GA CC 2 -.88660 736 0.51 0 CC 1 0.94616 737 0.55 GG CT 1 -1.5739 738 0.455 GG CC 1 -1.4593 739 0.55 GG CT 2 -.19931 740 0.43 0 CT 2 -1.0011 741 0.5 GG CT 2 -.31386 742 0.475 GG CC 1 -1.8030 743 0.53 GG CC 2 1.74800 744 0.485 0 CC 2 -.19931 745 0.52 GG TT 2 -.31386 746 0.48 GG CT 2 -.19931 747 0.475 GG CT 1 -1.0011 748 0.555 0 CC 2 0.60252 749 0.47 GG CC 1 -.54296 750 0.595 GA CT 1 0.94616 751 0.48 GG CC 1 -.19931 752 0.68 GG CT 1 0.25888 753 0.515 GA CT 2 1.06071 754 0.44 GG CT 2 -1.2302 755 0.535 GG CC 2 1.51890 756 0.43 GG CC 2 1.40435 757 0.58 0 0 2 -.54296 758 0.545 GG CT 2 -.54296 759 0.55 GA TT 2 0.71707 760 0.64 GA CT 1 0.02978 761 0.505 GG CC 2 -1.4593 762 0.365 GG CT 2 -.77205 763 0.45 GG CC 2 0.37342 764 0.48 GG CT 2 -.08477 765 0.56 GG CT 1 0.02978 766 0.54 GA CC 1 0.37342 767 0.445 GA TT 1 0.25888 768 0.495 GA CC 2 -.31386 769 0.455 GG CC 2 0.48797 770 0.4 GG CT 2 -1.4593 771 0.455 GA CC 2 0.02978 772 0.46 GG CC 2 0.25888 773 0.45 GG CT 2 -1.4593 774 0.65 GG TT 2 1.28981 775 0.535 GG CC 2 0.83162 776 0.505 GG CC 1 -1.2302 777 0.43 0 0 2 -1.1157 thesias-3.1.1/examples/dataset1/para0.txt000066400000000000000000000001121360777755100202600ustar00rootroot000000000000004 0 0.447118 1 0.000000 1 0.313361 0 0 2 0.151684 0 0 3 0.087837 0 0 thesias-3.1.1/examples/dataset1/para1.txt000066400000000000000000000001121360777755100202610ustar00rootroot000000000000004 0 0.447118 1 0.000000 1 0.313361 1 0 2 0.151684 1 0 3 0.087837 1 0 thesias-3.1.1/examples/dataset1/result0.txt000066400000000000000000000016101360777755100206570ustar00rootroot00000000000000Total number of individuals: 777 Number of individuals with 0 missing data: 668 Number of individuals with 1 missing data: 68 Number of individuals with 2 missing data: 41 Allele frequency at locus 1 (G/A) 0.76048 / 0.23952 p(HWE) = 0.227897 Allele frequency at locus 2 (C/T) 0.59880 / 0.40120 p(HWE) = 0.293616 Frequencies of Plausible Haplotype under Linkage Equilibrium Haplotype [0] GC 0.455377 Haplotype [1] GT 0.305102 Haplotype [2] AC 0.143426 Haplotype [3] AT 0.096095 After 2501 iterations burn at step 1500 Frequencies of Plausible Haplotypes under Linkage Disequilibrium Estimation StError T-Test Haplotype [0] GC 0.447118 Haplotype [1] GT 0.313361 0.014063 22.282011 Haplotype [2] AC 0.151684 0.011646 13.024323 Haplotype [3] AT 0.087837 0.009514 9.232228 LD MATRIX -0.09 P-Value MATRIX 0.149 thesias-3.1.1/examples/dataset1/result1.txt000066400000000000000000000027411360777755100206660ustar00rootroot00000000000000Total number of individuals: 777 Number of individuals with 0 missing data: 668 Number of individuals with 1 missing data: 68 Number of individuals with 2 missing data: 41 Phenotypic Mean = 0.528129 Standard Error = 0.102162 Allele frequency at locus 1 (G/A) 0.76048 / 0.23952 p(HWE) = 0.227897 Allele frequency at locus 2 (C/T) 0.59880 / 0.40120 p(HWE) = 0.293616 Frequencies of Plausible Haplotype under Linkage Equilibrium Haplotype [0] GC 0.455377 Haplotype [1] GT 0.305102 Haplotype [2] AC 0.143426 Haplotype [3] AT 0.096095 After 2501 iterations burn at step 1500 Estimated Haplotype Frequencies under Linkage Disequilibrium Estimation StError T-Test Haplotype 1 [0] GC 0.447069 Haplotype 2 [1] GT 0.313410 0.014108 22.215651 Haplotype 3 [2] AC 0.151734 0.011732 12.933010 Haplotype 4 [3] AT 0.087787 0.009531 9.210329 Haplotype Effects Estimation StError T-Test Intercept 0.296338 0.005028 Global Standard Error 0.102162 Residual Standard Error 0.081730 Covariable Adjustment Covariate 1 Column Number 5 -0.039670 0.006505 -6.098345 Diff = -0.03967 [-0.05242 - -0.02692] p=0.000000 Covariate 2 Column Number 6 0.054967 0.003217 17.085495 Diff = 0.05497 [0.04866 - 0.06127] p=0.000000 Log-likelihood = -516.857287 (Nb studied subjects = 668) Conditionnal Log-likelihood = 725.543449 (df = 3) LD MATRIX -0.09 P-Value MATRIX 0.147 thesias-3.1.1/examples/dataset1/result2.txt000066400000000000000000000043051360777755100206650ustar00rootroot00000000000000Total number of individuals: 777 Number of individuals with 0 missing data: 668 Number of individuals with 1 missing data: 68 Number of individuals with 2 missing data: 41 Phenotypic Mean = 0.528129 Standard Error = 0.102162 Allele frequency at locus 1 (G/A) 0.76048 / 0.23952 p(HWE) = 0.227897 Allele frequency at locus 2 (C/T) 0.59880 / 0.40120 p(HWE) = 0.293616 Frequencies of Plausible Haplotype under Linkage Equilibrium Haplotype [0] GC 0.455377 Haplotype [1] GT 0.305102 Haplotype [2] AC 0.143426 Haplotype [3] AT 0.096095 After 2501 iterations burn at step 1500 Estimated Haplotype Frequencies under Linkage Disequilibrium Estimation StError T-Test Haplotype 1 [0] GC 0.447133 Haplotype 2 [1] GT 0.313346 0.014096 22.229222 Haplotype 3 [2] AC 0.151669 0.011670 12.996173 Haplotype 4 [3] AT 0.087852 0.009537 9.212055 Haplotype Effects (Haplotypic effect by comparison to the reference with its 95% CI) Estimation StError T-Test Intercept 1 GC 0.295749 0.005675 Haplotype 2 GT 0.00757 0.006076 1.245688 Diff = 0.00757 [-0.00434 - 0.01948] p=0.212879 Haplotype 3 AC -0.01729 0.010006 -1.727418 Diff = -0.01729 [-0.03690 - 0.00233] p=0.084093 Haplotype 4 AT 0.00044 0.009228 0.047999 Diff = 0.00044 [-0.01764 - 0.01853] p=0.961717 Global Standard Error 0.102162 Residual Standard Error 0.080890 Covariable Adjustment Covariate 1 Column Number 5 -0.038668 0.006488 -5.960242 Diff = -0.03867 [-0.05138 - -0.02595] p=0.000000 Covariate 2 Column Number 6 0.055734 0.003197 17.432123 Diff = 0.05573 [0.04947 - 0.06200] p=0.000000 Log-likelihood = -510.447366 (Nb studied subjects = 668) Conditionnal Log-likelihood = 731.953549 (df = 6) Polymorphism 1 G/A Haplotypic Background -C 1-3 Diff = -0.01729 [-0.03690 - 0.00233] p=0.084093 Haplotypic Background -T 2-4 Diff = -0.00713 [-0.02872 - 0.01447] p=0.517718 Polymorphism 2 C/T Haplotypic Background G- 1-2 Diff = 0.00757 [-0.00434 - 0.01948] p=0.212879 Haplotypic Background A- 3-4 Diff = 0.01773 [-0.01096 - 0.04641] p=0.225768 LD MATRIX -0.09 P-Value MATRIX 0.150 thesias-3.1.1/examples/dataset2/000077500000000000000000000000001360777755100165235ustar00rootroot00000000000000thesias-3.1.1/examples/dataset2/answer0.txt000066400000000000000000000000531360777755100206410ustar00rootroot00000000000000data.dat 13 6 5 6 7 8 9 10 n n 0thesias-3.1.1/examples/dataset2/answer1.txt000066400000000000000000000001021360777755100206350ustar00rootroot00000000000000data.dat 13 6 5 6 7 8 9 10 n n 3 3 4 n y n n n thesias-3.1.1/examples/dataset2/data.dat000066400000000000000000001616071360777755100201410ustar00rootroot00000000000000292 1 0 2.67 11 11 11 11 11 22 65 1 1 294 1 0 2.6685714286 11 11 12 11 12 12 71 0 0 295 1 0 2.6671428571 11 12 11 11 11 22 64 1 1 297 1 0 2.6685714286 11 11 11 11 11 22 71 1 1 298 1 0 2.6714285714 11 11 11 11 11 22 69 0 0 303 1 0 2.66 11 11 11 11 11 22 67 0 0 310 1 0 2.6528571429 11 11 11 11 11 12 69 0 1 313 1 0 2.6771428571 11 11 11 11 11 22 60 1 1 314 1 1 2.24 11 11 11 11 11 22 70 1 1 315 1 0 2.6428571429 11 11 12 11 12 11 67 0 0 316 1 0 2.6428571429 11 11 11 11 11 12 62 0 0 318 1 0 2.6414285714 11 11 11 11 11 22 61 1 1 319 1 0 2.6428571429 11 11 12 11 12 12 58 1 1 320 1 0 2.64 11 11 11 11 11 12 53 0 1 321 1 0 2.6414285714 11 11 11 11 11 22 67 0 0 322 1 0 2.64 11 11 11 11 11 11 67 1 1 323 1 0 2.64 11 11 11 11 11 22 39 1 1 324 1 0 1.6042857143 11 11 11 11 11 22 68 0 1 325 1 0 2.6328571429 11 11 11 11 11 12 68 1 0 326 1 0 2.6328571429 11 12 11 11 11 22 69 0 0 327 1 0 2.6314285714 11 12 11 11 11 22 65 1 1 328 1 0 2.6314285714 11 11 11 11 11 22 67 1 0 329 1 1 0.05 11 11 11 11 11 22 58 1 1 330 1 0 2.6285714286 11 11 11 11 11 22 67 1 0 331 1 0 2.6285714286 12 11 11 11 11 22 52 1 1 334 1 0 0.14 11 11 11 11 11 22 72 1 1 335 1 0 2.6214285714 11 11 11 11 11 11 60 0 0 336 1 0 2.6214285714 11 11 11 11 11 22 75 1 1 337 1 0 2.6228571429 11 11 11 11 11 12 47 1 1 338 1 0 2.6228571429 11 11 11 11 11 22 75 1 1 339 1 0 2.6228571429 11 11 11 11 11 22 62 1 1 341 1 0 2.6214285714 11 11 11 11 11 22 73 1 0 342 1 1 1.92 11 12 11 11 11 22 72 0 0 343 1 0 2.6685714286 11 11 11 11 11 22 43 1 1 346 1 0 2.6114285714 11 11 11 11 11 22 76 0 1 347 1 0 2.6114285714 11 11 11 11 11 22 52 0 1 348 1 0 2.6114285714 11 11 11 11 11 22 41 0 0 349 1 0 2.61 11 11 11 11 11 22 54 1 0 350 1 0 2.62 11 11 11 11 11 0 67 1 1 351 1 1 2.4 11 11 12 11 12 12 70 1 1 352 1 0 2.6028571429 11 11 11 11 11 12 47 0 1 353 1 1 2.36 11 11 11 11 11 22 71 1 1 354 1 0 2.6028571429 11 11 11 11 11 12 64 1 0 355 1 0 2.6014285714 12 11 11 11 11 12 65 0 0 356 1 1 0.52 11 11 11 11 11 22 62 1 1 357 1 0 2.6014285714 11 12 11 11 11 22 62 0 0 358 1 0 1.6 11 11 11 11 11 0 70 1 1 359 1 1 0.08 11 11 11 11 11 22 56 1 0 360 1 0 2.5985714286 11 11 11 11 11 0 69 1 0 361 1 0 2.6085714286 11 11 11 11 11 12 67 0 0 362 1 0 2.5928571429 11 11 11 11 11 0 46 0 1 363 1 0 2.5928571429 11 11 12 11 12 0 44 1 1 365 1 0 2.59 11 11 11 11 11 22 74 0 0 366 1 0 2.59 11 11 12 11 12 12 42 1 1 367 1 0 2.5885714286 11 11 11 11 11 12 71 1 1 368 1 0 2.5642857143 11 11 11 11 11 0 65 1 0 369 1 0 2.7071428571 12 11 11 11 11 22 74 1 0 373 1 0 2.6328571429 11 11 11 11 11 12 49 1 0 374 1 0 2.5614285714 11 11 11 11 11 12 69 1 1 375 1 0 2.5628571429 11 11 11 11 11 22 44 1 1 376 1 0 2.5614285714 11 11 11 11 11 12 57 1 1 377 1 0 2.56 11 11 11 11 11 22 60 1 0 378 1 1 1.32 11 11 11 11 11 11 74 1 1 379 1 0 2.5614285714 11 11 11 11 11 22 66 0 0 381 1 0 2.5257142857 11 11 11 11 11 22 48 1 1 385 1 1 1.94 11 11 11 11 11 12 60 1 1 388 1 0 2.5528571429 11 12 11 11 11 22 55 1 1 390 1 1 1.91 11 11 11 11 11 12 68 1 1 392 1 0 2.55 11 11 11 11 11 22 71 1 1 393 1 0 2.5442857143 11 12 11 11 11 22 54 1 1 394 1 1 0.92 11 11 11 11 11 11 76 0 0 395 1 0 2.5514285714 11 11 11 11 11 22 49 1 0 396 1 0 2.5414285714 11 11 11 11 11 22 47 1 0 397 1 0 2.5585714286 11 12 11 11 11 22 68 1 0 398 1 1 0.46 11 11 11 11 11 22 67 1 1 399 1 0 2.5442857143 11 12 11 11 11 22 54 1 1 400 1 0 2.5442857143 11 11 11 11 11 22 72 1 0 401 1 0 2.5428571429 11 11 11 11 11 12 55 1 1 411 1 0 2.5342857143 11 22 11 11 11 22 59 1 1 413 1 0 2.5342857143 11 11 11 11 11 11 58 1 0 415 1 0 2.5314285714 11 11 11 11 11 12 73 1 0 417 1 0 2.5314285714 12 11 11 11 11 12 50 1 1 418 1 0 2.5314285714 11 11 11 11 11 22 64 1 1 419 1 0 2.5314285714 11 11 12 11 12 0 61 1 1 420 1 0 2.5314285714 11 11 11 11 11 22 62 1 0 422 1 0 2.5328571429 11 11 11 11 11 22 66 0 1 425 1 1 0.26 11 11 11 11 11 22 72 1 1 430 1 0 2.5228571429 11 11 11 11 11 0 66 1 1 431 1 1 1.75 11 11 11 11 11 12 69 1 1 433 1 0 2.5228571429 11 11 11 11 11 22 75 1 1 434 1 1 0.54 11 12 11 11 11 22 66 1 1 437 1 0 2.5214285714 11 11 11 11 11 11 58 1 1 438 1 0 2.52 11 12 11 11 11 12 55 1 1 440 1 0 2.5214285714 11 11 11 11 11 0 58 0 0 441 1 0 2.5214285714 11 11 11 11 11 12 54 1 0 442 1 0 2.5214285714 11 11 11 11 11 12 52 1 1 443 1 0 2.5214285714 11 11 11 11 11 22 56 1 1 446 1 0 2.5128571429 11 11 11 11 11 22 53 1 1 447 1 1 0.27 11 11 11 11 11 12 63 1 1 448 1 0 2.4828571429 11 11 11 11 11 22 58 1 0 449 1 0 2.5128571429 11 11 11 11 11 22 69 0 0 450 1 0 2.5128571429 11 11 11 11 11 0 74 1 1 451 1 1 2.01 11 11 11 11 11 22 72 1 1 452 1 1 0.69 11 11 11 11 11 22 71 1 1 453 1 1 2.23 11 11 11 11 11 22 65 1 1 454 1 0 2.5028571429 11 11 11 11 11 12 66 1 1 457 1 0 2.5057142857 11 12 11 11 11 22 66 1 1 459 1 0 2.5057142857 11 11 11 11 11 12 59 1 0 460 1 0 2.5057142857 11 11 11 11 11 12 55 0 1 461 1 1 0.48 11 11 11 11 11 22 69 1 1 462 1 0 2.5028571429 11 11 12 11 12 11 56 1 1 463 1 0 2.5042857143 11 11 12 11 12 0 44 1 1 464 1 0 2.4957142857 11 11 11 11 11 22 59 1 0 465 1 0 2.5242857143 11 11 12 11 12 12 61 0 0 466 1 0 2.4957142857 12 11 11 11 11 22 71 1 1 469 1 0 2.4957142857 11 11 11 11 11 22 64 0 0 471 1 0 2.4942857143 11 22 11 11 11 22 61 1 1 472 1 0 2.4957142857 11 11 11 11 11 22 52 1 1 473 1 0 2.4928571429 11 11 11 11 11 12 59 1 1 474 1 0 2.4771428571 11 11 11 11 11 22 77 0 0 475 1 0 2.4942857143 11 11 11 11 11 22 51 1 1 476 1 0 2.4942857143 11 11 11 11 11 0 53 1 1 477 1 0 2.4957142857 11 11 11 11 11 0 50 0 1 479 1 0 2.4914285714 11 11 11 11 11 22 65 0 0 480 1 0 2.4914285714 11 11 11 11 11 22 65 0 0 481 1 1 0.35 11 11 12 11 12 12 65 1 1 482 1 0 2.4928571429 11 11 11 11 11 22 59 0 0 483 1 1 0.74 11 11 11 11 11 22 74 1 1 484 1 0 2.4857142857 11 11 11 11 11 22 62 1 1 486 1 0 2.4828571429 11 11 11 11 11 22 46 1 1 488 1 1 1.36 11 11 11 11 11 12 65 0 0 489 1 0 2.4828571429 11 11 11 11 11 12 53 1 1 490 1 0 2.4828571429 11 11 11 11 11 22 67 1 1 492 1 0 2.4114285714 11 11 11 11 11 22 46 1 1 493 1 1 0.26 11 11 11 11 11 22 75 0 0 494 1 0 2.4828571429 11 11 11 11 11 11 46 1 1 496 1 0 2.4828571429 11 11 11 11 11 22 59 1 0 497 1 0 2.4814285714 11 11 11 11 11 22 55 1 1 498 1 1 0.1 11 12 11 11 11 22 67 1 0 499 1 0 2.4785714286 11 11 11 11 11 22 70 1 0 500 1 0 2.48 11 11 11 11 11 12 69 1 0 501 1 0 2.4785714286 11 11 11 11 11 22 74 0 1 502 1 0 2.4785714286 11 11 11 11 11 22 57 1 1 503 1 0 2.4785714286 11 11 11 11 11 22 58 1 1 504 1 0 2.4728571429 11 11 11 11 11 12 67 0 1 505 1 0 2.4728571429 11 11 11 11 11 0 56 1 1 506 1 0 2.4714285714 11 11 11 11 11 22 49 1 1 508 1 0 2.4714285714 11 11 11 11 11 22 49 0 1 509 1 0 2.4714285714 11 12 11 11 11 12 43 1 1 510 1 0 2.4714285714 11 11 11 11 11 12 67 1 1 511 1 0 2.4728571429 11 11 11 11 11 22 63 1 1 512 1 0 2.4714285714 11 11 11 11 11 22 73 1 0 513 1 0 2.47 11 11 11 11 11 22 65 1 1 514 1 0 2.4714285714 11 11 11 11 11 22 71 1 1 515 1 0 2.47 11 11 11 11 11 12 48 1 1 516 1 0 2.47 11 11 11 11 11 22 45 1 1 517 1 0 2.47 11 11 11 11 11 22 75 1 0 519 1 0 2.4685714286 11 11 11 11 11 22 52 1 1 520 1 0 2.47 11 11 11 11 11 12 63 1 1 521 1 0 2.47 11 11 11 11 11 22 64 1 1 522 1 1 1.4 11 11 11 11 11 0 75 1 1 523 1 1 1.52 11 11 11 11 11 12 73 1 1 524 1 1 0.64 11 11 11 11 11 22 74 1 1 525 1 0 2.47 11 11 11 11 11 22 39 0 1 526 1 1 1.74 11 11 11 11 11 12 74 0 1 528 1 1 2.38 11 11 11 11 11 22 63 1 1 530 1 1 0.03 11 12 11 11 11 12 72 1 1 531 1 0 2.4628571429 11 11 11 11 11 22 48 1 1 532 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1 0 0.7085714286 11 11 11 11 11 0 70 1 1 1813 1 0 0.7085714286 11 12 11 11 11 0 71 1 1 1814 1 0 0.7085714286 11 11 11 11 11 0 67 0 0 1815 1 0 0.7085714286 12 11 11 11 11 0 50 1 0 1816 1 0 0.7071428571 11 11 11 11 11 0 63 1 1 1817 1 0 0.7071428571 11 11 11 11 11 0 58 0 0 1818 1 0 0.7071428571 11 11 11 11 11 0 69 0 0 1819 1 0 0.7071428571 11 11 11 11 11 0 69 0 0 1820 1 0 0.7071428571 11 11 11 11 11 0 58 1 1 1821 1 0 0.7057142857 11 11 11 11 11 0 62 1 0 1822 1 0 0.7 11 12 11 11 11 0 71 1 1 1823 1 0 0.7 11 11 11 11 11 0 67 0 0 1824 1 0 0.6985714286 11 12 11 11 11 0 48 1 1 1825 1 0 0.6971428571 11 11 11 11 11 0 71 1 1 1826 1 1 0.52 11 11 11 11 11 0 62 0 0 1827 1 0 0.6957142857 11 11 11 11 11 0 68 0 1 1828 1 0 0.6957142857 11 11 11 11 11 0 69 1 0 1829 1 1 0.61 11 11 11 11 11 0 52 1 1 1830 1 1 0.07 11 11 11 11 11 0 49 0 1 1831 1 0 0.69 11 12 11 11 11 0 72 1 0 1832 1 0 0.69 11 11 11 11 11 0 60 1 0 1833 1 0 0.69 11 11 11 11 11 0 70 0 1 1834 1 0 0.6857142857 11 11 11 11 11 0 58 1 1 1835 1 0 0.6857142857 11 11 11 11 11 0 71 0 0 1836 1 0 0.6857142857 11 11 11 11 11 0 71 0 1 1837 1 0 0.6814285714 11 11 11 11 11 0 63 1 1 1838 1 0 0.6785714286 11 11 11 11 11 0 59 1 1 1839 1 0 0.6785714286 11 12 11 11 11 0 68 1 1 1840 1 1 0.03 11 12 11 11 11 0 73 0 0 1841 1 0 0.6771428571 11 11 11 11 11 0 51 0 0 1842 1 0 0.6757142857 11 11 11 11 11 0 63 1 1 1843 1 0 0.6671428571 11 11 11 11 11 0 60 0 0 1844 1 0 0.6657142857 11 12 11 11 11 0 48 1 1 1845 1 1 0.16 11 11 11 11 11 0 75 1 1 1846 1 0 0.65 11 11 11 12 11 0 60 1 0 1847 1 0 0.6457142857 11 11 11 12 11 0 64 0 1 1848 1 1 0.39 11 11 11 11 11 0 65 0 1 1849 1 0 0.6371428571 11 11 11 11 11 0 61 1 1 1850 1 0 0.6371428571 11 12 11 11 11 0 52 1 1 1851 1 0 0.6371428571 11 11 11 11 11 0 71 1 0 1852 1 0 0.6314285714 11 11 11 11 11 0 51 1 1 1853 1 0 0.63 11 11 11 11 11 0 61 0 0 1854 1 0 0.63 11 11 11 11 11 0 73 1 1 1855 1 0 0.6214285714 11 11 11 11 11 0 54 0 0 1856 1 0 0.62 11 11 11 11 11 0 67 1 1 1857 1 0 0.62 12 11 11 11 11 0 42 0 1 1858 1 0 0.62 11 11 11 11 11 0 47 1 1 1859 1 0 0.6185714286 11 11 11 11 11 0 49 1 1 1860 1 0 0.6185714286 12 11 11 11 11 0 73 1 0 1861 1 0 0.6185714286 11 11 11 11 11 0 58 1 0 1862 1 0 0.6185714286 11 11 11 11 11 0 63 1 0 1863 1 0 0.6171428571 11 11 11 11 11 0 72 1 0 1864 1 0 0.6171428571 11 11 11 11 11 0 63 0 1 1865 1 0 0.6114285714 11 11 11 11 11 0 60 1 0 1866 1 0 0.6114285714 11 11 11 11 11 0 45 1 1 1867 1 0 0.6085714286 11 11 11 11 11 0 48 1 1 1868 1 0 0.6085714286 11 11 11 11 11 0 54 1 1 1869 1 0 0.6071428571 11 12 11 11 11 0 51 1 1 1870 1 0 0.6 11 11 11 11 11 0 68 1 0 1871 1 0 0.5985714286 11 12 11 11 11 0 43 1 1 1872 1 0 0.5971428571 11 11 12 11 12 0 71 0 0 1873 1 0 0.5928571429 11 11 11 11 11 0 66 1 1 1874 1 0 0.5928571429 11 11 11 11 11 0 61 1 0 1875 1 0 0.5914285714 11 11 11 11 11 0 50 0 1 1876 1 0 0.5914285714 11 11 11 11 11 0 67 0 1 1877 1 0 0.5914285714 11 11 11 11 11 0 61 1 0 1878 1 0 0.59 11 11 11 11 11 0 70 0 1 1879 1 0 0.59 11 11 11 11 11 0 50 0 1 1880 1 0 0.5885714286 11 11 11 11 11 0 58 1 1 1881 1 0 0.5885714286 12 11 11 11 11 0 59 1 1 1883 1 0 0.5814285714 11 12 11 11 11 0 63 1 1 1884 1 0 0.58 11 11 12 11 12 0 41 0 1 1885 1 1 0.05 11 11 11 11 11 0 75 1 1 1886 1 0 0.5785714286 11 11 11 11 11 0 73 0 0 1887 1 0 0.5785714286 11 11 11 11 11 0 63 1 1 1888 1 0 0.5785714286 11 11 11 11 11 0 72 1 1 1889 1 0 0.57 11 11 11 11 11 0 65 1 1 1890 1 0 0.57 11 12 11 11 11 0 65 1 1 1891 1 0 0.5685714286 11 11 12 11 12 0 70 1 1 1892 1 0 0.5685714286 11 11 11 11 11 0 65 1 1 1893 1 0 0.56 12 11 11 11 11 0 43 1 1 1894 1 0 0.5528571429 11 12 11 11 11 0 58 0 1 1895 1 0 0.5528571429 11 11 11 11 11 0 43 1 1 1896 1 0 0.5514285714 11 11 11 11 11 0 48 1 1 1897 1 0 0.5514285714 11 11 11 11 11 0 58 1 1 1898 1 0 0.55 11 11 12 11 12 0 38 1 1 1899 1 0 0.5428571429 11 11 11 11 11 0 52 1 1 1900 1 0 0.5428571429 11 11 11 11 11 0 64 0 0 1901 1 0 0.5428571429 11 11 11 11 11 0 43 1 0 1902 1 0 0.5428571429 11 11 11 11 11 0 47 1 1 1904 1 0 0.54 12 11 11 11 11 0 61 1 1 1905 1 0 0.54 11 11 11 11 11 0 60 1 1 1906 1 0 0.54 11 12 11 11 11 0 75 0 1 1907 1 0 0.5385714286 11 11 11 11 11 0 43 1 0 1908 1 0 0.5385714286 11 12 11 11 11 0 66 1 1 1909 1 0 0.5328571429 11 11 11 11 11 0 59 1 1 1910 1 0 0.5328571429 11 11 11 11 11 0 64 1 0 1911 1 0 0.5042857143 11 11 11 11 11 0 62 1 1 1912 1 0 0.5042857143 11 11 11 11 11 0 51 0 0 1913 1 0 0.5014285714 11 11 11 11 11 0 49 1 1 1914 1 1 0.4 11 11 11 11 11 0 67 1 1 1915 1 0 0.5014285714 11 11 11 11 11 0 44 1 1 1916 1 0 0.5014285714 11 11 11 11 11 0 41 1 1 1917 1 0 0.5 12 11 11 11 11 0 52 1 1 1918 1 0 0.4942857143 11 11 11 11 11 0 46 1 1 1919 1 0 0.4942857143 11 12 11 11 11 0 69 0 1 1920 1 0 0.4942857143 11 11 11 11 11 0 74 0 0 1921 1 0 0.4942857143 11 11 11 11 11 0 59 1 0 thesias-3.1.1/examples/dataset2/para0.txt000066400000000000000000000003201360777755100202620ustar00rootroot0000000000000012 0 0.721745 1 0.000000 1 0.163918 0 0 16 0.067965 0 0 32 0.018820 0 0 11 0.016326 0 0 4 0.003161 0 0 2 0.002322 0 0 9 0.002114 0 0 33 0.001728 0 0 3 0.000847 0 0 24 0.000528 0 0 6 0.000527 0 0 thesias-3.1.1/examples/dataset2/result0.txt000066400000000000000000000043721360777755100206700ustar00rootroot00000000000000Total number of individuals: 1295 Number of individuals with 0 missing data: 949 Number of individuals with 1 missing data: 346 Number of individuals with 2 missing data: 0 Number of individuals with 3 missing data: 0 Number of individuals with 4 missing data: 0 Number of individuals with 5 missing data: 0 Number of individuals with 6 missing data: 0 Allele frequency at locus 1 (1/2) 0.97945 / 0.02055 p(HWE) = 0.518100 Allele frequency at locus 2 (1/2) 0.93151 / 0.06849 p(HWE) = 0.430948 Allele frequency at locus 3 (1/2) 0.98103 / 0.01897 p(HWE) = 0.551441 Allele frequency at locus 4 (1/2) 0.99631 / 0.00369 p(HWE) = 0.000000 Allele frequency at locus 5 (1/2) 0.97998 / 0.02002 p(HWE) = 0.305307 Allele frequency at locus 6 (2/1) 0.81507 / 0.18493 p(HWE) = 0.583703 Frequencies of Plausible Haplotype under Linkage Equilibrium Haplotype [0] 111112 0.712293 Haplotype [1] 111111 0.161613 Haplotype [2] 111122 0.014552 Haplotype [3] 111121 0.003302 Haplotype [4] 111212 0.002637 Haplotype [5] 111211 0.000598 Haplotype [6] 111222 0.000054 Haplotype [8] 112112 0.013772 Haplotype [9] 112111 0.003125 Haplotype [10] 112122 0.000281 Haplotype [11] 112121 0.000064 Haplotype [16] 121112 0.052375 Haplotype [17] 121111 0.011883 Haplotype [18] 121122 0.001070 Haplotype [19] 121121 0.000243 Haplotype [24] 122112 0.001013 Haplotype [25] 122111 0.000230 Haplotype [26] 122122 0.000021 Haplotype [27] 122121 0.000005 Haplotype [32] 211112 0.014943 Haplotype [33] 211111 0.003390 Haplotype [48] 221112 0.001099 After 2501 iterations burn at step 1500 Frequencies of Plausible Haplotypes under Linkage Disequilibrium Estimation StError T-Test Haplotype [0] 111112 0.721745 Haplotype [1] 111111 0.163918 0.008637 18.977625 Haplotype [2] 111122 0.002322 0.000940 2.471133 Haplotype [3] 111121 0.000847 0.000725 1.167687 Haplotype [4] 111212 0.003161 0.001417 2.230501 Haplotype [6] 111222 0.000527 0.000577 0.912491 Haplotype [9] 112111 0.002114 0.001057 2.000000 Haplotype [11] 112121 0.016326 0.002936 5.561030 Haplotype [16] 121112 0.067965 0.005781 11.756979 Haplotype [24] 122112 0.000528 0.000528 1.000000 Haplotype [32] 211112 0.018820 0.003306 5.692822 Haplotype [33] 211111 0.001728 0.001380 1.251853 thesias-3.1.1/examples/dataset2/result1.txt000066400000000000000000000106231360777755100206650ustar00rootroot00000000000000Total number of individuals: 1295 Number of individuals with 0 missing data: 949 Number of individuals with 1 missing data: 346 Number of individuals with 2 missing data: 0 Number of individuals with 3 missing data: 0 Number of individuals with 4 missing data: 0 Number of individuals with 5 missing data: 0 Number of individuals with 6 missing data: 0 Total number of censored individuals: 129 Total number of censored individuals without missing data: 129 Allele frequency at locus 1 (1/2) 0.97945 / 0.02055 p(HWE) = 0.518100 Allele frequency at locus 2 (1/2) 0.93151 / 0.06849 p(HWE) = 0.430948 Allele frequency at locus 3 (1/2) 0.98103 / 0.01897 p(HWE) = 0.551441 Allele frequency at locus 4 (1/2) 0.99631 / 0.00369 p(HWE) = 0.000000 Allele frequency at locus 5 (1/2) 0.97998 / 0.02002 p(HWE) = 0.305307 Allele frequency at locus 6 (2/1) 0.81507 / 0.18493 p(HWE) = 0.583703 Frequencies of Plausible Haplotype under Linkage Equilibrium Haplotype [0] 111112 0.712293 Haplotype [1] 111111 0.161613 Haplotype [2] 111122 0.014552 Haplotype [3] 111121 0.003302 Haplotype [4] 111212 0.002637 Haplotype [5] 111211 0.000598 Haplotype [6] 111222 0.000054 Haplotype [8] 112112 0.013772 Haplotype [9] 112111 0.003125 Haplotype [10] 112122 0.000281 Haplotype [11] 112121 0.000064 Haplotype [16] 121112 0.052375 Haplotype [17] 121111 0.011883 Haplotype [18] 121122 0.001070 Haplotype [19] 121121 0.000243 Haplotype [24] 122112 0.001013 Haplotype [25] 122111 0.000230 Haplotype [26] 122122 0.000021 Haplotype [27] 122121 0.000005 Haplotype [32] 211112 0.014943 Haplotype [33] 211111 0.003390 Haplotype [48] 221112 0.001099 After 2501 iterations burn at step 1500 Estimated Haplotype Frequencies under Linkage Disequilibrium Estimation Haplotype 1 [0] 111112 0.721310 Haplotype 2 [1] 111111 0.164351 Haplotype 7 [2] 111122 0.002353 Haplotype 10 [3] 111121 0.000816 Haplotype 6 [4] 111212 0.003161 Haplotype 12 [6] 111222 0.000527 Haplotype 8 [9] 112111 0.002115 Haplotype 5 [11] 112121 0.016326 Haplotype 3 [16] 121112 0.067966 Haplotype 11 [24] 122112 0.000527 Haplotype 4 [32] 211112 0.019224 Haplotype 9 [33] 211111 0.001324 Estimated Haplotype Frequencies in Uncensored (=0) Censored (=1) individuals Haplotype 1 [0] 111112 0.714976 0.761578 Haplotype 2 [1] 111111 0.166725 0.149264 Haplotype 7 [2] 111122 0.002721 0.000012 Haplotype 10 [3] 111121 0.000944 0.000000 Haplotype 6 [4] 111212 0.003659 0.000000 Haplotype 12 [6] 111222 0.000610 0.000000 Haplotype 8 [9] 112111 0.002446 0.000012 Haplotype 5 [11] 112121 0.016457 0.015492 Haplotype 3 [16] 121112 0.069512 0.058140 Haplotype 11 [24] 122112 0.000610 0.000000 Haplotype 4 [32] 211112 0.020108 0.013605 Haplotype 9 [33] 211111 0.001234 0.001899 Haplotype Effects Estimation StError T-Test Intercept 1 111112 Haplotype 2 111111 -0.12857 0.158657 -0.810368 HRR = 0.87935 [0.64433 - 1.20009] p=0.417729 Haplotype 7 111122 0.00000 Haplotype 10 111121 0.00000 Haplotype 6 111212 0.00000 Haplotype 12 111222 0.00000 Haplotype 8 112111 0.00000 Haplotype 5 112121 -0.21458 0.515288 -0.416435 HRR = 0.80688 [0.29389 - 2.21528] p=0.677092 Haplotype 3 121112 -0.18738 0.258669 -0.724386 HRR = 0.82913 [0.49939 - 1.37660] p=0.468829 Haplotype 11 122112 0.00000 Haplotype 4 211112 -0.42152 0.601697 -0.700554 HRR = 0.65605 [0.20173 - 2.13359] p=0.483581 Haplotype 9 211111 0.00000 -2 x Log-likelihood (with covariates) = 1701.020546 (Nb studied subjects = 949) -2 x Log-likelihood (without covariates) = 1702.707953 (df = 4) Polymorphism 1 1/2 Haplotypic Background -11112 1-4 HRR = 0.65605 [0.20173 - 2.13359] p=0.483581 Haplotypic Background -11111 2-9 Polymorphism 2 1/2 Haplotypic Background 1-1112 1-3 HRR = 0.82913 [0.49939 - 1.37660] p=0.468829 Polymorphism 3 1/2 Haplotypic Background 11-111 2-8 Haplotypic Background 11-121 10-5 Haplotypic Background 12-112 3-11 Polymorphism 4 1/2 Haplotypic Background 111-12 1-6 Haplotypic Background 111-22 7-12 Polymorphism 5 1/2 Haplotypic Background 1111-2 1-7 Haplotypic Background 1111-1 2-10 Haplotypic Background 1112-2 6-12 Haplotypic Background 1121-1 8-5 Polymorphism 6 2/1 Haplotypic Background 11111- 1-2 HRR = 0.87935 [0.64433 - 1.20009] p=0.417729 Haplotypic Background 11112- 7-10 Haplotypic Background 21111- 4-9 thesias-3.1.1/examples/dataset3/000077500000000000000000000000001360777755100165245ustar00rootroot00000000000000thesias-3.1.1/examples/dataset3/data.txt000066400000000000000000001131141360777755100201770ustar00rootroot00000000000000626 1 1 AG 55 GG GG AA GG AA GG TT 750 1 0 AG 45 GA GG AA GG GA GG TG 627 2 1 AA 44 GG GA AA GG GA GG TG 751 2 0 AG 45 GG GG AA GG GA GG TG 628 3 1 GG 55 GA GG GG TG GG GG TT 752 3 0 AG 45 GG GA AA GG GA GG TG 629 4 1 AA 44 GG GG AA GG GG GG GG 753 4 0 GG 55 GG GG AA GG AA GG TT 630 5 1 AA 44 GG GA AA GG GG GG GG 754 5 0 AG 45 GG GG AA GG GA GG TG 631 6 1 AA 55 GG GA AA GG GA GG TG 755 6 0 AA 44 GG GG AA GG GG GA TG 632 7 1 AA 44 GG GG AA GG GG GG GG 756 7 0 AA 44 GG GA AA GG GG GA TG 633 8 1 AA 44 GG GG AA 0 GG GA TG 757 8 0 AA 44 GG GA AA GG GG GG GG 634 9 1 AA 44 GG GG AA GG GG GA TG 758 9 0 AG 45 GG GG AA GG GG GG TG 635 10 1 AG 45 GG GG AA GG GG AA TT 759 10 0 AA 44 GG GG AA GG GG GG GG 637 11 1 AG 45 GG GG AA GG GA GG TG 760 11 0 AG 45 GA GG GA TG GG GG TG 638 12 1 AG 45 GG GG AA GG GA GA TT 761 12 0 AA 44 GG GG AA GG GG GG GG 639 13 1 AA 45 GG GG AA GG GA GG TG 762 13 0 AA 45 GG GG AA GG 0 GG TG 640 14 1 AA 44 GG GG AA GG GG GG GG 763 14 0 AA 44 GG GG AA GG GG GA TG 641 15 1 AG 45 GG GA AA GG GA GG TG 764 15 0 GG 55 GA GG GA TG GG GG TG 642 16 1 AA 44 GG GG AA GG GG GG GG 765 16 0 AG 45 GA GG GA TG GG GA TT 643 17 1 AG 45 GG GG AA GG GG GA TG 766 17 0 AG 45 GG GG AA GG GA GG TG 644 18 1 AA 44 GG GG AA GG GG GG GG 767 18 0 GG 55 GG GG AA GG GA GA TT 645 19 1 AA 45 GG GG AA GG GA GG TG 768 19 0 AG 45 GA GG GA TG GA GG TT 646 20 1 AG 45 GG GG AA GG GA GG TG 769 20 0 AG 45 GG GG AA GG GA GG TG 647 21 1 AG 45 GG GG AA GG GA GA TT 770 21 0 AA 44 GG GG AA GG GG GA TG 648 22 1 AA 44 GG GG AA GG GG GA TG 771 22 0 AA 44 GG GG AA GG GA GG TG 649 23 1 AG 45 GA GG GA TG GG GG TG 772 23 0 GG 55 GG GG AA GG AA GG TT 650 24 1 GG 55 GA GG GA TG GA GG TT 773 24 0 AA 44 GG GA AA GG GG GG GG 651 25 1 AG 45 GG GA AA GG GA GG TG 774 25 0 AG 45 GG GG AA GG GA GA TT 652 26 1 AG 45 GG GG AA GG GA GA TT 775 26 0 GG 55 GG GG AA GG AA GG TT 653 27 1 AG 45 GG GG GA GG GG GA TT 776 27 0 AA 44 GG GA AA GG GG GG GG 654 28 1 AG 45 GG GG AA GG GA GA TT 777 28 0 AG 45 GG GG AA GG GG GA TG 655 29 1 AG 45 GG GA AA GG GA GG TG 778 29 0 AA 44 GG GG AA GG GG GG GG 656 30 1 GG 55 GG GG AA GG AA GG TT 779 30 0 AG 45 GA GG GA TG GG GG TG 657 31 1 AG 45 GG GG AA GG GA GG TG 780 31 0 AG 45 GG GG GA GG GA GG TT 659 32 1 AG 45 GG GG AA GG GA GA TT 782 32 0 AA 44 GG GG AA GG GG GA TG 660 33 1 AA 44 GG AA AA GG GG GG GG 783 33 0 AA 44 GG GG AA GG GG GA TG 661 34 1 AG 45 GG GG AA GG GA GA TT 784 34 0 AA 44 GG GG AA GG GA GG TG 662 35 1 AA 45 GG GG AA GG GA GG TG 785 35 0 AG 45 GG GG AA GG GA 0 0 663 36 1 AG 45 GA GG GA TG GA GG TT 786 36 0 GG 55 GG GG AA GG GA GA TT 664 37 1 AG 45 GG GG AA GG GA GG TG 787 37 0 AA 45 GG GA AA GG GA GG TG 665 38 1 AG 45 GG GG AA GG GG GA TG 788 38 0 AG 45 GG GG GA GG GG GG TG 666 39 1 AG 45 GG GG AA GG GA GG TG 789 39 0 AA 45 GG GA AA GG GA GG TG 667 40 1 AA 44 GG GG AA GG GA GG TG 790 40 0 GG 55 GA GG GA TG GA GG TT 668 41 1 AG 45 GG GA AA GG GA GG TG 791 41 0 AG 45 GG GG AA GG GG GA TG 669 42 1 AG 45 GA GG GA TG GG GG TG 792 42 0 GG 55 GA GG GA TG GG GA TT 670 43 1 AG 55 GG GG AA GG AA GG TT 793 43 0 AA 44 GG GG AA GG GA GG TG 671 44 1 AG 45 GG GG GA GG GG GG TG 794 44 0 AA 44 GG GA AA GG GG GG GG 672 45 1 AG 45 GG GG AA GG GG GA TG 795 45 0 AG 45 GA GG GA TG GG GG TG 673 46 1 AG 45 GA GG GA TG GG GG TG 796 46 0 AG 45 GG GG GA TG GG GA TT 674 47 1 AG 45 GA GG GA TG GG GG TG 797 47 0 GG 55 GG GG AA GG GA GA TT 675 48 1 AA 44 GG GA AA GG GG GG GG 798 48 0 GG 45 GG GG GA GG GA GG TT 676 49 1 AG 45 GG GG AA GG GG GA 0 799 49 0 AA 44 GG GG AA GG GG GG GG 677 50 1 AG 45 GG GG AA GG AA GG TT 800 50 0 AA 44 GG GG AA GG GG GG GG 678 51 1 AG 45 GG GG AA GG AA GG TG 801 51 0 AG 45 GG GG AA GG GA GG TG 679 52 1 AA 44 GG GG AA GG GG GG GG 802 52 0 AA 45 GG GG AA GG GA GA TT 680 53 1 AG 45 GG GG GA GG GG GA TT 803 53 0 GG 55 GA GG GA TG GG GG TG 681 54 1 AG 45 GG GG AA GG GG GG GG 804 54 0 AA 44 GG GG AA GG GG GA TG 682 55 1 AG 45 GG GG AA GG GA GG TG 805 55 0 AG 45 GG GG AA GG GG GA TG 683 56 1 AA 44 GG GG AA GG GG GA TG 806 56 0 GG 55 GA GG GA TG GA GG TT 684 57 1 AG 45 GG 0 AA GG GA GG TG 807 57 0 AG 45 GG GG AA GG GG GA TG 685 58 1 GG 55 GG GG GA GG GG GG TG 808 58 0 AG 45 GA GG GA TG GG GG TG 686 59 1 AG 45 GA GG GA TG GG GA TT 809 59 0 AG 45 GG GG AA GG GA GG TG 687 60 1 GG 55 GA GG GG TG GG GG TT 810 60 0 AG 45 GA GG GA TG GG GG TG 688 61 1 AA 44 GG GG AA GG GG GG GG 811 61 0 AG 45 GA GG AA GG GA GG TG 689 62 1 AA 44 GG GA AA GG GG GG GG 812 62 0 AG 45 GG GG AA GG GA GG TG 690 63 1 GG 55 GG GG GG TG GG GG TT 813 63 0 AG 45 GG GG AA GG GA GG TG 691 64 1 AA 44 GG GG AA GG GG GG GG 814 64 0 AG 45 GG GG AA GG GA GA TT 1 65 0 0 0 0 0 0 0 0 0 0 692 65 1 AG 45 GG GA AA GG GA GG TG 693 66 1 AG 45 GG GG GA GG GG GG TG 815 66 0 GG 55 GG GG AA GG GA GA TT 694 67 1 AG 45 GA GG GA TG GG GA TT 816 67 0 AG 45 GG GG AA GG GA GG TG 695 68 1 AG 45 GA GG GA TG GG GG TG 817 68 0 GG 55 GA GG GA TG GA GG TT 696 69 1 AG 45 GG GG GA GG GG GG 0 818 69 0 AG 45 GG GG AA GG GA GG TG 697 70 1 AG 45 GG GG GA GG GG GG TG 819 70 0 AG 45 GG GG AA GG GA GG TG 698 71 1 GG 55 GA GG GG TG GG GG TT 820 71 0 AA 44 GG GG AA GG GG GA TG 699 72 1 AA 44 GG GG AA GG GG GA TG 821 72 0 GG 55 GG GG AA GG AA GG TT 700 73 1 AG 45 GG GG GA TG GG GG TG 822 73 0 AG 45 GA GG GA TG GG GG TG 701 74 1 AG 45 GG GG AA GG GG GA TG 823 74 0 AG 45 GG GG AA GG GA GG TG 702 75 1 AA 44 GG GG AA GG GA GG TG 824 75 0 AG 45 GG GG AA GG GA GG TG 703 76 1 AG 45 GG GG AA GG GA GG TG 825 76 0 AG 45 GG GG GA GG GG GG TG 704 77 1 AA 44 GG GA AA GG GG GG GG 826 77 0 AG 45 GG GG AA GG GG GG GG 705 78 1 AG 45 GG GG GA TG GA GG TT 827 78 0 GG 55 GA GG GA TG 0 GG TT 706 79 1 AG 45 GG GG AA GG GG AA TT 828 79 0 GG 55 GG GG AA GG AA GG TT 707 80 1 GG 55 GG GG AA GG GG GA TG 829 80 0 GG 55 GA GG GG TG GG GG TT 708 81 1 AG 45 GG GG AA GG GA GG TG 830 81 0 AA 45 GG GG AA GG GA GA TT 709 82 1 AG 45 GG GG AA GG GG GA TG 831 82 0 AG 55 GG GG AA GG GA GA TT 710 83 1 AA 44 GG GA AA GG GA GG TG 832 83 0 AG 45 GA GG GA TG GG GA TT 711 84 1 GG 55 GA GG GA TG GA GG TT 833 84 0 AG 45 GG GG AA GG GA GG TG 712 85 1 AA 44 GG GG AA GG GG GG 0 834 85 0 AA 45 GG GA AA GG GG GG GG 713 86 1 AG 45 GG GG GA GG GG GG TG 835 86 0 AG 45 GG GG GA GG GG GA TT 714 87 1 AG 55 GG GG AA GG AA GG TT 836 87 0 AA 44 GG GG AA GG GG GG GG 715 88 1 GG 55 GG GG AA GG GA GG TG 837 88 0 AG 45 GG GG GA GG GG GG TG 716 89 1 AA 44 GG GG AA GG GG GA TG 838 89 0 AA 44 GG GG AA GG GG GG GG 717 90 1 AG 45 GG GG AA GG GG GA TG 839 90 0 AA 44 GG GG AA GG GG GA TG 718 91 1 AA 44 GG GA AA GG GA GG TG 840 91 0 AG 45 GG GG GA GG GG GG TG 719 92 1 AG 45 GG GG AA GG GG GA TG 841 92 0 AA 44 GG GG AA GG GG GA TT 720 93 1 AA 44 GG GG AA GG GG GG GG 842 93 0 AG 45 GA GG GA TG GG GG TG 721 94 1 AG 45 GG GG AA GG GA GG TG 843 94 0 AA 44 GG GA AA GG GG GG GG 722 95 1 AA 44 GG GG AA GG GG GA TG 844 95 0 AA 44 GG GG AA GG GG GG GG 723 96 1 AA 45 GG GG AA GG GA GG TG 845 96 0 GG 55 GG GG AA GG GA GA TT 724 97 1 AG 55 GG GG AA GG GA GA TT 846 97 0 AG 45 GA GG GA TG GG GG TG 725 98 1 GG 55 GA GG GA TG GA GG TT 847 98 0 AA 44 GG GA AA GG GG GG GG 726 99 1 GG 55 GA GG GA TG GA GG TT 848 99 0 AG 45 GA GG GA TG GG GG TG 727 100 1 AA 44 GG GG AA GG GG AA TT 849 100 0 GG 55 GA GG GA TG GG GA TT 728 101 1 AG 45 GG GG AA GG GG AA TT 850 101 0 AA 55 GG GG AA GG AA GG TT 729 102 1 GG 55 GA GG GA TG GG GA TT 851 102 0 AG 45 GG GG AA GG GA GG TG 730 103 1 AG 45 GG GG GA GG GG GG TG 852 103 0 AG 45 GG GG GA GG GG GG TG 731 104 1 GG 55 GA GG GA TG GG GG TG 853 104 0 GG 55 GG GG GA GG GG GA TT 732 105 1 AG 55 GG GG AA GG AA GG TT 854 105 0 AG 45 GA GG GA TG GG GA TT 733 106 1 AG 45 GG GG AA GG GA GG TG 855 106 0 AG 45 GG GA AA GG GG GG GG 734 107 1 AG 45 GG GG AA GG GG GA TG 856 107 0 AG 45 GG GA AA GG GA GG TG 735 108 1 AG 45 GG GG AA GG AA GG TT 857 108 0 AA 44 GG GA AA GG GG GG GG 736 109 1 AA 44 GG GG AA GG GG GG GG 858 109 0 AG 45 GG GG GA GG GG GG TG 737 110 1 AA 45 GG GG AA GG GA GG TG 859 110 0 GG 55 GA GG GA TG GA GG TT 738 111 1 GG 55 GA GG GA TG GG GA TT 860 111 0 AA 44 GG GG AA GG GG GG GG 739 112 1 AA 44 GG GG AA GG GG GG GG 861 112 0 AG 45 GG GA AA GG GG GA TG 740 113 1 GG 55 AA GG GG TT GG GG TT 862 113 0 GG 55 GA GG GA TG GA GG TT 741 114 1 AA 45 GG GG AA GG GA GG TG 863 114 0 AG 55 GG GG AA GG AA 0 TT 742 115 1 AA 44 GG GG AA GG GG GA TG 864 115 0 AG 45 GA GA GA TG GG GG TG 743 116 1 AG 45 GG GG AA GG GA GG GG 865 116 0 AA 44 GG GG AA GG GG GG GG 744 117 1 AA 44 GG GG AA GG GG GA TG 866 117 0 AG 45 0 0 0 0 0 0 0 745 118 1 AA 44 GG GG AA GG GG GG GG 867 118 0 AG 45 GG GG GA TG GG GG TG 746 119 1 GG 55 GG GG AA GG 0 AA TT 868 119 0 AG 55 GG GG AA GG AA GG TT 747 120 1 AG 45 GG GG AA GG GA GG TG 869 120 0 AG 55 GA GG GA TG GA GG 0 748 121 1 AA 44 GG GA AA GG GG GG GG 870 121 0 AA 44 GG GG AA GG GG GG GG 749 122 1 AG 45 GG GG AA GG GA GG TG 871 122 0 GG 55 GA GG GA TG GA GG TT 872 123 1 AA 45 GG GG AA GG GA GG TG 916 123 0 AG 55 GG GG AA GG AA GG TT 873 124 1 AA 44 GG GG AA GG GA GG TG 917 124 0 GG 55 GA GG GA TG GA GG TT 874 125 1 GG 55 GA GG AA GG GA GG TG 918 125 0 AG 45 GA GG GA TG GG GG TG 875 126 1 AA 44 GG GA AA GG GG GG GG 919 126 0 AA 45 GG GG AA GG GA GA TT 876 127 1 AG 45 GG GA AA GG GG GG GG 920 127 0 AG 45 GG GA AA GG GG GG GG 877 128 1 AA 44 GG GG AA GG GG GA TG 921 128 0 AG 45 GG GG GA GG GG GA TT 878 129 1 AG 45 GG GG AA GG GG GA TG 922 129 0 AA 55 GG GG AA GG AA GG TT 879 130 1 GG 45 GG GG GA GG GA GG TG 923 130 0 AA 44 GG GG AA GG GG GG GG 880 131 1 AA 44 GG GA AA GG GG GG GG 924 131 0 AG 45 GA GG GA TG GG GG TG 881 132 1 AG 45 GG GG GA GG GG GG TG 925 132 0 AA 44 GG GG AA GG GA GG TG 882 133 1 AG 45 GA GG GA TG GG GG TG 926 133 0 AG 55 GA GG GA TG GA GG TT 883 134 1 AA 44 GG GG AA GG GG GG GG 927 134 0 AA 44 GG GG GA TG GG GG TG 884 135 1 AA 44 GG GG AA GG GG GG GG 928 135 0 AA 44 GG GG AA GG GG GA TG 885 136 1 AA 45 GG GG AA GG GA GG TG 929 136 0 GG 55 GA GG GA TG GG GA TT 886 137 1 AA 44 GG GG AA GG GG GG GG 930 137 0 AG 45 GG GG AA GG GG GG GG 887 138 1 AG 45 GG GG AA GG AA GG TT 931 138 0 AG 45 GA GG GA TG GG GG TG 888 139 1 AG 55 GG GG AA GG GA GA TT 932 139 0 AG 45 GG GA GA GG GG GG TG 889 140 1 GG 55 GG GG GG TG GG GG TT 933 140 0 AA 44 GG GG AA GG GG GA TG 890 141 1 AA 45 GG GG AA GG GA GA TT 934 141 0 AA 44 GG GG AA GG GG GG GG 891 142 1 AG 45 GG GG AA GG GA GA TT 935 142 0 AG 45 GA GG GA TG GG GG TG 892 143 1 AG 45 GG GG GA GG GG GG TG 936 143 0 AG 45 GG GG AA GG GA GG TG 894 144 1 AA 44 GG GG AA GG AA GG TT 938 144 0 AA 44 GG GG 0 0 GA GG TG 895 145 1 GG 55 GG GG AA GG GA GA TT 939 145 0 AA 44 GG GG AA GG GG GG GG 896 146 1 AA 44 GG GA AA GG GG GG GG 940 146 0 AA 45 GG GG AA GG GA GA TT 897 147 1 AG 45 GA GG GA TG GG GA TT 941 147 0 AG 45 GG GG AA GG GA GG TG 898 148 1 AG 45 GA GG GA TG GG GG TG 942 148 0 AG 45 GG GG AA GG GA GG TG 899 149 1 AG 55 GG GG AA GG GA GA TT 943 149 0 AA 44 GG GG AA GG GG GA TG 5 150 0 0 0 0 0 0 0 0 0 0 900 150 1 AA 44 GG AA AA GG GG GG GG 901 151 1 AG 45 GA GG GA TG GG GG TG 944 151 0 AA 44 GG GA AA GG GG GG GG 902 152 1 AG 45 GA GG GA TG GG GG TG 945 152 0 AA 44 GG GG AA GG GG GG GG 903 153 1 AG 45 GA GG GA TG GG GG TG 946 153 0 AG 45 GG GG AA GG GA GG TG 904 154 1 AG 45 GG GG AA GG GA GA TT 947 154 0 AA 45 GG GG AA GG AA GG TT 905 155 1 GG 55 GG GG AA GG AA GG TT 948 155 0 AG 45 GG GG AA GG GA GA TT 906 156 1 AA 44 GG GG AA GG GG GG GG 949 156 0 AA 44 GG GG AA GG GA GG TG 907 157 1 AG 45 GG GG AA GG GA GG TG 950 157 0 AG 45 GG GG AA GG GA GG TG 908 158 1 AG 45 GG GG GA GG GG GG TG 951 158 0 AA 44 GG GG AA GG GG GA TG 909 159 1 AG 45 GA GG GA TG GG GG TG 952 159 0 GG 55 GG GG AA GG AA GG TT 910 160 1 AG 45 GG GG AA GG GG GA TG 953 160 0 AA 45 GG 0 AA GG GA GG TG 911 161 1 AA 45 GG GG AA GG GA GA TT 954 161 0 AG 45 GG GG AA GG GG GA TG 912 162 1 AA 44 GG GA AA GG GG GG GG 955 162 0 AA 44 GG GG AA GG GG GA TG 913 163 1 AA 44 GG GA AA GG GG GG GG 956 163 0 AA 44 GG GG AA GG GG GG GG 914 164 1 AG 45 GG GG GA GG GG GG TG 957 164 0 AG 45 GG GG AA GG GG GA TG 915 165 1 GG 55 GG GG AA GG GA GA TT 958 165 0 AG 45 GA GG GA TG GG GA TT 959 166 1 AG 45 GA GG GA TG GG GG TG 970 166 0 AG 45 GA GG GA TG GA GG TT 960 167 1 AG 45 GA GA GA TG GG GG TG 971 167 0 AA 44 GG GG AA GG GG GG GG 961 168 1 AA 44 GG GG AA GG GA GG TG 972 168 0 AG 45 GG GG AA GG GA GG TG 962 169 1 AG 45 GG GG AA GG GA GG TG 973 169 0 AA 44 GG GG AA GG GG GG GG 963 170 1 AA 44 GG GG AA GG GG GG GG 974 170 0 AA 44 GG GG AA GG GG GA TG 964 171 1 AA 44 GG GG AA GG GG GA TG 965 172 1 AG 45 GG GG AA GG GA GG TG 976 172 0 AG 45 GG GA AA GG GG GA TG 966 173 1 AG 55 GG GG AA GG AA GG TT 977 173 0 AG 45 GG GG GA GG GG GA TT 967 174 1 AG 45 GG GG GA GG GG GG TG 978 174 0 AG 45 GG GG AA GG GA GG TG 968 175 1 AG 45 GG GG AA GG GG GA TG 979 175 0 GG 55 GA GG GA TG GA GG TT 981 177 1 AG 45 GA GG GA TG GG GG TG 1013 177 0 AA 44 GG GG AA GG GG GG GG 982 178 1 GG 55 GA GG GA TG GA GG TT 1014 178 0 AG 45 GG GG AA GG GG 0 TG 983 179 1 GG 55 GA GG GA TG GA GG TT 1015 179 0 AA 44 GG GG AA GG GG GA TG 984 180 1 AA 44 GG GG AA GG GG GG GG 1016 180 0 AG 45 GG GA GA TG GG GG TG 985 181 1 AA 44 GG GA AA GG GG GG GG 1017 181 0 AA 44 GG GG AA GG GG GA TG 986 182 1 AA 44 GG GG AA GG GG 0 TG 1018 182 0 AG 45 GG GA AA GG GA GG TG 987 183 1 AG 45 GG GG GA GG GG 0 TG 1019 183 0 GG 55 GG GG GA GG GA GG TT 988 184 1 GG 55 GG GG GA GG GA GG TT 1020 184 0 GG 55 GA GG AA GG GA GG TG 989 185 1 AA 44 GG GG AA GG GG GA TG 1021 185 0 GG 55 GA GG GA TG GA GG TT 1022 187 0 AG 45 GA GG GA TG GG GG GG 990 188 1 AA 44 GG GA AA GG GG GG GG 1023 188 0 AG 45 GG GG GA GG GG GG TG 991 189 1 AG 45 GA GG GA TG GG GG TG 1024 189 0 AG 45 GG GG AA GG GG GA TG 1025 190 0 GG 55 GA GG GG TT GG GG TT 992 192 1 AG 45 GG GG AA GG GA GG TG 1026 192 0 AG 55 GG GG AA GG AA GG TT 993 193 1 GG 55 GG GG GA GG GG GA TT 1027 193 0 AG 45 GA GG GA TG GG GG TG 994 194 1 AA 44 GG GG AA GG GG GG GG 1028 194 0 AG 45 GG GG GA GG GG GG TG 995 195 1 AG 55 GG GG AA GG GA GA TT 1029 195 0 AG 45 GA GG GA TG GG GG TG 996 196 1 AG 45 GG GG GA GG GG GA TT 1082 196 0 AG 55 GA GG GA TG GA GG TT 997 197 1 AG 45 GG GG AA GG AA GG TT 1030 197 0 AG 45 GG GG AA GG GG GA TG 998 198 1 GG 55 GA GG GA TG GG GA TT 1031 198 0 AA 44 GG GG AA GG GG GG GG 1033 199 0 AG 55 GG GG AA TG AA GG TT 1060 199 1 AA 44 GG GG AA GG GG GG GG 1083 199 0 AA 45 GG GG AA GG GA GG TG 999 200 1 AG 45 GG GG GA TG GG GG TG 1034 200 0 0 0 0 0 0 0 0 0 0 1039 200 0 AG 45 GG GG AA 0 GA GA TT 1000 201 1 AA 45 GG 0 AA GG GA GG TG 1035 201 0 AA 44 GG GG AA GG GA GA TT 1061 216 1 AA 44 GG GG AA GG GG GA TG 1070 216 0 AG 45 GG GG AA GG GG AA TT 1062 217 1 AG 55 GG GG AA GG GA GA 0 1071 217 0 AG 45 GA GG GA TG GG GG TG 1063 218 1 AG 45 GG 0 AA GG 0 GG 0 1072 218 0 AA 44 GG GG AA GG GG GG GG 1064 219 1 GG 45 GG GA AA GG GA GG TG 1073 219 0 GG 55 GA GG GA TG GA GG TT 1065 220 1 AA 44 GG GG AA GG GG GG GG 1074 220 0 GG 55 AA GG GG TT GG GG TT 1066 222 1 AG 55 GG GG AA GG AA GG TT 1075 222 0 AA 45 GG GG AA GG GA GA TT 1076 223 0 AG 45 GG GG GA GG GG GG TG 1077 225 0 AG 45 GG GG AA GG GG GA TG 1067 226 1 AG 45 GA GG GA TG GG GG TG 1078 226 0 AG 45 GG GG GA GG GG GG TG 1079 227 0 0 0 0 0 0 0 0 0 0 1068 230 1 AA 44 GG GA AA GG GG GA TG 1080 230 0 AG 45 GG GG AA GG GA GA TT 1081 230 0 AG 45 GA GG GA TG GG GG TG 1040 232 1 GG 55 GG GG AA GG AA GG TT 1052 232 0 AG 45 GG GA AA GG GA GG TG 1041 233 1 AG 45 GA GG GA TG GG GG TG 1053 233 0 AG 45 GG GA AA GG GG GG GG 1042 234 1 AG 45 GA GG GA TG GG GG TG 1054 234 0 GG 55 GG GG AA GG GA GA TT 1043 236 1 AG 45 GG GG AA GG GG GA TG 1055 236 0 AG 45 GG GG AA GG GG GA TG 1044 237 1 AG 45 GA GG GA TG GG GG TG 1056 237 0 AG 45 GG GG AA GG GA GG TG 1045 238 1 AG 45 GG GG GA GG GG GG TG 1057 238 0 GG 55 GA GG GG TT GG GG TT 1046 239 1 AA 45 GG GG AA GG GA GG TG 1058 239 0 AG 45 GA GG GA TG GG GG TG 1059 239 0 AG 45 GG GG AA GG GA GG TG 405 240 1 AG 45 GG GG AA GG 0 GA TG 504 240 0 AG 45 GA GG GA TG GG GG TG 406 241 1 AG 55 GA GG GA TG GA GG TT 505 241 0 AG 55 GA GG GA TG GA GG TT 407 242 1 AA 45 GG GG AA GG GA GG TG 506 242 0 AA 44 GG GA AA GG GG GG GG 408 243 1 AA 45 GG GG AA GG GA GG TG 507 243 0 AG 45 GG GG AA GG GA GG TG 409 244 1 AG 45 GG GG GA GG GG GG TG 508 244 0 AG 55 GG GG AA GG AA GG TT 410 245 1 AA 44 GG GA AA GG GG GG GG 509 245 0 AG 45 GG GG GA GG GG GG TG 411 246 1 AG 45 GG GA AA GG GA 0 TG 510 246 0 AG 45 GG GG AA GG GA GG TG 412 247 1 AG 45 GA GG GA TG GG GG TG 511 247 0 AA 45 GG GG AA GG GA GG TG 413 248 1 AA 45 GG GG AA GG GA GG TG 512 248 0 AA 44 GG GG AA GG GA GG TG 414 249 1 AG 45 GG GG AA GG GG GA TG 513 249 0 AA 44 GG GG AA GG GG GA TG 415 250 1 AG 45 GG GG AA GG AA GG TT 514 250 0 AG 45 GG GG AA GG AA GG TT 416 251 1 AG 45 GG GG AA GG GG GA TG 515 251 0 AA 44 GG AA AA GG GG GG GG 417 252 1 AG 45 GG GG AA GG GG GA TG 516 252 0 AA 44 GG GA AA GG GG GA TG 418 253 1 AA 44 GG GG AA GG GA GG TG 517 253 0 AA 44 GG GG AA GG GG GA TG 419 254 1 GG 55 GG GG GA TG GA GG TT 518 254 0 AG 45 GA GG GA TG GG GA TT 420 255 1 AG 45 GG GG AA GG GA GA TT 519 255 0 GG 55 GG GG GA GG GG GG TT 421 256 1 AG 55 GG GG AA GG GA GA TT 520 256 0 AG 45 GG GG AA GG GG GA TG 422 257 1 AG 45 GG GG AA GG GA GG TG 521 257 0 AG 55 GG GG AA GG AA GG TT 423 258 1 AG 45 GG GG AA GG GA GG TG 522 258 0 AG 45 GG GG AA GG GG GA TG 424 259 1 AA 45 GG GG AA GG AA GG TT 523 259 0 AG 45 GG GA AA GG GG GA TG 425 260 1 AA 45 GG GG AA GG GA GG TG 524 260 0 AA 44 GG GG AA GG GG GG GG 426 261 1 AG 45 GA GG GA TG GG GG TG 525 261 0 AG 45 GG GG AA GG GG GG GG 427 262 1 AA 44 GG GG AA GG GG GG GG 526 262 0 AG 45 GG GG AA GG GA GA TT 428 263 1 AG 45 GG GG GA GG GG GG TT 527 263 0 AG 45 GG GG AA GG GG GA TG 429 264 1 AA 44 GG GG AA GG GG GG GG 528 264 0 AG 45 GA GG GA TG GA GG TT 430 265 1 AG 45 GG GG GA TG GG GG TG 529 265 0 AA 45 GG GG AA GG GA GA TT 530 266 0 AA 44 GG GG AA GG GG AA TT 432 267 1 AG 45 GG GG AA GG GA GG TG 531 267 0 AA 44 GG GG AA GG GG GA TG 433 268 1 AG 45 GG GG AA GG GA GA TT 532 268 0 AG 45 GA GG GA TG GG GG TG 434 269 1 AG 45 GA GG GA TG GG GG TG 533 269 0 AA 45 GG GG AA GG GA GG TG 435 270 1 AA 44 GG GG AA GG GG GG GG 534 270 0 GG 55 GA GG GG TG GG GG TT 436 271 1 AA 44 GG GG AA GG GG GA TG 535 271 0 AG 45 GG GA GA GG GG GA TT 437 272 1 AG 45 GG GG GA GG GG GG TG 536 272 0 0 55 GG GG AA GG GA GA TT 438 273 1 AA 44 GG GG AA GG GG GG GG 537 273 0 AG 45 GG GG AA GG GA GG TG 439 274 1 AG 45 GG GG AA GG GA GG TG 539 274 0 AA 44 GG GG AA GG GG GG GG 440 275 1 AG 45 GG GG GA TG GG GG TG 538 275 0 GG 55 GA GG GA TG GG GA TT 441 276 1 AG 45 GG GG AA GG GG GA TG 540 276 0 AA 44 GG GG AA GG GG GG GG 442 277 1 GG 55 GA GG GA TG GA GG TT 541 277 0 AG 45 GA GG GA TG GG GG TG 443 278 1 AA 44 GG GG AA GG GG GG GG 542 278 0 AA 44 GG GG AA GG GG GA TG 444 279 1 AA 44 GG GG AA GG GG GA TG 543 279 0 AA 44 GG GG 0 GG GG GA TG 445 280 1 AG 45 GG GA GA GG GG GG TG 544 280 0 AG 45 GA GG GA TG GG GG TG 446 281 1 AG 45 GG GG AA GG GA GG TG 545 281 0 AA 44 GG GG AA GG GG GG GG 447 282 1 GG 55 GA GG GA TG GG GA TT 546 282 0 GG 55 GA 0 GA TG GG GA TT 448 283 1 AG 45 GG GG AA GG GG GA TG 547 283 0 AG 45 GG GG AA GG GA GG TG 449 284 1 GG 55 GG GG GA GG GA GG TT 548 284 0 AG 45 GG GG AA GG GG GG GG 450 285 1 AG 45 GA GG GA TG GG GG TG 549 285 0 GG 55 GG GG AA GG GA GA TT 451 286 1 AG 45 GG GG AA GG GA GG TG 550 286 0 AG 45 GA GG GA TG GG GG TG 452 287 1 AA 44 GG GA AA GG GG GG GG 551 287 0 GG 55 GG GG GG TG GG GG GG 6 288 1 0 0 0 0 0 0 0 0 0 552 288 0 AA 44 GG GG AA GG GA GG TG 453 289 1 AG 45 GG GG GA GG GG GG TG 553 289 0 AG 45 GA GA GA TG GG GG TG 554 289 0 AA 44 GA 0 GA TG GG GG TG 555 290 0 AG 45 GG GG AA GG GA GG TG 556 290 0 AG 45 GG GG AA GG GA GA TT 455 291 1 AA 44 GG GG AA GG GA GG TG 557 291 0 AG 45 GG 0 GA GG GG GG TG 558 291 0 GG 55 GG GG GA GG GA GG TT 456 292 1 AG 45 GG GG AA GG GA GG TG 559 292 0 GG 55 GA GG GA TG GA GG TT 560 292 0 AA 44 GG GG AA GG GA GG TG 457 293 1 AA 44 GG GG AA GG GG GG 0 561 293 0 AA 44 GG GG AA GG GG GG GG 562 293 0 AG 45 GA GG GA TG GG GG TG 458 294 1 GG 55 GA GG GA TG GA GG TT 563 294 0 AA 44 GG GG AA GG GG GA TG 564 294 0 AG 45 GG GG GA GG GG GA 0 459 295 1 AA 44 GG GG AA GG GA GG TG 565 295 0 AG 45 GG GG AA GG GA GG TG 566 295 0 AG 45 GG GG AA GG GA GG TG 460 296 1 AA 44 GG GG AA GG GG GG GG 567 296 0 AG 45 GG GG GA 0 GG GG TG 568 296 0 AG 45 GA GG GA TG GA GG TT 461 297 1 AA 44 GG GG AA GG GG GA TG 569 297 0 AG 45 GG GG AA GG GG GA TG 570 297 0 AG 45 GG GG AA GG GG AA TT 462 298 1 GG 55 GA GG GG TG GG GG TG 571 298 0 AA 44 GG GG AA GG GG GG GG 572 298 0 AA 44 GG GG AA GG GG GG GG 463 299 1 AA 44 GG GA AA GG GG GG GG 573 299 0 GG 55 GA GG GA TG GA GG TG 574 299 0 GG 55 GG GG GG GG GG GG TT 464 300 1 GG 55 GA GG GG TG GG GG TT 575 300 0 AG 45 GG GA AA GG GG GG GG 576 300 0 AG 45 GG GG AA GG GA GG TG 465 301 1 GG 55 GA GG GA TG GA GG TT 577 301 0 AA 44 GG GG AA GG GG GA TG 578 301 0 AG 45 GG GG GA GG GG GG TG 466 302 1 AA 44 GG GA AA GG GG GA TG 579 302 0 AG 45 GG GG AA GG GA GA TT 580 302 0 AG 45 GG GG AA GG GA GG TG 467 303 1 AG 45 GG GG GA GG GA GG TT 581 303 0 AG 45 GA GG GA TG GG GG TG 582 303 0 AA 45 GG GG AA GG GA GG TG 468 304 1 AA 45 GG GG AA GG GA GG TG 583 304 0 AG 45 GA GG GA TG GG GA TT 584 304 0 AA 44 GG GG GA GG GG GG TG 2 305 0 0 0 0 0 0 0 0 0 0 469 305 1 AG 45 GG GG GA GG GG GG TG 585 305 0 AG 55 GG GG GA GG GA GG TT 470 306 1 GG 55 GA GG GG TG GG GG TT 586 306 0 AA 44 GG 0 AA GG GG GG GG 587 306 0 AG 55 GG GG GA GG GA GG TT 471 307 1 GG 55 AA GG GG TT GG GG TT 588 307 0 AA 44 GG GG AA GG GG GA TG 589 307 0 GG 55 GG GG GA GG GA GG TT 472 308 1 AG 45 GG GG AA GG GA GA TT 590 308 0 AG 45 AA GG GG TT GG GG TT 591 308 0 AA 44 GG GG AA GG GA GG TG 592 309 0 GG 55 GA GG GG TG GG GG TT 593 309 0 AA 44 GG GG AA GG GG GG GG 474 310 1 AG 45 GG GG GA GG GG GG TG 594 310 0 AG 45 GG GG GA TG GG GG TG 595 310 0 AG 45 GG GG AA GG GA GA TT 475 311 1 GG 55 GA GG GA TG GA GG TT 596 311 0 GG 55 GG GG AA GG GA GG TG 597 311 0 AG 45 GA GG GA TG GA GG TT 476 312 1 AG 45 GG GG AA GG GA GA TT 598 312 0 AG 45 GA GA GA TG GG GG TG 599 312 0 AG 45 GG GG AA GG GG GA TG 477 313 1 AG 45 GG GA GA TG GG GG 0 600 313 0 AG 45 GG GA GA GG GG GG TG 601 313 0 GG 55 GG GG AA GG GA GA TT 478 314 1 AG 45 GA GG GA TG GA GG TT 602 314 0 AA 44 GG GG AA GG GG GG GG 603 314 0 GG 55 GG GG AA GG GG AA TT 479 315 1 AA 44 GG GG AA GG GG GG GG 604 315 0 AG 45 GG GG GA GG GG GG TG 605 315 0 AG 45 GG GG AA 0 AA GG TT 480 316 1 GG 55 GG GG AA GG GG GG TG 606 316 0 AG 45 GG GG GA GG GG GG TG 607 316 0 AA 44 GG GG AA GG GG GA TG 481 317 1 AA 44 GG GG AA GG GG GG GG 608 317 0 AG 45 GG GG GA GG GG GA TT 609 317 0 AG 45 GG GG AA GG GA GG TG 482 318 1 AA 45 GG GA AA GG GA GG TG 610 318 0 AA 44 GG GA GA TG GG GG TG 611 318 0 AG 45 GG GG AA GG AA GG TT 483 319 1 AA 44 GG GG AA GG GG GG GG 612 319 0 GG 55 GA GG GA TG GA GG TT 613 319 0 AG 45 GG GG AA GG GG GA TG 484 320 1 AG 45 GG GA AA GG GA GG TG 614 320 0 AG 55 GA GG GA TG GA GG TT 615 320 0 AG 45 GA GG GA TG GG GG TG 485 321 1 AG 45 GG GG AA GG GA GG TG 616 321 0 AG 45 GG GG AA GG GA GG TG 617 321 0 AA 45 GG GG AA GG GA GG TG 486 322 1 AA 44 GG GG AA GG GG GG GG 618 322 0 AG 45 GA GG GA TG GG GA TT 619 322 0 AG 55 GG GG AA GG GA GA TT 487 323 1 AA 44 GG GG AA GG GG GG GG 620 323 0 GG 55 GA GG GA TG GA GG TT 621 323 0 AG 45 GG GG GA GG GG GA TT 488 324 1 AG 45 GG GG GA GG GG GG TG 622 324 0 AG 55 GG GG GA TG GA GG TT 623 324 0 AA 44 GG GA AA GG GG GG GG 489 325 1 AA 44 GG GG AA GG GA GG TG 624 325 0 GG 55 GA GG GG TG GG GG TT 625 325 0 AG 45 GA GG GA TG GG GG TG 7 326 1 AG 45 GA GG GA 0 GG GA TT 207 326 0 AG 45 GG GG GA TG GG GG TG 8 327 1 AG 55 GG GG AA GG GA GA TT 208 327 0 AG 45 GG GA AA GG GA GG TG 9 328 1 AG 45 GG GG AA GG GG GG GG 209 328 0 AA 44 GG GG AA GG GG GG GG 10 329 1 AG 55 GG GG AA GG AA GG TT 210 329 0 AG 45 GG GG GA GG GG GG TG 11 330 1 AG 45 GG GG GA GG GA GG TT 211 330 0 AG 45 GG GG GA 0 GG GG 0 12 331 1 GG 55 GA GG GG TG GG GG TT 212 331 0 GG 55 GA GG GG TG GG GG TT 13 332 1 GG 55 GA GG GA TG GA GG TT 213 332 0 AG 45 GA GG GA GG GG GG TG 14 333 1 AA 44 GG GG GA TG GG GG TG 214 333 0 AA 44 GG GG AA GG GG GG GG 15 334 1 AA 45 GG GG AA GG GA GG TG 215 334 0 GG 55 GA GG GG TG GG GG TT 16 335 1 AG 45 GG GG AA GG GG GA TG 216 335 0 AG 45 GG GG GA GG GG GG TG 17 336 1 AG 45 0 0 0 TG GG GG 0 217 336 0 AG 45 GA GG 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45 GG GG GA GG GG GA TT 32 351 1 AA 44 GG GG AA 0 GG GA TG 232 351 0 AG 55 GG GG GA GG GA GG TT 33 352 1 AA 44 GG GG AA GG GA GG TG 233 352 0 AA 44 GG GG AA GG GA GG TG 34 353 1 GG 45 GG GG GA GG GA GG TT 1108 353 0 AA 44 GG GG AA GG GG GG GG 35 354 1 0 0 0 0 0 0 0 0 0 234 354 0 AG 45 GG GG AA GG GG GA TG 36 355 1 GG 55 GG GG AA GG 0 GG TT 235 355 0 AG 45 GA GG GA TG GG GG TG 37 356 1 AA 44 GG GG AA GG GG GG 0 236 356 0 AA 44 GG GG AA GG GA GG TG 38 357 1 AG 45 GA GG GA TG GA GG TT 237 357 0 AG 45 GA GG GA TG GG GG TG 39 358 1 GG 55 GG GG GG TG GG GG TT 238 358 0 AG 45 GA GG GA TG GG GG TG 40 359 1 AG 55 GG GG AA GG GA GG TG 239 359 0 AG 45 GG GG AA GG GG GA TG 41 360 1 AG 45 GG GG GA GG GG GG TG 240 360 0 GG 55 GG GG GA GG GG GG TG 42 361 1 AG 45 GA GG GA TG GG GG TG 241 361 0 AG 45 GA GG GA TG GG GG TG 43 362 1 AA 45 GG GG AA GG GA GG TG 242 362 0 AA 44 GG GG AA GG GG GG 0 44 363 1 AA 44 GG GG AA GG GG GA TG 243 363 0 AA 44 GG GG AA GG GA GG TG 45 364 1 GG 55 GG 0 GA 0 GG GA 0 244 364 0 AG 45 GA GG GA TG GG GG TG 46 365 1 AG 45 GG 0 AA GG GG GG 0 245 365 0 AG 45 GG GG AA GG GA GG TG 47 366 1 GG 55 GA GG GA GG GG GG TG 246 366 0 AG 45 GA GG GA TG GG GG TG 48 367 1 AA 44 GG GG AA 0 GA GG TG 247 367 0 GG 55 GG GG GG GG GG GG TT 49 368 1 AG 45 0 GG AA GG GA GG TG 248 368 0 GG 55 GG GG GA TG GG GA TT 50 369 1 AG 45 GG GG AA GG GG GA TG 249 369 0 AA 44 GG GA AA GG GG GG GG 51 370 1 AG 45 GA GG GA TG GG GG TG 250 370 0 AA 44 GG GG AA GG GG GG GG 52 371 1 AG 45 GG GG GA GG GG GG TG 251 371 0 AA 44 GG GG AA GG GG GG GG 53 372 1 AG 45 GA GG GA TG GG GG TG 252 372 0 AA 45 GG GG AA GG GA GG TG 54 373 1 AG 55 GG GG AA GG AA GG TT 253 373 0 AA 44 GG GA GA GG GG GG GG 55 374 1 GG 55 GA GG GA TG GG GA TT 254 374 0 GG 55 AA GG GG TT GG GG TT 56 375 1 AA 44 GG GG AA GG GG GG GG 255 375 0 AA 44 GG GG AA GG GA GG TG 57 376 1 AG 55 GG GG AA GG AA GG TT 256 376 0 AG 45 GG GG GA GG GG GG TG 58 377 1 AG 45 GG GG GA TG GG GG TG 257 377 0 AG 45 GA GG GA TG GG GG TG 59 378 1 GG 55 GA GG GA TG GA GG TT 258 378 0 GG 55 AA GG GG TT GG GG TT 60 379 1 AG 45 GG GG GA GG GG GG TG 259 379 0 GG 55 GG GG AA 0 AA GG TT 61 380 1 AA 44 GG GG AA GG GG GG GG 260 380 0 AG 45 GG GG AA GG GG GA TG 62 381 1 AG 45 GG GG GA TG GG GG TG 261 381 0 AG 45 GA GG GA TG GG GG TG 63 382 1 AG 45 GA GG GA TG GG GG TG 262 382 0 AA 44 GG GG AA GG GA GG TG 64 383 1 AG 55 GG GG AA GG GA GG TT 263 383 0 AG 45 GG GA GA GG GG GG TG 65 384 1 AA 44 GG GG AA GG GA GG TG 264 384 0 AG 45 GG GG GA GG GG GG TG 66 385 1 GG 55 GG GG GA GG GA GG TT 265 385 0 AG 45 GA GG GA TG GG GG TG 67 386 1 AG 45 GA GG GA TG GG GG TG 266 386 0 AG 45 GG GG AA GG GA GG TG 68 387 1 AG 45 GG GG GA GG GG GG TG 267 387 0 AG 45 GG GG AA GG GA GG TG 69 388 1 AG 45 GG GG GA TG GG GG TG 268 388 0 AG 45 GA GG GA TG GG GG TG 70 389 1 AG 45 GG GG GA GG GG GG TG 269 389 0 AA 44 GG GG AA GG GG GA TG 71 390 1 AA 44 GG GG AA GG GG GG GG 270 390 0 AG 45 GG GG AA GG GA GG TG 72 391 1 AG 45 GG GG GA GG GG GG TG 271 391 0 AG 55 GG GG GA TG GA GG 0 73 392 1 AG 45 GG GG GA TG GA GG TT 272 392 0 AG 45 GA GG GA TG GG GA TT 74 393 1 AG 45 0 GA GA TG GG GG TG 273 393 0 AA 45 GG GG AA GG GA GG TG 75 394 1 AG 45 GA GG GA TG GG GA TT 274 394 0 AA 44 GG GG AA GG GG GG GG 76 395 1 AG 45 GG GG GA TG GG GG TG 275 395 0 AA 44 GG GG AA GG GA GG TG 77 396 1 AA 44 GG GG AA GG GG GA TG 276 396 0 AA 44 GG GG GA GG GG GG TG 78 397 1 AG 45 GG GG GA GG GG GG TG 277 397 0 AG 45 GA GA GA TG GG GG TG 79 398 1 AG 45 GG GG GA GG GG GG TG 278 398 0 AA 44 GG GG AA GG GG GG GG 80 399 1 AG 45 GG GG GA GG GG GG TG 279 399 0 AG 45 GG GA AA GG GG GG GG 81 400 1 GG 55 GA GG GG TG GG GG TT 280 400 0 GG 55 GA GG GA TG GA GG TT 82 401 1 AA 44 GG GG AA GG GG GA TG 281 401 0 AG 45 GG GG AA GG GA GG TG 83 402 1 AG 45 GG GG 0 TG GG GG TG 282 402 0 AG 45 GG GG GG TT GG GG TT 84 403 1 GG 55 GG GG GG TG GG GG 0 283 403 0 GG 55 GG GG GA GG GG GA TT 85 404 1 AG 45 GG GG GA GG GG GG TG 284 404 0 AG 45 GG GG GA GG GG GG TG 86 405 1 AA 44 GG GG AA GG GG GG 0 285 405 0 AG 45 GA GG GA TG GG GG TG 87 406 1 AG 45 GG GG AA GG AA GG TT 286 406 0 GG 45 GG GG AA GG GG GA TG 88 407 1 AG 45 GG GG GA GG GG GA TT 287 407 0 AG 45 GG GG GA GG GG GG TG 89 408 1 AA 44 GG GG AA GG GG GG GG 288 408 0 AG 45 GG GG GA TG GA GG TT 90 409 1 AA 44 GG GG AA 0 GG GG GG 289 409 0 GG 55 GG 0 GA GG GA GG TT 91 410 1 GG 45 GG GG GA GG GG GA TT 290 410 0 AG 45 GG GG AA 0 GA GG TG 92 411 1 AG 45 GG GG AA GG GA GG TG 291 411 0 AG 45 GA GG GA 0 GG GG TG 93 412 1 AA 44 GG GG AA GG GG GG GG 292 412 0 AA 44 GG GG AA 0 GG GA TG 94 413 1 GG 55 AA GG GA TG GG GG TG 293 413 0 AA 44 GG GG GA GG GG GG TG 95 414 1 AG 55 GG GG GA TG GA GG TT 294 414 0 AG 55 GA GG GA TG GA GG TT 96 415 1 AG 45 GA GG GA TG GG GA TT 295 415 0 GG 55 GG GG GA GG GA GG TT 97 416 1 AG 45 GG GG AA GG GG AA TT 296 416 0 AA 44 GG GG AA GG GG GA TG 98 417 1 AA 44 GG GG AA GG GG GA TG 297 417 0 GG 55 GA GG GA TG GG GA TT 99 418 1 AG 45 GA GG GA TG GG GG TG 298 418 0 AG 45 GG GG AA GG GA GG TG 100 419 1 AA 45 GG GG AA GG GA GG TG 299 419 0 AG 45 GG GG AA GG 0 GG GG 101 420 1 AA 44 GG GG AA 0 GA GG TG 300 420 0 AG 45 GA GG GA TG GG GG TG 102 421 1 0 0 0 0 0 0 0 0 0 301 421 0 AG 55 GG GG AA GG GA GA TT 103 422 1 AG 45 GG GG GA GG GG GG TG 302 422 0 AG 45 GA GG GA TG GG GG TG 104 423 1 AA 44 GG GG AA GG GG GG GG 303 423 0 GG 55 GA GG GA TG GG GA TT 105 424 1 AG 55 GG GG GA GG GA GG TT 304 424 0 AA 44 GG GG AA GG GG GG GG 106 425 1 AG 45 GG GG GA TG GG GG TG 305 425 0 AA 45 GG GG AA GG GG GG TG 658 426 1 AG 45 GG GG AA GG GA GG 0 781 426 0 AG 45 GG GG AA GG GG GA TG 893 427 1 GG 55 GA GG GA TG GA GG TT 937 427 0 AG 45 GG GG AA GG GA GG TG 969 428 1 AA 44 GG GG AA GG GG GA TG 980 428 0 AG 45 GG GG AA GG GG GA TG 107 432 1 AA 44 GG GG AA GG GG GG GG 306 432 0 GG 55 GG GG GA TG GG GA TT 108 433 1 AG 55 0 GG GA TG GA GG TT 307 433 0 AA 44 GG GG AA GG GG GG GG 109 434 1 AA 44 GG GG AA GG GG GG GG 308 434 0 AA 44 GG GA AA 0 GG GG GG 110 435 1 AA 45 GG GG AA GG GA GG TG 309 435 0 AG 45 GG GA AA GG GG GA TG 111 436 1 AG 55 GG GG AA GG GA GA TT 310 436 0 AG 45 GG GG AA GG GA GG TG 112 437 1 AA 44 GG GG GA TG GG GG TG 311 437 0 AA 45 GG GG AA GG GA GG TG 113 438 1 AG 45 GG GG GA GG GG GG TG 312 438 0 AG 45 GA GG GA TG GG GG TG 114 439 1 AG 45 GG GG AA GG GG AA TT 313 439 0 AG 45 GA GG GA TG GG GG TG 115 440 1 AA 44 GG GG AA GG GG 0 GG 314 440 0 AA 44 GG GG GA TG GG GG TG 116 441 1 GG 55 GG GG AA GG AA GG TT 315 441 0 GG 55 GG GG AA GG GG AA TT 117 442 1 GG 55 GG GG GA GG GG GA TT 316 442 0 AG 45 GG GA GA GG GG GG TG 118 443 1 GG 55 GG GG GA GG 0 GA TT 317 443 0 AA 44 GG GA AA GG GG GA TG 119 444 1 GG 55 GA GG GA TG GG GA TT 318 444 0 GG 55 GG GG GG TG GG GG TT 120 445 1 GG 55 GG GG GA GG GA GG TT 319 445 0 GG 55 GA GG GA TG GA GG TT 121 446 1 AG 45 GA GG GA TG GG GG TG 320 446 0 AG 45 GG GG GA GG GG GG TG 122 447 1 GG 55 GA GG GG TG GG GG TT 321 447 0 AG 45 GG GG GA GG GG GG TG 123 448 1 AA 44 GG GG AA GG GG GA TG 322 448 0 AG 45 GG GG GA TG GG GA TT 124 449 1 AG 45 GG GG AA GG GG GA TG 323 449 0 AG 45 GA GG GA TG GG GG TG 125 450 1 GG 55 GG GG GA TG GA GG TT 324 450 0 AA 44 GG GG AA GG GA GG TG 126 451 1 AA 44 GG GG AA GG GG GA TG 325 451 0 GG 55 GG GG GA GG GA GG TT 127 452 1 AG 45 GG GG GA GG GG GA TT 326 452 0 AG 45 GG GG GA GG GG GG TG 128 453 1 AG 45 GG GG AA GG GG GA TG 327 453 0 GG 45 GG GG GG GG GG GG TT 129 454 1 AG 45 GG GG AA GG GA GG TG 328 454 0 AG 45 GG GG GG TG GG GG TT 130 455 1 AG 45 GG GG GA GG GG GG TG 329 455 0 AA 45 GG GG AA GG GA GG TG 131 456 1 AG 45 GG GG GA GG GG GG TG 330 456 0 AG 45 GG GG AA GG GA GG TG 132 457 1 AA 45 GG GG AA GG GG GA TG 331 457 0 AG 45 GG GG AA GG GG GA TG 133 458 1 AA 44 GG GG 0 0 GG GG 0 332 458 0 AA 44 GG GA AA GG GG GG GG 134 459 1 AG 45 GG GG 0 0 GG GG 0 333 459 0 AG 45 GA GG GA TG GG GG TG 135 460 1 GG 55 GG GG GA GG GA GG TT 334 460 0 GG 45 GG GG AA GG GG GA TG 136 461 1 GG 55 GA GG GA TG GA GG TT 335 461 0 GG 55 GG GG GA GG GA GG TT 137 462 1 AG 45 GA GA GA TG GG GG TG 336 462 0 AG 45 GG GG AA GG GA GG TG 138 463 1 AA 44 GG GA AA GG GG GG GG 337 463 0 AA 44 GG GG AA GG GG GG GG 139 464 1 AA 44 GG GG AA GG GG GG GG 338 464 0 AA 45 GG GG AA GG GA GG TG 140 465 1 AG 45 GG GG AA GG AA GG TT 339 465 0 AA 44 GG GG AA GG GG GG GG 141 466 1 GG 55 GG GG AA GG AA 0 TT 142 467 1 AG 45 GA GG 0 TG GG GG TG 340 467 0 AG 45 GG GA GA TG GG GG TG 143 468 1 GG 55 GG GG AA GG AA GG TT 341 468 0 AA 44 GG GG AA GG GA GG TG 144 469 1 AG 45 GA GG GA TG GG GG TG 342 469 0 AG 45 GA GG GA TG GG GG TG 145 470 1 AG 45 GG GG AA GG GG GA TG 343 470 0 AG 45 GA GG GA TG GG GA TT 146 471 1 AG 45 0 0 GA 0 GG GG 0 344 471 0 AG 45 GG GA GA TG GG GG TG 147 472 1 AA 45 GG GG AA 0 GA GG TG 345 472 0 AA 44 GG GG AA GG GA GG TG 148 473 1 AA 44 GG GA AA GG GG GG GG 346 473 0 AA 44 GG GG GA GG GG GG GG 149 474 1 AG 45 GG GG GA GG GG GG TG 347 474 0 AG 45 GG GG AA 0 GG GG GG 150 475 1 AG 55 GG GG GA GG GA GG TT 348 475 0 GG 55 GG GG AA GG GG GA TG 151 476 1 AG 55 GG GG AA GG GA GG TG 349 476 0 AA 44 GG GA AA GG GG GG GG 152 477 1 AA 44 GG GG AA GG GG GG GG 350 477 0 AA 44 GG GG GA TG GG GG TG 153 478 1 AA 45 GG GG AA GG GA GG TG 351 478 0 AA 44 GG 0 AA GG GA GA TT 154 479 1 GG 55 GG GG AA GG GG GG GG 352 479 0 AG 45 GG GG GA GG GG GG TG 155 480 1 AG 45 GG GG GA TG GG GG TG 353 480 0 GG 55 GG GG GA GG GG GA TT 156 481 1 GG 55 GA GG GG TG GG GG TT 354 481 0 GG 55 GG GG AA GG GA GA TT 157 482 1 GG 55 GG GG GA GG GA GG TT 355 482 0 GG 55 GG GG AA GG GA GA TT 158 483 1 AG 45 GG GG AA GG GA GG TG 356 483 0 AG 45 GG GA GA GG GG GG TG 159 484 1 AG 45 GG GG AA GG GA GG TG 357 484 0 AG 45 GA GG GA TG GG GG TG 160 485 1 GG 55 GA GG GA TG GA GG TT 358 485 0 0 0 0 0 0 0 0 0 0 161 486 1 AG 45 GA GG GA TG GG GG TG 359 486 0 AG 45 GA GA GA TG GG GG TG 162 487 1 AA 44 GG GG AA GG GG GG GG 360 487 0 GG 55 GA GG GA TG GA GG TT 163 488 1 AG 45 GA GG GA TG GG GG TG 361 488 0 AG 45 GG GG AA GG GG GA TG 164 489 1 0 0 GG 0 GA 0 0 GG TT 362 489 0 AA 45 GG GG AA GG GA GG TG 165 490 1 AA 44 GG GG AA GG GA GG TG 363 490 0 AG 45 GG GG GA GG GG GG TG 166 491 1 AG 45 GA GG GA TG GG GG TG 364 491 0 AG 45 GA GG AA GG GA GG TG 167 492 1 AG 45 GA GG GA TG GG GG TG 365 492 0 AA 44 GG GG AA 0 GG GA TG 168 493 1 AG 45 GG GA AA GG GA GG TG 366 493 0 AG 45 GA GG GA TG GG GG TG 169 494 1 0 0 GG 0 GA GG GG GA TG 367 494 0 AA 44 GG GG AA GG GG GG GG 170 495 1 0 0 0 0 0 0 0 0 0 368 495 0 AA 44 GG GG AA 0 GA GG TG 171 496 1 GG 55 GG GG GA GG GA GG TT 369 496 0 GG 55 GG GG GA GG GG GA TT 172 497 1 GG 55 GG GG GA TG GG GA TT 370 497 0 AG 45 GG GG GA 0 GG GG TG 173 498 1 AG 45 GG GG GA GG GG GG TG 371 498 0 AG 55 GG GG AA 0 GA GG TG 174 499 1 AG 45 GA GG GA TG GG GG TG 372 499 0 AA 44 GG GA AA 0 GG GG GG 175 500 1 AG 45 GG GG AA GG GG GG GG 373 500 0 AG 45 0 GG GA 0 GG GG TG 176 501 1 AA 44 GG GG AA GG GG GG GG 374 501 0 GG 55 GG GG GA TG GG GA TT 177 502 1 0 0 GG 0 AA 0 GG GA 0 375 502 0 AG 45 0 GG GA 0 0 GG TG 178 503 1 AA 44 GG GG AA GG GG GG GG 376 503 0 AG 45 GG GG AA GG AA GG TT 179 504 1 AA 44 GG GG AA GG GG GA TG 377 504 0 AG 45 GG GG AA GG GA GG TG 180 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0.1921617452 1.64941783867672 1 22 0 22 12 1 68 0.31411223 1.15800493655117 1 22 11 22 12 1 63 0.2095793814 1.56265270255722 2 22 12 12 12 1 63 0.2095793814 1.56265270255722 1 22 11 22 22 0 67 0.290933662 1.2346600034345 1 22 12 22 11 0 59 0.1467080014 1.91931105271664 2 22 12 22 11 1 59 0.1467080014 1.91931105271664 1 22 12 12 12 1 72 0.4164761525 0.87592607591724 2 22 12 22 12 0 57 0.121705894 2.10614784959441 2 22 22 22 11 1 56 0.1106555065 2.20133344869846 1 22 11 22 12 thesias-3.1.1/examples/dataset3/pafah.txt000066400000000000000000001103531360777755100203470ustar00rootroot000000000000002 0 0.267 TC CC RR II AV 1 0 0.267 TT CC RR II VV 3 0 0.2669 TC CC RR II AV 4 0 0.2667 TT CC RR II VV 5 0 0.2671 TC CC RH II AA 7 0 0.2669 TT CC RR II AA 8 0 0.2671 TT CC RR II AV 9 0 0.2687 TT CC RR II AV 10 0 0.2677 TT CC RR II AV 11 0 0.2661 CC GG HH II AA 13 0 0.266 TC CG RR II AV 14 1 0.240 TC CG RH II AA 18 0 0.2657 TC CG RH II AV 19 0 0.2657 TC CC RR II AA 22 0 0.2657 TT CC RR II AA 24 0 0.2653 TC CG RH II AA 30 1 0.224 TC CG RH II AA 31 0 0.2643 CC CG RH IT AA 32 0 0.2643 TT CC RH II AA 36 0 0.2641 CC CG RH II AA 41 0 0.2643 TC CG RH II AV 42 0 0.264 TC CC RH II AA 43 0 0.2641 TC CC RH II AA 44 0 0.264 TC CC RR II AA 45 0 0.264 TC CG RH II AA 46 0 0.1604 TC CG RH II AA 47 0 0.2633 TC CG RH II AA 49 0 0.2631 TC CC RR II AV 50 0 0.2631 TT CC RR II AV 51 1 0.005 TT CC RR II VV 52 0 0.2629 TC CG RH II AA 53 0 0.2629 TC CC RR II AA 55 0 0.2633 TC CG RH II AA 56 0 0.014 TC CC RR IT AA 57 0 0.2621 TT CC RR II AA 58 0 0.2621 TT CC RR II VV 59 0 0.2623 TC CC RR IT AA 60 0 0.2623 CC CG RH II AA 61 0 0.2623 TC CC RH II AA 63 0 0.2621 CC CC RH II AA 64 1 0.192 TC CG RH II AA 65 0 0.2669 TC CC RH II AA 66 1 0.052 TC CG RH II AV 69 0 0.2611 TC CC RR IT AA 71 0 0.2611 CC GG HH II AA 72 0 0.2611 TT CC RR II AA 73 0 0.261 TT CC RR II AV 75 1 0.240 CC CG RH II AA 77 0 0.2603 CC CC RR IT AV 78 1 0.236 TT CC RR II AV 79 0 0.2603 TC CG RH II AA 80 0 0.2601 TC CG RH II AA 81 1 0.052 TT CC RR II AA 83 0 0.2601 TC CG RH II AA 85 0 0.160 TC CG RH II AA 86 1 0.008 TC CC HH II AA 88 0 0.2609 TT CC RR II AV 93 0 0.259 TT CC RR II AA 94 0 0.259 TC CG RH II AA 97 0 0.2589 TT CC RR II AV 103 0 0.2707 TC CC RR IT AA 104 0 0.2563 TC CC RH II AA 105 0 0.2564 TT CC RR II AA 108 0 0.2633 TC CG RH II AA 109 0 0.2561 TC CC RR IT AA 110 0 0.2563 TT CC RR II VV 111 0 0.2561 TT CC RR II VV 114 0 0.256 CC CG RH IT AV 115 0 0.256 TC CG RH II AV 116 0 0.2561 CC GG HH II AA 117 0 0.264 CC CG RH II AA 118 0 0.2526 CC CC RR II AV 119 0 0.256 TC CC RH II AA 120 0 0.2559 CC CC RH II AA 122 0 0.2554 TC CC RR IT AA 123 1 0.194 TT CC RR II AA 125 0 0.2561 TT CC RR II AA 127 0 0.2554 TT CC RR II AA 129 0 0.2553 CC GG HH II AA 132 1 0.191 TT CC RR II AA 135 0 0.2571 TC CC RR IT AV 136 0 0.255 TT CC RR II AA 137 0 0.2544 TT CC RR II AA 138 1 0.092 TT CC RR II AV 139 0 0.2551 TT CC RR II AA 140 0 0.2541 TT CC RR II AA 141 0 0.2559 TC CG RH II AA 145 0 0.255 TT CC RR II AV 147 0 0.2544 CC CG RH II AA 150 0 0.2544 TC CC RR II AV 151 0 0.2543 TC CC RR IT AV 152 0 0.2544 TC CG RH II AA 153 0 0.2544 TC CG RH II AV 154 0 0.2544 TC CG RH II AV 156 0 0.2541 TT CC RR II AV 163 0 0.2534 TT CC RR II AV 166 0 0.2534 TC CC RR II AA 172 0 0.2531 TC CC RH II AA 174 0 0.2531 TT CC RR II VV 175 0 0.2531 TC CG RH II AA 177 0 0.2531 TC CC RH II AV 178 0 0.2531 TT CC RR II AA 179 0 0.2533 TC CG RH II AA 184 1 0.026 TT CC RR II AV 186 0 0.2524 CC GG RH II AA 192 0 0.2524 CC CG RH IT AA 193 0 0.2523 TT CC RR II VV 194 1 0.054 TT CC RR II AA 197 0 0.2521 TT CC RR II AA 198 0 0.252 CC GG RH II AA 201 0 0.2521 TC CG RR II AA 202 0 0.2521 CC CG RH IT AV 203 0 0.2521 TT CC RR II AA 207 0 0.2513 TT CC RR II AA 208 1 0.027 CC CC RR II AA 209 0 0.2483 TC CG RH II AA 210 0 0.2513 TT CC RR IT AA 212 1 0.201 TC CC RR II AV 213 1 0.069 TT CC RR II AV 214 1 0.223 TT CC RR II AV 216 0 0.2503 TT CC RR II AV 217 0 0.2503 TT CC RR II AA 219 0 0.2506 TC CG RH II AA 221 0 0.2506 CC CC RR II AA 222 0 0.2506 TT CC RR II AA 223 1 0.048 TT CC RR II AA 225 0 0.2503 TC CG RH II AV 228 0 0.2496 TC CG RH II AA 229 0 0.2524 TC CC RH II AV 231 0 0.2496 TC CG RH II AV 234 0 0.2496 CC CG HH II AA 235 0 0.2496 TC CC RR II AA 236 0 0.2494 TT CC RR II AV 238 0 0.2496 TT CC RR II AA 239 0 0.2493 TT CC RR II AV 240 0 0.2477 TC CG RH II AV 241 0 0.2494 TC CC RH II AV 246 0 0.2491 TT CC RR II AV 247 0 0.2491 TC CC RR II AA 250 0 0.2493 TC CC RR II AV 251 1 0.074 TT CC RR II AA 253 0 0.2486 TC CG RH II AA 256 0 0.2483 TC CC RH II AA 258 1 0.136 TC CG RH II AA 259 0 0.2483 TC CG RH II AA 260 0 0.2483 TC CG RH II AA 262 0 0.2411 TT CC RR II AV 264 0 0.2483 TT CC RR II AV 267 0 0.2483 TC CC RH II AV 268 0 0.2481 TT CC RH II AV 277 0 0.2479 TT CC RR II AA 278 0 0.248 TT CC RR II AA 280 0 0.2479 TT CC RR II AA 281 0 0.2479 CC CC RR IT AA 282 0 0.2479 TT CC RR II AA 283 0 0.2473 TC CG RH II AA 285 0 0.2471 TT CC RR II AA 287 0 0.2471 TC CC RR II AV 290 0 0.2471 TT CC RR II AA 291 0 0.2471 CC CG RH II AA 292 0 0.2473 TT CC RR II AV 293 0 0.2471 TT CC RR II AV 294 0 0.247 TC CG HH II AA 295 0 0.2471 CC GG HH II AA 296 0 0.247 TC CC RR IT AA 297 0 0.247 TC CG RH II AA 298 0 0.247 TT CC RR II AA 300 0 0.2469 TT CC RR II AV 301 0 0.247 TT CC RR II AA 307 0 0.247 TC CG RH II AA 310 1 0.152 CC GG HH II AA 312 0 0.247 TT CC RR II AA 313 1 0.174 TC CC RR II AV 316 1 0.238 TC CG RH II AA 318 1 0.003 TC CG RH IT AA 319 0 0.2463 TC CC RR IT AA 320 0 0.2463 TC CC RR IT AA 322 0 0.2461 TT CC RR II AV 324 0 0.2463 TC CC RH II AV 326 0 0.246 TT CC RR II AA 327 0 0.246 TT CC RR II AV 329 0 0.246 CC CG RH II AV 330 0 0.2461 TT CC RR II AA 331 0 0.1959 TT CC RR II AA 332 0 0.246 TT CC RR II AA 334 1 0.030 CC CG RH II AA 335 1 0.180 TT CC RR II AV 336 0 0.2459 TC CG RH II AA 339 0 0.2473 TC CC RR II AA 340 0 0.2459 TC CC HH II AA 341 1 0.192 TC CG RH II AV 342 0 0.2451 TC CG RH II AV 345 0 0.2451 TC CC RR IT AA 346 0 0.2453 TT CC RR II AV 347 0 0.2453 TT CC RR II AV 348 0 0.2451 TT CC RR II VV 349 0 0.2007 CC CG RH IT AA 352 0 0.2447 TC CC RH II AA 353 0 0.2451 TT CC RR II AV 354 0 0.245 TT CC RR II AV 357 0 0.2404 CC CG HH II AA 360 0 0.2443 TC CC RR IT AV 361 0 0.2431 TC CG RH II AA 362 0 0.2443 TC CC RR II AA 365 0 0.244 TC CC RR II AA 366 0 0.2441 TT CC RR II VV 368 0 0.244 TC CC RR II AA 374 1 0.076 CC CG RH II AA 376 0 0.2434 TC CC RH II AA 377 1 0.002 TT CC RR II AV 380 0 0.2434 TT CC RR II VV 381 0 0.2434 TC CC RR IT AA 385 1 0.009 TT CC RH II AV 389 0 0.2433 TC CG RH II AA 390 0 0.2433 TT CC RR II AV 391 0 0.2434 TT CC RR II AA 392 0 0.2431 TC CC RR IT AV 394 0 0.2431 TC CG RH II AV 395 0 0.243 TC CG RH II AV 396 0 0.2433 TC CC RH II AA 397 0 0.2431 CC GG HH II AA 398 0 0.2431 TC CC RR II AA 401 0 0.243 TT CC RR II AA 402 0 0.202 TC CG RH II AA 403 0 0.243 TT CC RR II AV 404 0 0.243 TC CG RH II AV 406 0 0.2429 TC CG RH II AA 407 0 0.2429 CC CG HH II AA 409 0 0.2424 CC CC RH II AA 410 0 0.2424 TC CG RH II AA 412 0 0.2607 TC CC RR IT AA 413 0 0.2424 CC GG HH II AA 414 0 0.2423 TT CC RR II AA 415 1 0.098 TC CG RH II AA 417 0 0.2423 CC CG HH II AA 418 0 0.2423 TC CC RR II AV 420 0 0.2421 TC CC RH II AV 425 0 0.1927 TC CC RH II AA 428 0 0.242 CC CG RH II AA 429 1 0.002 TT CC RR II AA 432 1 0.182 TC CC RR II AV 438 0 0.2414 TC CG RH IT AA 439 0 0.2414 TT CC RR II AA 440 1 0.220 CC CG HH II AA 443 0 0.2414 TC CG RH TT AV 445 0 0.2414 TC CG RH II AV 447 0 0.2413 TT CC RR II AV 448 0 0.2413 TC CC RR IT VV 449 0 0.2413 TC CG RH II AV 450 0 0.2414 TC CC RR II AA 451 0 0.241 TC CG RH II AA 457 0 0.241 TT CC RR II AA 460 0 0.2404 TC CC RR II AA 462 0 0.2403 TT CC RR II AV 464 0 0.2404 TC CG RH II AA 465 0 0.2404 TT CC RR II AA 468 0 0.2404 TT CC RR II AA 469 0 0.2404 CC GG HH II AA 471 0 0.1916 TC CG RH II AV 473 0 0.240 TT CC RR II AA 475 0 0.264 TC CG RH II AA 476 1 0.204 TC CG RH II AA 480 0 0.2394 CC CG HH II AA 481 0 0.2394 CC CG RH II AA 482 1 0.195 CC CC RR II AA 484 0 0.2394 TC CC RR II AA 485 0 0.2393 TC CC RR II AA 487 0 0.2393 TC CG RH II AA 489 0 0.2391 CC CG RH II AA 490 0 0.2391 CC GG HH II AA 491 0 0.2389 TC CC RH II AA 493 0 0.2391 CC CC RR IT AA 494 0 0.2389 TT CC RR II AA 497 0 0.2394 TT CC RR II AA 498 0 0.2391 CC CG HH II AA 499 0 0.2391 TT CC RR II AA 501 1 0.030 TC CC RR II AA 502 0 0.2384 TC CG RH II AA 503 0 0.2384 CC CG RH IT AV 504 0 0.2384 TT CC RR II AA 505 0 0.2384 TC CG RH II AA 506 0 0.2383 TC CG RH II AV 507 0 0.2383 TT CC RR II AA 508 0 0.2384 TC CC RR IT AV 511 0 0.2383 CC CC RH II AA 512 0 0.2383 TT CC RR II AA 513 0 0.2383 CC CG HH II AA 514 0 0.2381 CC CG RH II AA 515 0 0.056 TC CG RH II AA 516 0 0.2381 TT CC RR II AA 526 0 0.2373 TT CC RR II AA 527 0 0.2373 CC CG RH IT AA 529 0 0.2373 TC CC RR IT AA 530 0 0.2371 TT CC RR II AA 531 0 0.2371 TC CG RH II AA 535 0 0.237 TC CC RH II AA 538 0 0.2364 TC CC RH II AA 539 0 0.2364 TT CC RR II AA 540 1 0.140 TT CC RR II AA 541 0 0.2363 TT CC RR II AV 543 0 0.2363 TT CC RR II AV 544 0 0.2361 TT CC RR II AV 548 0 0.2357 TC CC RH II AA 549 0 0.2357 TT CC RR II AV 550 0 0.2357 TT CC RR II AV 551 0 0.2357 TC CG RH II AA 553 0 0.2354 CC CC RH II AV 554 0 0.2354 TC CG RH II AA 558 0 0.2354 TT CC RR II AA 563 0 0.2351 CC CG RH II AA 564 0 0.2346 CC CC RR II AA 565 0 0.2346 TT CC RR II AA 566 0 0.2346 TC CC RH II AV 567 0 0.2346 TC CG RH II AA 573 0 0.2346 TC CG HH II AA 574 0 0.2346 CC CC HH II AA 578 1 0.104 TT CC RR II AV 579 0 0.2343 TT CC RR II AV 593 0 0.2524 TC CC RH II AV 598 0 0.2344 TC CC RR II AV 600 0 0.2334 TC CG RH II AV 603 0 0.2334 TC CC RR IT AV 604 0 0.2334 CC CG HH II AA 605 0 0.2334 TT CC RR II AV 607 0 0.2333 TC CC RH II AA 612 0 0.2333 TC CG RH II AV 613 0 0.2293 CC GG RH II AA 625 0 0.2326 CC GG RH II AA 626 0 0.234 TC CC RH II AV 629 0 0.2323 TC CG RH II AV 630 0 0.2324 TC CG RH II AA 634 0 0.2321 TC CC RR II VV 635 0 0.2314 TC CC RH II AV 636 0 0.2313 TC CC RR II AV 640 0 0.2189 CC CG HH II AA 641 1 0.047 TT CC RR II AA 643 0 0.2314 TC CC RR II VV 645 0 0.2314 CC CG RH IT AV 646 0 0.2314 TT CC RR II AV 650 0 0.2314 TT CC RR II VV 651 0 0.2314 TC CC RR IT AV 655 0 0.2313 TT CC RR II AA 656 0 0.2313 TC CC RR II AV 657 1 0.013 TC CG RH II AA 658 0 0.2313 CC CG RH IT AA 659 0 0.204 CC CC RR TT AA 660 0 0.2311 CC GG HH II AA 662 0 0.065 TC CG RH II AA 663 0 0.2311 TC CG RH II AA 665 0 0.2311 TC CG RH II AV 668 0 0.2296 TC CG RH II AA 669 0 0.2307 TT CC RR II AA 670 0 0.2291 TC CG RH II AV 671 0 0.229 TT CC RR II AV 672 0 0.2287 TT CC RR II AA 673 0 0.2287 TT CC RR II AA 674 0 0.192 TT CC RR II AA 676 0 0.2286 TT CC RR II AA 677 0 0.2286 TC CG RH II AA 685 0 0.2276 TT CC RR II AA 687 0 0.2276 TT CC RR II AA 688 0 0.2276 TT CC RR II VV 689 0 0.2276 TT CC RR II AA 690 0 0.228 TC CC RR II AA 691 0 0.2276 CC CG RH II AV 697 0 0.2271 TT CC RR II AV 698 0 0.2271 TC CC RH II AV 700 0 0.2257 TC CG RH II AA 703 0 0.2271 CC GG HH II AA 704 0 0.2267 TT CC RR II AV 705 0 0.227 TC CG RH II AA 707 0 0.2271 TC CG RH II AA 709 0 0.2271 CC CG RH II AA 710 0 0.2263 TC CG RH II AA 712 0 0.228 TT CC RR II VV 713 0 0.2264 TT CC RR II AA 716 0 0.2263 TT CC RR II AV 717 0 0.2261 TC CG RH II AV 718 0 0.2256 TC CG RH II AV 719 0 0.2261 TC CG RH II AV 720 0 0.2257 TT CC RR II AV 721 0 0.2254 TC CG RH II AA 723 0 0.2217 TC CG RH II AV 724 0 0.2214 TC CG RH II AA 726 0 0.2209 TC CG RH II AA 729 0 0.2251 TC CC RH II AA 733 0 0.2206 TT CC RR II AV 734 0 0.2206 TT CC RR II AV 735 1 0.154 CC CG HH II AA 736 0 0.2213 TT CC RR II AA 737 0 0.2204 CC CG HH II AA 740 0 0.2204 TT CC RR II AA 741 0 0.2206 TC CC RH II AA 742 0 0.2204 TC CG RR II AA 743 0 0.2204 CC CG RH IT AA 745 0 0.2314 TC CC RR II AA 747 1 0.104 TC CG RH II AA 748 0 0.2231 CC CC RH II AA 749 0 0.2197 TC CG RH II AA 750 0 0.2204 TC CG RR II AV 751 0 0.2196 TC CG RH II AA 754 0 0.2199 TC CG RH II AV 757 0 0.2197 TT CC RR II VV 760 0 0.2196 CC CG RH II AA 762 0 0.2196 TC CG RH II AA 764 0 0.2194 TT CC RH II AV 767 0 0.2186 TT CC RR II AA 768 0 0.2189 TC CG RH II AA 769 0 0.2186 TC CG RH II AA 771 0 0.2189 CC GG RH II AA 772 0 0.2186 TT CC RR II AV 775 0 0.2186 TT CC RR II AV 777 0 0.2181 TC CC RR II AA 778 1 0.036 TC CC RR II AA 779 0 0.2181 TC CC RH II AV 780 0 0.2184 TC CC RR IT AV 781 0 0.2179 TT CC RR II AA 786 0 0.2177 TT CC RR II VV 787 0 0.2176 TT CC RR II AA 788 0 0.2176 TC CC RR II AA 790 0 0.2176 TC CC RH II AA 791 0 0.2176 TC CG RH II AA 797 0 0.2167 TT CC RR II AA 798 0 0.2219 TC CG RH II AV 800 0 0.2169 TT CC RR II AV 801 0 0.2169 CC CG RH II AA 807 0 0.2163 TC CG RH II AA 809 0 0.2166 CC CG RH IT AA 811 0 0.2167 TC CC RR IT AA 812 0 0.2164 TT CC RR II AA 813 0 0.2164 TC CC RR II AA 815 0 0.216 TT CC RR II AA 817 0 0.2611 TT CC RR II AA 818 1 0.010 TT CC RR II AA 819 0 0.2159 CC CC HH II AA 820 1 0.150 TT CC RR II AA 821 0 0.2157 TC CC RR II AA 822 0 0.2164 TC CG RH II AV 824 0 0.2156 TC CC RR II AV 825 0 0.2156 TC CG RH II AA 826 0 0.2154 CC CC RH IT AA 827 1 0.024 TC CG RH II AA 829 0 0.2156 CC CG HH II AA 830 0 0.2156 CC CG RH II AA 831 0 0.2157 TT CC RR II VV 832 0 0.2153 TT CC RR II AV 834 1 0.240 TC CC RR IT AA 835 1 0.052 TC CG RH II AA 836 0 0.2149 TC CG RH II AV 837 0 0.2149 TT CC RR II AV 838 0 0.2146 TC CC RR IT AV 839 1 0.010 TC CC RR II AA 840 0 0.2143 TC CG RH II AV 843 0 0.2146 CC GG HH II AA 845 0 0.2146 TT CC RR II AA 846 0 0.2143 TC CG RH II AV 847 0 0.2143 TT CC RR II AV 849 0 0.2141 TC CC RH II AA 850 0 0.2143 TC CC RH II AA 851 0 0.2143 TT CC RR II AV 852 0 0.2139 TT CC RR II AV 853 0 0.2139 CC CG HH II AA 855 0 0.214 TT CC RR II VV 857 0 0.2137 TC CG RH II AA 859 0 0.2139 TC CC RR II AA 860 0 0.2139 TC CC RR II AA 861 0 0.2139 TC CC RH II AV 862 0 0.214 TT CC RR II AA 865 0 0.2137 TC CC RR IT AA 866 0 0.2137 TT CC RR II AV 867 0 0.2146 TC CG RH II AA 869 0 0.2136 TC CG RH II AA 870 0 0.2136 CC CG RH II AA 871 0 0.190 TC CG RH II AA 872 0 0.2134 TC CG RH II AA 873 0 0.2134 CC CC RR TT AA 875 0 0.213 TC CG RH II AV 876 0 0.213 CC CC RH II AA 878 0 0.2129 TT CC RR II AA 879 1 0.025 CC CG RH II AA 880 0 0.2127 TT CC RR II AV 881 0 0.213 TT CC RR II AV 882 0 0.2127 TC CC RH II AV 883 0 0.2127 TC CC RR II AA 886 1 0.100 TT CC RR II AA 887 0 0.2126 TC CC RR IT AV 888 0 0.2127 TC CG RH II AA 889 0 0.2123 TT CC RR II AA 896 0 0.2117 TT CC RR II AV 897 0 0.2116 CC CG RH II AA 898 1 0.142 TC CC RH II AA 899 0 0.2124 TC CG RH II AA 900 0 0.2119 TT CC RR II AV 901 0 0.2116 TC CC RR II AV 902 0 0.2116 TT CC RH II AA 903 0 0.2116 TC CG RH II AV 904 0 0.2114 TT CC RR II AV 907 0 0.2107 TC CG RH II AA 908 0 0.2107 TC CC RH II AA 909 1 0.172 CC CG HH II AA 910 0 0.2114 TC CC RH II AA 912 0 0.2109 TT CC RR II AA 913 0 0.2109 TC CG RH II AA 915 0 0.211 TT CC RR II AA 917 0 0.2107 TT CC RH II AV 918 0 0.2107 TC CC RR IT VV 919 0 0.2107 TT CC RR II AV 921 0 0.2107 TT CC RR II AA 922 0 0.1593 TC CG RH II AA 923 0 0.2086 TC CG RH II AV 924 0 0.2107 CC CG RH II AA 928 0 0.2106 CC CC RR II AA 930 0 0.2106 TT CC RR II AV 931 1 0.156 TT CC RR II AA 932 0 0.2667 TT CC RR II VV 933 0 0.2106 TC CC RR IT AA 938 0 0.2106 TC CC RR IT AV 939 0 0.2099 CC CG RH II AA 941 0 0.2099 TC CC RR II AV 943 0 0.210 TT CC RR II VV 944 0 0.210 TC CG RH II AA 946 0 0.2079 TC CG RH II AA 948 0 0.2097 TT CC RR II AA 951 0 0.2096 TC CG RR II VV 952 0 0.2097 TT CC RR II AV 953 0 0.2097 TC CG RH II AV 954 0 0.2097 TT CC RH II AA 955 0 0.2097 TC CC RR II AA 957 0 0.2097 TC CG RH II AA 959 0 0.2097 TC CG RH II AA 961 0 0.120 TT CC RR II AA 964 0 0.2094 TC CG RH II AA 965 0 0.2094 TT CC RR II AA 966 0 0.2094 CC CG RH IT AA 968 1 0.083 TT CC RR II AV 971 0 0.209 TC CG RH II AA 974 0 0.208 TC CC RH II AA 975 0 0.2084 TC CG RH II AA 979 0 0.2087 TT CC RR II VV 980 0 0.120 TT CC RR II AA 981 0 0.2087 TC CG RH II AA 982 0 0.2086 TT CC RR II AA 984 0 0.2086 TT CC RR II VV 986 0 0.2346 TC CC RR IT AA 987 0 0.202 TT CC RR II AA 989 1 0.099 TC CC RR II AA 992 0 0.2079 TC CG RH II AV 993 0 0.2077 TC CG RH II AA 995 0 0.2079 TT CC RR II VV 997 0 0.208 TT CC RR II AA 998 0 0.2081 CC GG HH II AA 1000 1 0.055 TC CC RR IT AA 1002 0 0.2076 TT CC RR II AA 1005 1 0.038 TC CC RR IT AA 1006 0 0.2077 CC CG HH II AA 1007 0 0.1561 TT CC RR II AA 1008 0 0.2096 CC GG HH II AA 1009 0 0.2053 TT CC RR II AA 1010 0 0.2051 TT CC RR II AA 1013 0 0.205 CC GG HH II AA 1014 0 0.2049 TC CC RR II AA 1015 0 0.2049 TC CG RH II AA 1016 0 0.205 TC CC RH II AV 1018 1 0.008 TT CC RR II AA 1019 0 0.2049 TT CC RR II AA 1020 0 0.2049 CC GG HH II AA 1021 0 0.2049 TT CC RR II AV 1022 0 0.205 TC CC RR II AA 1023 0 0.205 TC CC RR IT AV 1026 0 0.2046 TC CG RH II AA 1028 0 0.2053 TT CC RR II AV 1029 0 0.2014 TT CC RR II AV 1031 0 0.204 TT CC RR II AV 1032 1 0.125 TC CG RH II AA 1033 0 0.2041 TT CC RR II AA 1034 1 0.130 TT CC RR II AA 1035 0 0.204 TC CC RR IT AA 1039 0 0.2041 TC CC RR II AV 1040 0 0.2039 TC CG RH II AV 1041 0 0.2336 TT CC RR II AV 1042 0 0.2041 TT CC RR II AV 1044 0 0.2046 TT CC RR II AA 1045 0 0.2046 TC CC RH II AV 1046 0 0.2039 TT CC RR II AA 1048 0 0.2037 TT CC RR II AA 1050 0 0.2036 TC CG RH TT AA 1052 0 0.2033 TT CC RH II AA 1053 0 0.2037 TT CC RR II AA 1055 0 0.2036 TC CG RH II AV 1056 0 0.203 TT CC RR II VV 1057 1 0.018 TT CC RR II AA 1058 0 0.2031 TC CC RH II AA 1060 0 0.2031 CC CG HH II AA 1062 0 0.203 TC CC RR IT AA 1064 0 0.203 TC CC RR IT AA 1065 1 0.126 TC CG RH II AA 1067 0 0.2029 TT CC RR II AV 1068 0 0.2029 TC CC RR IT AA 1070 0 0.2029 TC CG RH II AA 1071 0 0.2029 CC CG RH II AA 1072 0 0.2027 TT CC RR II VV 1073 0 0.143 TT CC RR II AV 1074 1 0.005 TC CG RH II AA 1075 0 0.2021 TC CC RR IT AA 1077 0 0.2026 TT CC RR II AA 1079 1 0.120 TT CC RR II AV 1082 0 0.2026 TC CC RH II AA 1083 0 0.2026 TT CC RR II AV 1085 0 0.2021 TT CC RR II AA 1087 0 0.2027 TC CG RH II AA 1089 0 0.2027 TT CC RR IT AA 1090 0 0.2079 TC CC RH II AA 1092 0 0.2014 CC CC RH II AV 1095 0 0.2021 TC CG RH II AV 1096 0 0.2021 TC CC RR IT AA 1097 0 0.202 TT CC RR II AV 1098 0 0.2463 TC CC RH II AV 1099 0 0.202 TC CC RR II AA 1102 0 0.202 CC CG HH II AA 1103 0 0.202 TC CC RR IT AA 1104 0 0.2004 CC CG RH II AA 1105 0 0.2009 TT CC RR II AA 1106 1 0.159 TT CC RR II AA 1108 0 0.2007 TC CC RR II AV 1109 1 0.016 TC CG RH II AV 1110 0 0.2003 TT CC RR II AA 1112 0 0.2001 TC CC RH II AA 1114 0 0.2001 TC CG RH II AA 1117 0 0.2003 CC CC RR IT AA 1118 0 0.2003 TC CC RH II AA 1121 0 0.2001 TT CC RR II AA 1123 1 0.133 TC CC RR II AA 1126 0 0.200 TC CC RH II AV 1127 1 0.008 TC CG RH II AA 1128 1 0.040 TC CG RH II AA 1130 0 0.1907 TC CC RH IT AA 1132 0 0.1999 TC CC RH II AA 1133 0 0.1997 TC CG RH II AA 1134 1 0.085 TC CC RH II AA 1135 0 0.1999 CC CG RH II AA 1137 0 0.1999 CC GG HH II AA 1138 0 0.010 TC CC RH II AA 1142 0 0.1993 TC CC RH II AA 1143 0 0.1993 TC CG RH II AA 1144 0 0.1991 TT CC RR II AA 1145 0 0.1993 TT CC RR II AA 1146 0 0.1993 TC CC RH II AV 1148 0 0.199 TC CG RH II AV 1149 0 0.1991 TC CG RH II AA 1150 0 0.199 CC CC RR IT AA 1151 0 0.199 TT CC RR II VV 1152 0 0.199 TC CC RR II AA 1154 0 0.199 TT CC RR II AV 1156 1 0.158 TC CC RH II AV 1158 0 0.199 TT CC RR II AA 1159 0 0.1989 TC CG RH II AA 1160 0 0.1989 TC CC RH II AA 1161 0 0.1989 TT CC RR II VV 1162 1 0.022 TT CC RR II AA 1163 0 0.1989 TT CC RR II AA 1165 0 0.199 TT CC RR II VV 1168 0 0.160 TT CC RR II AA 1171 0 0.198 CC CG RH II AA 1172 0 0.198 TT CC RR II AA 1175 0 0.170 TC CG RH II AA 1177 0 0.120 TC CC RR II AA 1180 0 0.197 TC CG RH II AA 1181 1 0.038 TC CG RH II AA 1182 1 0.056 CC CC RR II AA 1183 0 0.197 TT CC RR II AV 1184 0 0.199 TC CC RR II AA 1188 0 0.1969 CC CG HH II AA 1189 1 0.106 TC CG RH II AA 1191 0 0.1969 TC CG RH II AA 1192 1 0.014 TC CG RH II AA 1193 0 0.1969 TT CC RR II AV 1194 0 0.1969 TC CG RH II AA 1196 0 0.1967 TT CC RR II AV 1197 0 0.1967 CC CG HH II AA 1198 1 0.052 TC CC RH II AA 1200 0 0.1966 TT CC RR II AA 1201 0 0.1964 TT CC RR II AA 1203 0 0.1964 TC CC RR II AA 1204 0 0.196 TC CG RH II AA 1211 0 0.196 TT CC RR II AV 1212 0 0.196 TT CC RR II AV 1214 0 0.1959 TC CG RH II AA 1215 0 0.1743 TT CC RR II AV 1217 0 0.1957 TC CC RH II AA 1219 1 0.135 TC CC RR II AA 1220 0 0.1957 CC CG RH II AA 1221 0 0.1957 TC CG HH II AA 1222 0 0.1956 TC CG RH II AA 1226 0 0.1956 TT CC RR II AA 1227 0 0.1954 TC CC RH II AA 1228 0 0.194 TC CC RR IT AA 1229 0 0.194 TC CG RH II AV 1230 0 0.194 TC CG RH II AA 1233 0 0.194 TT CC RR II AA 1235 1 0.009 TT CC RR II AA 1238 0 0.1937 TT CC RR II AA 1239 0 0.1937 TC CC RR II AA 1248 1 0.002 TC CG RH II AV 1250 1 0.061 TT CC RR II AV 1252 0 0.1929 TT CC RR II AA 1255 0 0.1929 CC CG HH II AA 1256 0 0.1929 TT CC RR II AA 1258 0 0.1929 TC CG RH II AA 1259 0 0.1929 TT CC RH II AA 1260 0 0.1929 TC CC RH II AA 1261 0 0.1929 TC CC RR IT AA 1263 0 0.1927 TC CG RH II AA 1264 0 0.1927 TC CG RH II AA 1268 0 0.1921 TT CC RR II AA 1269 0 0.1921 TT CC RR II AA 1270 0 0.1921 TC CC RR II AA 1271 1 0.153 TT CC RR II AV 1272 0 0.1919 TT CC RR II AV 1273 0 0.1919 TT CC RR II AV 1274 0 0.161 TT CC RR II AA 1276 0 0.1917 CC GG HH II AA 1278 0 0.1917 TC CC RR II AA 1279 0 0.1917 TC CC RH II AV 1280 0 0.1917 TC CC RR II VV 1284 0 0.191 TC CG RH II AV 1285 0 0.1909 TT CC RR II AA 1286 1 0.116 TC CG RH II AA 1287 0 0.1909 TC CG RH II AA 1288 0 0.1907 CC CG RH IT AA 1289 0 0.1907 TT CC RR II AA 1290 0 0.1907 TT CC RR II AA 1291 0 0.1907 TT CC RR II VV 1292 0 0.1907 TC CC RH IT AA 1297 0 0.1841 TC CC RR IT AA 1300 0 0.1841 TC CG RR II AV 1303 0 0.184 TC CG RH II AA 1304 0 0.184 TT CC RR II AV 1305 0 0.184 CC CC RH IT AA 1306 0 0.184 TT CC RR II AV 1308 0 0.184 CC GG HH II AA 1309 0 0.1839 TC CC RR II AA 1310 0 0.180 TC CG RH II AA 1311 0 0.1839 TC CC RH II AV 1312 0 0.2346 TC CC RH II AV 1315 0 0.1839 TT CC RR II VV 1316 0 0.1839 TC CG RH II AA 1317 1 0.022 TC CC RH II AA 1318 0 0.1833 TC CC RH II AA 1321 0 0.1833 CC GG RH II AA 1322 0 0.1833 TC CG RH II AA 1324 0 0.1833 CC CG HH II AA 1325 0 0.1831 TC CC RH II AA 1326 0 0.1833 TC CC RR IT AV 1327 0 0.1831 TT CC RR II AV 1328 1 0.008 TT CC RR II AV 1331 0 0.1831 TT CC RR II AV 1332 0 0.1831 TT CC RR II AV 1334 0 0.183 TC CG RH II AV 1336 0 0.183 TT CC RR II AV 1337 0 0.1837 TT CC RR II AA 1339 0 0.1836 TC CC RR IT AV 1340 0 0.1836 TT CC RR II AA 1342 0 0.1813 CC CG RH IT AA 1343 0 0.1811 TC CC RR II AA 1344 0 0.183 TC CG RH II AV 1345 0 0.183 TT CC RR II AV 1348 0 0.1827 TT CC RR II AV 1349 0 0.1823 TT CC RR II AV 1350 0 0.1823 TT CC RR II AA 1351 0 0.2263 TC CG RH II AA 1352 0 0.1813 TT CC RR II AA 1356 0 0.1811 TT CC RR II AV 1358 0 0.1811 TC CC RH II AA 1359 0 0.181 CC GG HH II AA 1360 0 0.181 CC GG HH II AA 1361 0 0.181 TC CC RR II AA 1362 0 0.181 TC CC RR II AV 1364 0 0.181 TT CC RR II AV 1365 0 0.181 TC CC RR II AV 1367 0 0.1809 TT CC RR II AV 1368 0 0.1809 CC CC RH IT AA 1369 0 0.1809 TT CC RR II AA 1371 0 0.1809 TT CC RR II AA 1372 0 0.1809 TC CC RH II AV 1376 0 0.1807 TT CC RR II AV 1378 1 0.052 TC CG RH II AA 1379 0 0.105 TT CC RR II AV 1381 1 0.039 TT CC RR II AA 1383 0 0.180 TC CC RR IT AV 1384 0 0.180 CC CC HH II AA 1385 0 0.180 TC CC RH II AV 1387 0 0.180 TT CC RR II AA 1389 0 0.1851 TC CC RH II AA 1390 0 0.180 CC GG HH II AA 1391 1 0.001 TT CC RR II AA 1393 0 0.1781 CC CC RH IT AA 1394 0 0.1783 TC CG RH II AA 1395 0 0.178 TC CC RH II AA 1397 0 0.1767 TC CG RH II AA 1399 0 0.1286 CC CG RH II AA 1400 0 0.1286 TT CC RR II VV 1401 0 0.126 CC CC HH II AA 1402 0 0.126 TC CG RH II AA 1403 0 0.1257 TT CC RR II AV 1404 0 0.1256 TT CC RR II AA 1407 0 0.125 TC CG RH II AV 1408 0 0.125 TT CC RR II AA 1409 0 0.1247 TC CC RR II AA 1410 0 0.1247 TT CC RR II AA 1411 0 0.1241 CC CG RH II AA 1412 0 0.124 TC CC RR IT AA 1413 0 0.1239 TT CC RR II AV 1414 0 0.1221 TT CC RR II AA 1416 0 0.122 TT CC RR II AV 1417 0 0.122 TT CC RR II VV 1418 0 0.1219 TC CC RH II AA 1419 0 0.1217 TC CC RR II AA 1420 0 0.1216 TC CC RR II AA 1421 0 0.1216 TC CG RH II AA 1422 0 0.1209 CC CG HH II AA 1423 0 0.1209 TC CG RH II AA 1425 0 0.1209 TC CC RR IT AA 1426 0 0.1209 TC CG RH II AV 1428 0 0.120 TC CC RR II VV 1429 0 0.120 TC CC RR IT AA 1431 0 0.120 TT CC RR II AV 1432 0 0.1197 TC CG RH IT AV 1433 0 0.1191 TC CC RH II AV 1434 1 0.076 TC CC RR IT AV 1438 0 0.1189 TC CC RH II AA 1439 0 0.1187 TC CG RR II AV 1440 0 0.1183 TC CG RH II AV 1441 0 0.118 TC CG HH II AA 1442 0 0.118 TC CG RH II AA 1443 0 0.1179 TC CG RH II AA 1444 0 0.1179 TC CC RR II VV 1445 0 0.1173 TC CG RH II AA 1446 0 0.068 TT CC RR II AA 1447 1 0.052 CC GG HH II AA 1448 0 0.1173 TC CG RH II AV 1449 0 0.1171 TT CC RR II AV 1450 0 0.1171 TT CC RR II AV 1452 0 0.1169 CC GG HH II AA 1453 0 0.1169 TT CC RR II AV 1454 0 0.1163 CC CG HH II AA 1455 0 0.1163 CC GG HH II AA 1456 0 0.116 CC CG RH IT AA 1457 0 0.116 TC CG RH II AA 1458 0 0.116 TT CC RR II VV 1459 0 0.1157 TC CG RH II AA 1460 0 0.1157 CC CC RH II AV 1461 0 0.1157 TC CC RR II AV 1462 0 0.1151 TC CG HH II AA 1463 0 0.1151 CC GG HH II AA 1464 0 0.1151 TT CC RR II AA 1465 0 0.115 TC CC RR II AA 1466 0 0.115 TT CC RR II AV 1467 0 0.115 TC CG RH II AA 1468 0 0.1149 CC CC RH II AA 1469 0 0.1149 TT CC RR II AV 1470 0 0.1149 TT CC RR II VV 1471 0 0.1143 TC CG RH II AV 1472 0 0.1143 TC CG RH II AV 1473 0 0.1143 TT CC RR II AA 1474 0 0.114 TC CC RH II AV 1476 1 0.027 CC CG RH IT AA 1478 0 0.114 TT CC RR II AV 1479 0 0.1139 TC CG RH II AV 1480 1 0.006 TT CC RR IT AA 1482 0 0.1131 TT CC RR II AA 1483 0 0.1131 TC CC RH II AA 1484 0 0.113 TC CG HH II AA 1485 1 0.065 TT CC RR II VV 1486 0 0.1123 CC CC RR IT AV 1488 0 0.1111 TT CC RR II AV 1489 0 0.111 TC CC RH II AA 1490 0 0.111 TC CG RR II VV 1491 0 0.111 TT CC RR II AA 1492 0 0.1104 TC CG RH II AA 1493 0 0.1099 TT CC RR II AA 1494 0 0.1091 TT CC RR II AA 1495 0 0.1091 CC CG RH II AA 1496 0 0.1091 TC CC RH II AA 1497 1 0.082 TC CC RH II AA 1498 0 0.109 CC CG RH II AV 1499 0 0.1083 CC CG RH IT AA 1500 0 0.1081 TT CC RR II AV 1501 0 0.1079 TT CC RR II AA 1502 0 0.1079 TT CC RR II AV 1503 0 0.1064 TC CC RR II AA 1504 0 0.1064 TT CC RR II AA 1505 1 0.027 TT CC RR II AA 1506 0 0.105 CC CC RR IT AA 1509 0 0.0956 TT CC RR II AA 1510 0 0.0956 TC CC RR II AA 1511 0 0.0956 CC CG RH IT AV 1512 0 0.0954 TC CC RR II AA 1513 0 0.0954 TT CC RR II AA 1514 0 0.0954 TC CC RH II AV 1516 0 0.0953 TT CC RR II AV 1517 0 0.0951 TC CC RR II AV 1518 0 0.0951 CC CG RH II AA 1519 0 0.0947 TC CC RR IT AA 1520 1 0.068 TC CC RH II AA 1521 0 0.0943 TT CC RH II AA 1522 0 0.0943 TC CG RH II AA 1523 0 0.0943 CC GG HH II AA 1524 0 0.0943 CC CG RH II AA 1525 0 0.0943 CC CG RH II AA 1527 0 0.0943 TT CC RR II AV 1528 0 0.0943 TC CG RH II AA 1529 0 0.0941 TT CC RR II AV 1530 0 0.0941 TC CG RH II AA 1531 0 0.0941 TT CC RR II VV 1532 0 0.094 TT CC RR II AV 1534 0 0.0933 CC GG HH II AA 1535 0 0.0933 CC CC RR IT AV 1536 0 0.0931 TC CG RH II AA 1537 0 0.093 CC CG RR II AA 1538 0 0.093 CC CC RH II AV 1539 0 0.0926 TC CG RH II AA 1541 0 0.0924 TC CG RR II AA 1542 0 0.0924 TT CC RR II AA 1544 0 0.0923 TC CG RH II AV 1545 0 0.0921 TC CG RH II AA 1546 0 0.0921 TC CG RH II AA 1548 0 0.092 TT CC RR II AV 1549 0 0.0916 CC GG HH II AA 1550 0 0.117 TT CC RR II AV 1551 0 0.1177 TT CC RR II AA 1552 0 0.116 TC CC RR IT AV 1553 0 0.1143 TC CC RR IT AV 1554 0 0.1143 TC CC RH II AA 1555 0 0.1141 TC CG RH II AA 1556 0 0.1153 TC CG RH II AV 1557 0 0.1157 TT CC RR II AV 1558 0 0.1153 TC CG RH II AA 1559 0 0.1153 TC CG RR II AA 1560 0 0.1149 CC CG HH II AA 1561 0 0.1117 TC CC RH II AA 1562 0 0.004 TT CC RR II AA 1563 0 0.1113 TC CG RH II AV 1564 1 0.026 CC GG HH II AA 1565 0 0.1091 TC CC RR IT AV 1566 0 0.1103 TC CG RH II AA 1567 0 0.1104 TC CC RR IT AA 1568 0 0.1104 TC CC RR II AV 1569 0 0.1084 TT CC RR II AA 1570 0 0.0921 TT CC RR II VV 1571 0 0.092 TT CC RR II AA 1573 0 0.114 TT CC RR II AA 1574 0 0.1139 TT CC RR II AA 1575 0 0.1139 TC CC RH II AV 1576 0 0.1137 TT CC RR II AA 1577 0 0.1133 TC CG RH II AA 1579 0 0.1129 CC CG RH II AA 1580 0 0.1129 TT CC RR II AV 1581 0 0.1129 TT CC RR II AV 1582 0 0.1123 TC CC RH II AA 1583 1 0.037 TC CG HH II AA 1584 0 0.1113 TC CC RR II AA 1585 0 0.1099 TC CG RH II AA 1586 0 0.1089 TT CC RR II AA 1587 0 0.1094 TT CC RR II AV 1588 0 0.1093 TC CG RH II AV 1589 0 0.1083 TC CG RH II AA 1590 0 0.108 TT CC RR II AA 1591 0 0.1089 TT CC RR II AA 1592 0 0.1084 TC CC RH II AA 1593 0 0.1079 TT CC RH II AA 1594 0 0.0981 TT CC RR II AV 1595 0 0.1011 CC CG HH II AA 1596 0 0.038 TC CG RH II AV 1597 0 0.1011 TT CC RR II AV 1598 0 0.105 TT CC RR II AV 1599 0 0.1013 TT CC RR II AV 1600 0 0.0996 TC CC RR II AA 1601 0 0.1001 TC CG RH II AA 1602 0 0.0977 TT CC RR II AA 1603 0 0.0994 TC CC RH II AV 1604 0 0.0994 TT CC RR IT AA 1605 0 0.0994 TT CC RR II AV 1606 0 0.0983 TC CG RH II AA 1607 0 0.0977 TC CC RH II AV 1609 0 0.0963 TT CC RR II AV 1610 0 0.0973 TC CG RH II AA 1611 0 0.0951 TC CG RH II AA 1612 0 0.0964 CC GG HH II AA 1613 0 0.0976 TC CC RH II AA 1614 0 0.0973 CC CG HH II AA 1615 0 0.0934 TT CC RR II VV 1616 0 0.0961 TT CC RR II AV 1617 0 0.0963 CC GG HH II AA 1619 0 0.0903 TC CC RH II AV 1620 0 0.0916 TT CC RR II AA 1621 0 0.0924 TC CC RH II AA 1622 0 0.0941 CC CC RH IT AA 1623 0 0.0924 TT CC RR II AV 1625 0 0.013 CC CG HH II AA 1626 0 0.0913 TC CC RH II AA 1627 0 0.0914 TT CC RR II AV 1628 0 0.0903 TC CC RH II AA 1629 0 0.0913 TT CC RR II AA 1630 1 0.032 TT CC RR II AV 1631 0 0.0883 CC GG HH II AA 1632 0 0.090 TC CC RR II AA 1633 0 0.0886 TC CC RR II AA 1634 0 0.0866 TC CG RH II AV 1635 1 0.019 TT CC RR II AA 1636 0 0.0886 TC CC RH II AA 1637 0 0.0887 TC CC RH II AV 1638 0 0.0891 TC CG RH II AA 1639 0 0.0891 TC CG RH II AA 1640 0 0.0873 TC CG RH II AA 1641 0 0.0876 TT CC RH II AA 1642 0 0.0864 TT CC RR II AV 1644 0 0.0861 TT CC RR II AA 1645 0 0.0857 TC CC RH II AV 1646 0 0.0874 TT CC RR II AV 1647 0 0.0856 TC CC RR IT AA 1648 0 0.0854 TC CC RR IT AA 1649 0 0.0856 TC CG RH II AA 1651 0 0.0843 TC CC RR IT AV 1652 0 0.0837 TT CC RR II AV 1654 0 0.0846 TC CG RH II AA 1655 0 0.0831 TT CC RR II AV 1656 0 0.0831 TT CC RR II AA 1657 0 0.0836 TT CC RR II AA 1658 0 0.0824 TT CC RR II AV 1659 0 0.0826 TT CC RR II AV 1660 0 0.0776 CC CC RR IT AA 1661 0 0.0824 TT CC RR II AV 1662 0 0.0827 TC CG RH II AA 1663 0 0.0797 TT CC RR II AV 1664 0 0.0817 TC CC RH II AA 1665 0 0.0797 TT CC RR IT AA 1666 0 0.0817 TC CC RH II AA 1667 0 0.0809 TT CC RR II AA 1668 0 0.0823 TT CC RR II AA 1669 0 0.0796 TC CC RR II AA 1670 0 0.0796 TT CC RR II AA 1671 0 0.0789 TC CC RR IT AV 1672 0 0.0779 TC CG RH II AA 1673 0 0.0789 CC CC RH IT AA 1675 0 0.0776 TC CC RR II AA 1676 0 0.0759 TT CC RR II AV 1677 0 0.0763 TC CC RR IT AA 1678 0 0.0771 TT CC RR II AV 1679 0 0.0736 TC CG RH II AA 1680 0 0.0949 TC CG RH II AA 1681 0 0.0747 TC CC RR II AV 1682 0 0.0726 TT CC RR II AV 1683 0 0.0737 TT CC RR II AA 1684 0 0.0727 TT CC RR II AA 1685 0 0.0726 TT CC RH II AV 1686 0 0.0729 TT CC RR II AA 1687 0 0.071 CC GG HH II AA 1688 0 0.0717 TC CC RR II AA 1689 0 0.071 CC GG HH II AA 1690 0 0.0639 TC CG RH II AA 1691 0 0.0609 TT CC RR II VV 1692 0 0.0551 TC CG RH II AV 1693 0 0.0631 TC CG RH II AA 1694 0 0.0657 TC CG RH II AA 1695 0 0.0549 TT CC RR II AA 1696 0 0.0549 TT CC RR II AV 1697 0 0.0547 TC CG RH II AV 1698 0 0.0543 TC CG RH II AA 1699 0 0.054 TT CC RR II AV 1700 0 0.0533 TC CG RH II AA 1701 0 0.0916 TC CG RH II AV 1702 0 0.0916 TC CC RR IT AV 1703 0 0.0914 TC CG RH II AA 1704 0 0.0914 TC CC RR II AA 1705 0 0.051 TC CC RR II AA 1706 0 0.0913 TT CC RH II AA 1707 0 0.0913 TT CC RR II AA 1708 0 0.0913 TT CC RR II AA 1709 0 0.0911 TT CC RR II AA 1710 1 0.064 CC CG RH IT AA 1711 0 0.0911 CC GG HH II AA 1712 0 0.0911 TC CC RH II AA 1713 0 0.0906 TT CC RR II AV 1714 0 0.0906 TC CC RR II AV 1715 0 0.0906 TT CC RR II AV 1716 0 0.0906 TT CC RR II AA 1717 0 0.0904 TC CG RH II AV 1718 0 0.0904 TC CC HH II AA 1719 0 0.0903 TC CG RH II AA 1720 1 0.012 CC GG HH II AA 1721 0 0.0903 CC GG HH II AA 1722 0 0.0903 TT CC RR II AV 1723 0 0.0903 TC CC RH II AA 1724 0 0.090 TC CC RR II AV 1725 0 0.090 TC CC RR IT AV 1726 0 0.090 TT CC RR II AV 1727 0 0.0897 TT CC RH II AA 1728 0 0.0897 TC CG RH II AA 1729 0 0.0897 TC CG RH II AA 1730 0 0.0897 TC CG RH II AA 1731 0 0.0896 TC CC RR IT AA 1732 0 0.0896 TC CC RR IT AV 1733 0 0.0896 CC CG HH II AA 1734 0 0.0896 CC GG HH II AA 1735 0 0.0893 TC CG RH II AA 1736 0 0.0893 TC CC RR II AV 1737 0 0.0891 TC CC RH II AA 1738 0 0.0891 TC CG RH II AA 1739 0 0.0887 TT CC RR II AV 1740 0 0.0887 CC GG HH II AA 1741 0 0.0886 TT CC RR II AV 1742 0 0.0886 TC CG RH II AV 1743 0 0.0886 TC CC RH II AV 1744 0 0.0886 CC GG HH II AA 1745 0 0.0884 TC CC RR II AA 1746 0 0.0884 TC CG RH II AA 1747 0 0.0884 CC CG HH II AA 1748 0 0.0884 TT CC RR II AA 1749 0 0.0884 CC GG HH II AA 1751 0 0.0883 TC CG RH II AV 1752 0 0.0883 TT CC RR II AA 1753 0 0.0881 TT CC RR II AV 1754 0 0.0861 TT CC RR II AV 1755 0 0.0861 TC CG RH II AA 1756 0 0.0739 TT CC RR II AV 1757 1 0.024 TC CG RH II AA 1758 1 0.010 TC CG RH II AA 1759 0 0.0737 TC CG RH II AV 1760 0 0.0736 TT CC RR II AA 1761 0 0.0736 CC CG RH IT AA 1762 0 0.0736 TC CC RR IT AV 1763 0 0.0736 CC GG HH II AA 1764 0 0.0734 TC CG RR II AA 1765 0 0.0734 TT CC RR II AV 1766 0 0.0733 TC CC RR IT AA 1767 0 0.0733 TC CC RR IT AA 1768 0 0.0729 TC CG RH II AA 1769 0 0.0729 TC CC RR IT AV 1770 0 0.0729 TC CG RH II AA 1772 0 0.0727 CC CC RR IT AA 1773 0 0.0727 TT CC RR II AV 1774 1 0.052 TT CC RR II AA 1775 0 0.0727 TT CC RR II AA 1776 0 0.0726 TT CC RR II AV 1777 0 0.0726 TC CG RH II AA 1778 0 0.0726 TC CG RH II AA 1779 0 0.0724 TT CC RR II AA 1780 0 0.0717 CC CG RH IT AA 1781 0 0.0717 CC CC RR IT AV 1782 0 0.0717 TT CC RR II VV 1783 0 0.0717 TT CC RR II AA 1784 0 0.0717 TT CC RR II AV 1785 0 0.0717 TT CC RR II VV 1786 0 0.0716 TC CC RR IT AV 1787 0 0.0716 TC CC RR IT AV 1788 0 0.071 TC CG RH II AA 1789 0 0.071 TT CC RR II AV 1790 0 0.071 TC CC RR IT AV 1791 0 0.0709 TC CC RR IT AA 1792 0 0.0709 CC CC RR II AA 1793 0 0.0709 TT CC RR II AV 1794 0 0.0709 TC CC RH II AV 1795 0 0.0707 TC CC RR II AA 1796 0 0.0707 TC CG RH II AA 1797 0 0.0707 TC CG RH II AA 1798 0 0.0707 TT CC RR II AA 1799 0 0.0707 TT CC RR II AV 1800 0 0.0706 TC CG RH II AA 1801 0 0.070 CC CG RH II AA 1802 0 0.070 TT CC RH II AV 1803 0 0.0699 TT CC RR II AV 1804 0 0.0697 TC CG RH II AA 1805 1 0.052 TT CC RR II VV 1806 0 0.0696 TC CG RH II AA 1807 0 0.0696 CC CG RH II AA 1808 1 0.061 TC CG RH II AA 1809 1 0.007 TT CC RR II AV 1810 0 0.069 TC CC RR II AV 1811 0 0.069 TT CC RR II AA 1812 0 0.069 TT CC RR II AA 1813 0 0.0686 TC CC RH II AV 1814 0 0.0686 TC CG RH II AV 1815 0 0.0686 TT CC RR II AV 1816 0 0.0681 TT CC RR II AV 1817 0 0.0679 TT CC RH II AA 1818 0 0.0679 TT CC RR II AA 1819 1 0.003 CC CC RR IT AA 1820 0 0.0677 TC CC RH II AV 1821 0 0.0676 CC CG RH IT AA 1822 0 0.0667 TC CC RR IT AA 1823 0 0.0666 TT CC RR II AA 1824 1 0.016 CC CG RH II AA 1825 0 0.065 TC CG RH II AV 1826 0 0.0646 TC CG RH II AV 1827 1 0.039 TC CC RR II AA 1828 0 0.0637 TC CG RH II AA 1829 0 0.0637 TC CG RH II AA 1830 0 0.0637 CC CG RH II AA 1831 0 0.0631 TC CC RR II AV 1832 0 0.063 TC CC RR IT AV 1833 0 0.063 TT CC RR II AA 1834 0 0.0621 TC CC RH II AA 1835 0 0.062 TC CG RH II AA 1836 0 0.062 TC CG HH II AA 1837 0 0.062 TT CC RR II AA 1838 0 0.0619 TT CC RR II AV 1839 0 0.0619 TT CC RR II AV 1840 0 0.0619 TT CC RR II AV 1841 0 0.0619 TT CC RR II AV 1842 0 0.0617 TC CC RH II AA 1843 0 0.0617 TT CC RR II AA 1844 0 0.0611 TC CG RH II AV 1845 0 0.0611 TT CC RR II AA 1846 0 0.0609 TC CG RH II AV 1847 0 0.0609 TC CC RR II AA 1848 0 0.0607 TC CC RR II AA 1849 0 0.060 TT CC RR II AV 1850 0 0.0599 TT CC RR II AA 1851 0 0.0597 TC CC RR II AV 1852 0 0.0593 TC CG RH II AV 1853 0 0.0593 CC CG RH II AA 1854 0 0.0591 TC CC RR II AA 1855 0 0.0591 TC CG RH II AA 1856 0 0.0591 TT CC RR II AV 1857 0 0.059 TT CC RR II AV 1858 0 0.059 TC CC RR IT AA 1859 0 0.0589 TC CG RH II AA 1860 0 0.0589 CC CG RH II AA 1861 0 0.0587 CC GG HH II AA 1862 0 0.0581 TC CG RH II AV 1863 0 0.058 TC CG RH II AV 1864 1 0.005 TC CG RH II AA 1865 0 0.0579 TT CC RR II AA 1866 0 0.0579 TC CG RH II AA 1867 0 0.0579 TT CC RR II AA 1868 0 0.057 CC GG HH II AA 1869 0 0.057 TC CG RH II AA 1870 0 0.0569 TC CC RR II AA 1871 0 0.0569 TT CC RR II VV 1872 0 0.056 TC CC RR II AA 1873 0 0.0553 CC CG RH II AV 1874 0 0.0553 TC CG RH II AA 1875 0 0.0551 TC CG RH II AV 1876 0 0.0551 CC CG RH II AA 1877 0 0.055 TT CC RR II AV 1878 0 0.0543 CC GG HH II AA 1879 0 0.0543 TC CG RH II AV 1880 0 0.0543 TT CC RR II AA 1881 0 0.0543 TT CC RR II AV 1882 0 0.0541 TT CC RR II AA 1883 0 0.054 CC GG HH II AA 1884 0 0.054 TT CC RR II AA 1885 0 0.054 TT CC RR II AA 1886 0 0.0539 TT CC RR II AA 1887 0 0.0539 TT CC RR II AA 1888 0 0.0533 CC GG HH II AA 1889 0 0.0533 TC CC RR II AA 1890 0 0.0504 TC CC RR IT AA 1891 0 0.0504 TC CC RR II AA 1892 0 0.0501 TC CG RH II AA 1893 1 0.040 TC CG RH II AA 1894 0 0.0501 TT CC RR II AV 1895 0 0.0501 TC CG RH II AV 1896 0 0.050 TT CC RR II AA 1897 0 0.0494 TC CC RR IT AA 1898 0 0.0494 TT CC RR II AV 1899 0 0.0494 TC CC RR IT AA 1900 0 0.0494 TT CC RR II AA thesias-3.1.1/examples/dataset3/polytest.txt000066400000000000000000002622751360777755100211660ustar00rootroot000000000000001 51 3.288688537 2 1 11 22 2 63 0.928906543 1 1 11 22 2 59 1.237569187 1 0 12 22 2 62 0.928906543 1 0 12 22 1 42 2.710334052 1 0 12 22 1 43 2.619401323 1 1 11 22 2 59 2.525148028 2 0 11 12 1 46 2.348745456 1 0 12 22 2 39 2.98487959 1 0 11 12 2 47 2.170429777 1 1 11 22 1 47 2.259350845 1 1 12 22 2 62 0.928906543 1 1 11 12 2 52 1.734475431 1 0 11 12 2 52 1.820349819 1 0 22 22 2 63 2.199007031 2 1 11 12 2 59 1.237569187 1 1 12 22 2 54 1.649368446 1 0 12 22 2 60 1.158444154 1 1 12 12 2 62 1.00403308 1 1 12 22 1 42 2.710334052 1 1 11 22 2 45 3.811612884 2 1 12 22 2 44 2.528804928 1 0 11 11 2 62 2.360758581 2 0 11 22 2 34 3.446950546 1 0 11 12 2 58 2.691809497 2 1 11 11 2 58 1.317870115 1 1 11 22 2 60 2.442647433 2 0 11 12 2 62 0.928906543 1 1 11 12 2 62 0.928906543 1 0 11 22 1 40 2.893098125 1 0 12 12 2 54 1.649368446 1 0 11 22 2 58 1.237569187 1 1 12 22 2 53 3.116373685 2 0 11 22 2 62 2.360758581 2 0 11 12 2 29 4.006345092 1 0 12 12 1 61 1.080572405 1 0 11 12 1 63 0.855273778 1 1 11 12 1 49 1.994175919 1 0 12 22 1 63 0.928906543 1 1 11 12 2 59 2.525148028 2 0 11 12 2 53 3.116373685 2 0 11 12 2 62 0.928906543 1 1 12 22 1 61 1.080572405 1 1 12 12 1 45 2.43857533 1 0 12 12 2 62 0.928906543 1 1 11 22 2 61 2.360758581 2 1 12 12 1 38 3.07689735 1 0 11 12 2 57 1.399271734 1 0 22 22 1 62 0.928906543 1 0 12 22 1 58 1.317870115 1 1 12 12 2 44 2.528804928 1 1 22 22 1 56 1.481701382 1 1 11 22 2 55 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0.620780287474333 1 1280 0 SS NN LV TT 0.458781656399726 1 1281 0 SS ND LL TT 0.405338809034908 1 1282 0 SN ND LL TT 0.472032854209446 1 1286 0 SS NN LL TP 0.522108145106092 1 1288 0 SS NN LL TP 0.447446954140999 1 1289 0 SS ND LL TT 0.437973990417522 1 1290 0 SS ND LL TP 0.633319644079398 1 1291 0 SS NN VV TT 0.439315537303217 1 1293 0 SS ND LV TT 0.526926762491444 1 1294 0 SS ND LV TT 0.511594798083504 1 1295 0 SS ND LL TT 0.607337440109514 1 1296 0 SS ND LL TP 0.507542778918549 1 1297 0 NN ND LV TT 0.379000684462697 1 1298 0 SS ND LL TP 0.476440793976728 1 1299 0 SS ND LL TT 0.557946611909651 1 1300 0 SS NN LL TT 0.348336755646817 1 1301 0 SS NN LV TT 0.622422997946612 1 1302 0 NN ND LV TT 0.394579055441478 1 1303 0 SS DD LL TT 0.355619438740589 1 1304 0 SN ND LV TT 0.549322381930185 1 1305 0 SS NN LL TT 0.574565366187543 1 1306 0 SS NN LV TT 0.524955509924709 1 1307 0 SN DD LL TT 0.460342231348392 1 1308 0 SN NN LV TP 0.573744010951403 1 1311 0 NN ND LL TT 0.409472963723477 1 1312 0 SS ND LL TT 0.437782340862423 1 1314 0 SN ND LL TT 0.643367556468173 1 1315 0 SN DD LL TT 0.430746064339493 1 1316 0 SN NN LL TT 0.354633812457221 1 1317 0 SN DD LL TT 0.354113620807666 1 1318 0 SS ND LL TT 0.555756331279945 1 1319 0 SN NN LL TT 0.583353867214237 1 1320 0 SS DD LL TT 0.374647501711157 1 1322 0 SS NN VV TT 0.550171115674196 1 1323 0 SS NN LL TT 0.637590691307324 1 1324 0 SS ND LL TT 0.642026009582478 1 1325 0 SN ND LL TT 0.419411362080767 1 1326 0 SS ND LV TT 0.633429158110883 1 1327 0 NN ND LL TT 0.528268309377139 1 1329 0 SN ND LV TT 0.629130732375086 1 1332 0 SS ND LL TT 0.393292265571526 1 1334 0 SS NN LL TT 0.48062970568104 1 1335 0 SS DD LL TT 0.551594798083504 1 1336 0 SS ND LL TT 0.474414784394251 1 1337 0 SS NN LV TP 0.460260095824778 1 1338 0 SN ND LL TP 0.603148528405202 1 1339 0 SS DD LL TT 0.624777549623545 1 1340 0 SS NN LL TT 0.55047227926078 1 1341 0 SS ND LL TT 0.435537303216975 1 1342 0 SS ND LV TT 0.340041067761807 1 1343 0 SS DD LL TT 0.356413415468857 1 1344 0 SN NN LL TP 0.578891170431211 1 1345 0 SN ND LL TP 0.436659822039699 1 1346 0 SN ND LV TT 0.385681040383299 1 1348 0 SS NN LL TP 0.540232717316906 1 1349 0 SS ND LL TT 0.463655030800821 1 1350 0 NN ND LL TT 0.557371663244353 1 1351 0 SS ND LL TT 0.513100616016427 1 1352 0 SS NN LL TT 0.434277891854894 1 1353 0 SN DD LL TT 0.558220396988364 1 1354 0 SS NN LL TT 0.580205338809035 1 1355 0 SS NN LL TT 0.499986310746064 1 1356 0 SS NN LV TT 0.620780287474333 1 1357 0 SN NN LL TT 0.583600273785079 1 1358 0 SS NN LV TT 0.622505133470226 1 1359 0 SN ND LL TP 0.480602327173169 1 1360 0 SS ND LL TT 0.513511293634497 1 1361 0 SS NN LV TT 0.370047912388775 1 1362 0 SS ND LL TP 0.594168377823409 1 1363 0 SS NN LV TP 0.520027378507871 1 1364 0 SN ND LL TT 0.54444900752909 1 1365 0 SS NN LV TT 0.412731006160164 1 1366 0 SN NN LL TT 0.443367556468172 1 1368 0 SS NN LV TT 0.469185489390828 1 1370 0 SS NN LL TT 0.452621492128679 1 1371 0 SS DD LL TT 0.603394934976044 1 1372 0 SS NN LV TT 0.524435318275154 1 1373 0 SS ND LL TT 0.436413415468857 1 1374 0 SS NN LL TT 0.609801505817933 1 1375 0 SS ND LL TT 0.622286105407255 1 1376 0 SN ND LL TT 0.615003422313484 1 1377 0 SS ND LL TT 0.526817248459959 1 1378 0 NN DD LL TT 0.466255989048597 1 1379 0 SS NN LV TT 0.555838466803559 1 1380 0 SS ND LL TT 0.448761122518823 1 1382 0 SS ND LL TT 0.467542778918549 1 1383 0 SS DD LL TT 0.434140999315537 1 1385 0 SS ND LL TT 0.520191649555099 1 1386 0 SS ND LL TT 0.542696783025325 1 1387 0 SS ND LL TT 0.351567419575633 1 1388 0 SS ND LV TT 0.363915126625599 1 1389 0 SS ND LL TT 0.448651608487337 1 1390 0 NN ND LL TT 0.440383299110199 1 1391 0 SS DD LL TT 0.524490075290897 1 1392 0 SS ND LL TT 0.467734428473648 1 1393 0 SS NN LV TT 0.525201916495551 1 1394 0 SS NN LV TP 0.430171115674196 1 1395 0 SS NN LL TP 0.366707734428474 1 1396 0 SS NN LV TT 0.529336071184121 1 1397 0 SS ND LL TT 0.458726899383984 1 1398 0 SS ND LL TT 0.405776865160849 1 1399 0 SS ND LV TT 0.429459274469541 1 1400 0 NN NN LL TT 0.461820670773443 1 1401 0 SS DD LL TT 0.536180698151951 1 1402 0 SN DD LL TT 0.53864476386037 1 1403 0 SN ND LL TT 0.481095140314853 1 1404 0 SN NN LV TT 0.555373032169747 1 1405 0 SN ND LL TT 0.425160848733744 1 1406 0 SS NN LV TP 0.467624914442163 1 1407 0 SS DD LL TT 0.465954825462012 1 1409 0 SS ND LL TT 0.356139630390144 1 1410 0 SN ND LL TT 0.434579055441478 1 1411 0 SN ND LV TT 0.59460643394935 1 1413 0 SN DD LL TT 0.451553730321697 1 1414 0 SS NN VV TT 0.624640657084189 1 1415 0 SN ND LV TT 0.621108829568789 1 1416 0 SN NN LL PP 0.501793292265571 1 1417 0 SS NN LL TT 0.618425735797399 1 1418 0 SS DD LL TT 0.624613278576318 1 1419 0 SS DD LL TT 0.423901437371663 1 1420 0 SS ND LL TP 0.389404517453799 1 thesias-3.1.1/examples/dataset3/psgl1.txt000066400000000000000000000767331360777755100203330ustar00rootroot00000000000000292 6.0330862218 GG MM AA MM CC CC 65 294 5.7104270174 GG MM aA MV CC CT 71 295 5.9763509093 GG MI AA MM CC CC 64 298 6.0185932145 GG MM AA MM CC CC 69 310 5.5529595849 GG MM aA MM CC CC 69 313 5.9738096119 GG MM AA MM CC CC 60 314 5.8777357818 GG MM AA MM CC CC 70 315 5.8051349689 GG MM aa MV CC CT 67 316 5.9712618398 GG MM aA MM CC CC 62 318 5.811140993 GG MM AA MM CC CC 61 319 5.3471075307 GG MM aA MV CC CT 58 320 5.8833223885 GG MM aA MM CC CC 53 321 5.7683209958 GG MM AA MM CC CC 67 322 5.8607862235 GG MM aa MM CC CC 67 323 5.8998973536 GG MM AA MM CC CC 39 324 5.2203558251 GG MM AA MM CC CC 68 326 5.8260001074 GG MI AA MM CC CC 69 327 5.7430031878 GG MI AA MM CC CC 65 328 5.6835797673 GG MM AA MM CC CC 67 329 5.6970934865 GG MM AA MM CC CC 58 331 5.6312117818 GA MM AA MM CC CC 52 334 6.1527326947 GG MM AA MM CC CC 72 335 5.7990926545 GG MM aa MM CC CC 60 337 5.7960577508 GG MM aA MM CC CC 47 338 5.7714411231 GG MM AA MM CC CC 75 339 5.8944028343 GG MM AA MM CC CC 62 340 5.8550719222 GG MM aA MM CC CC 67 341 5.579729826 GG MM AA MM CC CC 73 342 6.1569789856 GG MI AA MM CC CC 72 343 6.0038870671 GG MM AA MM CC CC 43 346 5.6489742382 GG MM AA MM CC CC 76 347 6.0520891689 GG MM AA MM CC CC 52 348 6.0980742822 GG MM AA MM CC CC 41 349 5.9864520053 GG MM AA MM CC CC 54 351 5.7776523232 GG MM aA MV CC CT 70 352 5.6869753563 GG MM aA MM CC CC 47 353 6.1246833909 GG MM AA MM CC CC 71 354 5.7651911028 GG MM aA MM CC CC 64 355 5.8579331545 GA MM aA MM CC CC 65 356 5.5834963088 GG MM AA MM CC CC 62 357 5.9532433343 GG MI AA MM CC CC 62 359 5.598421959 GG MM AA MM CC CC 56 365 5.910796644 GG MM AA MM CC CC 74 366 5.8318824773 GG MM aA MV CC CT 42 367 5.5683445038 GG MM aA MM CC CC 71 369 5.926926026 GA MM AA MM CC CC 74 373 5.8692969131 GG MM aA MM CC CC 49 374 5.7004435734 GG MM aA MM CC CC 69 375 6.1136821798 GG MM AA MM CC CC 44 376 5.5174528965 GG MM aA MM CC CC 57 377 5.8289456176 GG MM AA MM CC CC 60 378 5.5568280617 GG MM aa MM CC CC 74 379 6.001414878 GG MM AA MM CC CC 66 385 5.6454468976 GG MM aA MM CC CC 60 388 5.7683209958 GG MI AA MM CC CC 55 390 5.730099783 GG MM aA MM CC CC 68 392 6.0637852087 GG MM AA MM CC CC 71 393 5.8021183754 GG MI AA MM CC CC 54 394 6.0844994131 GG MM aa MM CC CC 76 395 5.8200829304 GG MM AA MM CC CC 49 397 5.4847969335 GG MI AA MM CC CC 68 398 5.8861040315 GG MM AA MM CC CC 67 399 5.8833223885 GG MI AA MM CC CC 54 400 5.843544417 GG MM AA MM CC CC 72 401 5.8749307309 GG MM aA MM CC CC 55 411 5.8805329864 GG II AA MM CC CC 59 413 5.5093883366 GG MM aa MM CC CC 58 415 5.9738096119 GG MM aA MM CC CC 73 417 5.463831805 GA MM aA MM CC CC 50 418 5.8888779583 GG MM AA MM CC CC 64 425 6.0258659738 GG MM AA MM CC CC 72 431 6.2245584293 GG MM aA MM CC CC 69 433 5.723585102 GG MM AA MM CC CC 75 434 6.1484682959 GG MI AA MM CC CC 66 437 5.6970934865 GG MM aa MM CC CC 58 438 5.7071102647 GG MI aA MM CC CC 55 441 5.7620513828 GG MM aA MM CC CC 54 442 5.7776523232 GG MM aA MM CC CC 52 443 5.5490760849 GG MM AA MM CC CC 56 446 5.537334267 GG MM AA MM CC CC 53 447 5.843544417 GG MM aA MM CC CC 63 448 5.7333412769 GG MM AA MM CC CC 58 449 5.8377304472 GG MM AA MM CC CC 69 452 5.7397929122 GG MM AA MM CC CC 71 453 5.9712618398 GG MM AA MM CC CC 65 454 5.5721540322 GG MM aA MM CC CC 66 457 5.7170277014 GG MI AA MM CC CC 66 459 5.7397929122 GG MM aA MM CC CC 59 460 5.5254529391 GG MM aA MM CC CC 55 461 5.4847969335 GG MM AA MM CC CC 69 462 5.6058020663 GG MM aa MV CC CT 56 464 5.8550719222 GG MM AA MM CC CC 59 465 5.7037824747 GG MM aA MV CC CT 61 466 5.8833223885 GA MM AA MM CC CC 71 469 5.7104270174 GG MM AA MM CC CC 64 471 5.8493247799 GG II AA MM CC CC 61 472 5.7071102647 GG MM AA MM CC CC 52 473 5.8636311756 GG MM aA MM CC CC 59 474 5.8260001074 GG MM AA MM CC CC 77 475 5.8721177895 GG MM AA MM CC CC 51 479 5.8051349689 GG MM AA MM CC CC 65 480 5.7990926545 GG MM AA MM CC CC 65 481 5.7930136084 GG MM aA MV CC CT 65 483 5.9532433343 GG MM AA MM CC CC 74 484 6.0958245624 GG MM AA MM CC CC 62 486 5.6419070709 GG MM AA MM CC CC 46 488 5.811140993 GG MM aA MM CC CC 65 489 5.4553211154 GG MM aA MM CC CC 53 490 5.5174528965 GG MM AA MM CC CC 67 492 5.926926026 GG MM AA MM CC CC 46 493 5.7990926545 GG MM AA MM CC CC 75 494 5.7104270174 GG MM aa MM CC CC 46 496 5.7930136084 GG MM AA MM CC CC 59 497 5.8348107371 GG MM AA MM CC CC 55 499 6.3491389914 GG MM AA MM CC CC 70 500 5.7868973814 GG MM aA MM CC CC 69 501 6.2304814476 GG MM AA MM CC CC 74 502 5.6167710977 GG MM AA MM CC CC 57 503 5.8493247799 GG MM AA MM CC CC 58 504 5.8777357818 GG MM aA MM CC CC 67 506 6.1841488909 GG MM AA MM CC CC 49 508 5.96870756 GG MM AA MM CC CC 49 509 5.8636311756 GG MI aA MM CC CC 43 510 5.6524891803 GG MM aA MM CC CC 67 511 5.5214609179 GG MM AA MM CC CC 63 512 5.5872486584 GG MM AA MM CC CC 73 513 5.6347896032 GG MM AA MM CC CC 65 514 5.7589017739 GG MM AA MM CC CC 71 515 5.9215784196 GG MM aA MM CC CC 48 516 5.9295891434 GG MM AA MM CC CC 45 517 6.0497334552 GG MM AA MM CC CC 75 519 5.8021183754 GG MM AA MM CC CC 52 520 5.5134287462 GG MM aA MM CC CC 63 521 5.7268477476 GG MM AA MM CC CC 64 523 5.6383546693 GG MM aA MM CC CC 73 524 5.9989365619 GG MM AA MM CC CC 74 525 6.0330862218 GG MM AA MM CC CC 39 526 5.5134287462 GG MM aA MM CC CC 74 528 6.0684255882 GG MM AA MM CC CC 63 530 5.7838251823 GG MI aA MM CC CC 72 531 5.9427993751 GG MM AA MM CC CC 48 532 5.537334267 GG MM AA MM CC CC 76 533 5.8200829304 GG MM AA MM CC CC 67 535 5.9939614273 GG MM aA MM CC CC 74 536 6.0185932145 GG MM aA MV CC CT 69 537 5.6204008657 GG MM AA MM CC CC 53 540 5.4205349993 GG MM aA MV CC CT 57 541 5.9788857649 GG MI AA MM CC CC 75 542 5.8021183754 GG MM aa MM CC CC 73 544 5.8289456176 GG MM AA MM CC CC 64 545 6.154858094 GG MM AA MM CC CC 75 546 5.4889377262 GG MM AA MM CC CC 53 548 5.7651911028 GG MM aA MM CC CC 56 549 5.7714411231 GG MM AA MM CC CC 44 550 5.6903594543 GG MM aA MM CC CC 67 551 5.8805329864 GG MM AA MM CC CC 64 553 5.8200829304 GG MI aA MM CC CC 59 554 6.1092475828 GG MM AA MM CC CC 46 555 6.0844994131 GG MI aA MM CC CC 66 556 5.7651911028 GG MM AA MM CC CC 74 557 5.9401712527 GG MI AA MM CC CC 71 559 5.843544417 GG MM AA MM CC CT 60 560 5.96870756 GG MM aA MV CC CT 45 561 5.9053618481 GG MM aA MM CC CT 70 563 5.8636311756 GG MM aA MM CC CC 65 564 5.7525726388 GG MM AA MM CC CC 50 565 5.8607862235 GG MM AA MM CC CC 58 566 5.8406416574 GG MM AA MM CC CC 61 567 5.730099783 GG MM aA MM CC CC 68 568 5.9738096119 GG MM AA MM CC CC 52 569 6.3526293963 GG II AA MM CC CC 56 570 5.6524891803 GG MM AA MM CC CC 57 575 5.7170277014 GG MM AA MM CC CC 58 577 6.1862086239 GG MM AA MM CC CC 57 580 5.8377304472 GG MM AA MM CC CC 45 584 6.1246833909 GG MI aA MM CC CC 62 585 6.0980742822 GG MI aA MM CC CC 61 586 5.9295891434 GG MM AA MM CC CC 43 587 5.8692969131 GG MM aA MV CC CT 79 588 5.8141305318 GG MM AA MM CC CC 26 593 5.8550719222 GG MM AA MM CC CC 45 594 5.8141305318 GG MM aA MM CC CC 62 595 5.7776523232 GG MI AA MM CC CC 72 596 6.1696107325 GG MM AA MM CC CC 52 598 5.926926026 GG MM AA MM CC CC 67 599 5.910796644 GG MM aA MM CC CC 56 600 5.9914645471 GG MM aA MM CC CC 66 601 6.1398845522 GG MM aA MM CC CC 60 604 5.7838251823 GG MM AA MM CC CC 54 605 5.7104270174 GG MM AA MM CC CC 70 606 5.8464387751 GG II AA MM CC CC 66 609 5.6937321388 GG MI AA MM CC CC 63 610 5.7137328055 GG MM aa MM CC CC 39 614 5.7745515455 GG MM aA MM CC CC 43 618 5.5909869805 GG MM AA MM CC CC 64 620 6.238324625 GG MM aA MM CC CC 77 621 6.0520891689 GG MM AA MM CC CC 73 623 5.8944028343 GG MM AA MM CC CC 75 627 5.9889614169 GG MM AA MM CC CC 62 629 5.7170277014 GG MM AA MM CC CC 56 631 5.6629604801 GG MM AA MM CC CC 69 632 5.6903594543 GG MM AA MM CC CC 70 635 6.1246833909 GG MM AA MM CC CC 59 636 6.0890448754 GG MI AA MM CC CC 76 640 5.9295891434 GG MM AA MM CC CC 61 642 5.1239639794 GG MM AA MM CC CC 77 646 5.8664680569 GG MM AA MM CC CC 65 648 5.5529595849 GG MM aA MM CC CC 75 649 6.0354814325 GG MM AA MM CC CC 79 651 5.9738096119 GG MM AA MM CC CC 26 653 5.7525726388 GG MI AA MM CC CC 69 655 6.070737728 GG MM AA MM CC CC 39 660 5.8721177895 GG MM aA MV CC CT 73 664 6.0185932145 GG MI AA MM CC CC 67 665 5.6021188209 GG MM AA MM CC CC 57 667 5.8833223885 GG MM aA MM CC CC 54 669 6.1136821798 GG MM AA MM CC CC 70 670 6.3716118472 GG MM AA MM CC CC 63 672 5.9348941956 GG MM AA MM CC CC 67 673 6.1612073217 GG MM AA MM CC CC 55 676 6.0844994131 GG MM AA MM CC CC 56 678 6.1290502101 GG MM aA MM CC CC 77 680 5.8579331545 GG MM AA MM CC CC 74 681 5.8607862235 GG MM AA MM CC CC 54 682 5.7868973814 GG MM AA MM CC CC 57 683 6.0497334552 GG MM aA MM CC CC 69 685 6.1398845522 GG MM aA MM CC CC 69 686 5.9348941956 GA MM AA MM CC CC 75 687 6.1312264895 GA MM AA MM CC CC 70 689 5.8141305318 GG MM aA MM CC CC 75 696 5.8493247799 GG MI aA MM CC CC 77 701 6.0567840132 GG MM aA MM CC CC 69 703 5.9506425526 GG MM AA MM CC CC 46 704 5.8777357818 GG MI AA MM CC CC 48 706 6.0637852087 GA MM AA MM CC CC 73 708 5.7004435734 GG MM AA MM CC CC 69 709 5.7899601709 GG MM AA MM CC CC 42 710 5.8888779583 GG MM AA MM CC CC 53 711 6.1612073217 GG MM AA MM CC CC 74 712 5.6767538023 GG MM AA MM CC CC 57 713 6.1590953885 GG MM aA MM CC CC 60 716 6.1092475828 GG MM aA MM CC CC 65 717 5.9712618398 GG MM AA MM CC CC 56 718 6.1224928095 GG MM AA MM CC CC 58 720 5.6733232672 GG MM aA MM CC CC 50 724 5.669880923 GG MM AA MM CC CC 48 726 5.958424693 GA MI AA MM CC CC 60 730 5.9889614169 GG MM aA MM CC CC 59 732 6.0637852087 GG MM AA MM CC CC 69 733 6.0354814325 GG MM AA MM CC CC 72 736 5.8861040315 GG MM AA MM CC CC 74 737 5.7203117766 GG MM AA MM CC CC 68 740 5.7430031878 GG MM aA MV CC CC 61 745 5.6869753563 GG MM aA MM CC CC 77 746 5.7493929859 GG MM AA MM CC CC 59 749 5.4161004022 GG MM AA MM CC CC 68 752 5.7838251823 GG MM aA MM CC CC 56 753 5.8861040315 GG MM AA MM CC CC 57 754 5.9712618398 GG MM AA MM CC CC 53 757 5.6276211137 GG MM AA MM CC CC 69 760 5.7203117766 GG MM aA MM CC CC 65 761 5.5174528965 GG MM AA MM CC CC 66 766 5.4930614433 GA MM AA MM CC CC 62 768 5.8721177895 GG MM aA MM CC CC 60 769 5.6869753563 GG MM AA MM CC CC 76 772 5.8348107371 GA MM AA MM CC CC 68 774 5.7683209958 GG MM AA MM CC CC 69 775 5.3890717298 GA MM aA MM CC CC 74 776 5.5294290875 GG MM AA MM CC CC 64 777 5.6767538023 GG MM AA MM CC CC 55 778 5.6835797673 GG MM AA MM CC CC 67 779 6.1654178542 GG MM AA MM CC CC 62 780 6.0637852087 GG MM aA MM CC CC 64 781 5.7071102647 GG MM aA MM CC CC 74 783 5.4764635519 GG MM aA MM CC CC 53 786 5.8550719222 GG MI AA MM CC CC 72 790 5.7037824747 GG MM aA MM CC CC 55 792 5.3471075307 GG MM AA MM CC CC 72 793 6.1290502101 GG MM AA MM CC CC 59 794 5.9864520053 GG MI AA MM CC CC 59 800 5.9348941956 GG MM AA MM CC CC 63 801 5.6835797673 GG MM AA MM CC CC 76 802 5.80814249 GG MM AA MM CC CC 62 803 5.7557422136 GG MM aA MM CC CC 63 804 5.8522024798 GG MI AA MM CC CC 60 805 6.2265366693 GG MM AA MM CC CC 54 806 6.2441669007 GG MM AA MM CC CC 44 817 5.598421959 GG MM AA MM CC CC 72 818 6.0306852603 GG MM AA MM CC CC 59 819 5.5174528965 GG MM aA MM CC CC 73 821 5.6869753563 GG MM AA MM CC CC 68 823 5.5053315359 GG MM AA MM CC CC 73 824 5.7071102647 GG MM AA MM CC CC 75 826 6.0354814325 GG MI AA MM CC CC 74 827 5.537334267 GG MM AA MM CC CC 46 828 5.9026333334 GG MM AA MM CC CC 73 829 5.3706380281 GG MM AA MM CC CC 69 832 5.7104270174 GG MM AA MM CC CC 43 835 6.0890448754 GG MM aA MM CC CC 39 836 5.5412635452 GG MI AA MM CC CC 53 844 5.6767538023 GG MM AA MM CC CC 56 845 5.5683445038 GG MM aA MM CC CC 77 846 5.6733232672 GG MM AA MM CC CC 51 847 5.6489742382 GG MM aA MM CC CC 71 848 5.2832037287 GG MM AA MM CC CT 63 849 5.3471075307 GG MM aA MM CC CC 60 850 5.5053315359 GG MM AA MM CC CC 74 851 6.1758672701 GA MM AA MM CC CC 63 852 5.8348107371 GG MI aA MM CC CC 56 854 5.5412635452 GG MM AA MM CC CC 61 856 5.5053315359 GA MM AA MM CC CC 65 857 6.0497334552 GG MM aA MM CC CC 41 858 5.5834963088 GG MM aa MM CC CC 56 860 5.7268477476 GG MM AA MM CC CC 73 862 6.0112671744 GG MM aa MM CC CC 75 863 5.6970934865 GG MM aA MM CC CC 60 869 5.598421959 GG MM AA MM CC CC 69 871 5.4971682253 GG MM aA MV CC CT 60 872 5.3981627015 GG MM AA MM CC CC 59 873 5.4806389233 GG MM aA MV CC CT 58 877 5.9712618398 GG MM AA MM CC CC 73 879 5.8692969131 GG MM AA MM CC CC 57 880 5.7807435158 GA MM aA MM CC CC 61 881 5.7557422136 GG MI aA MV CC CT 58 883 5.7868973814 GG MI AA MM CC CC 64 885 5.7268477476 GA MM AA MM CC CC 61 886 5.7589017739 GG MM AA MM CC CC 68 890 6.0890448754 GG MM AA MM CC CC 75 894 6.1944053911 GG MM AA MM CC CC 75 896 5.7620513828 GG MM AA MM CC CC 72 897 5.6312117818 GG MM aA MM CC CC 71 899 5.7203117766 GG MM aA MM CC CC 64 900 5.7589017739 GG MM AA MM CC CC 47 901 5.9295891434 GG MI AA MM CC CC 59 903 5.9712618398 GG MM AA MM CC CC 51 904 5.7525726388 GG MM AA MM CC CC 54 906 5.9322451874 GG MI AA MM CC CC 56 907 6.0038870671 GG MM AA MM CC CC 42 908 6.045005314 GG MM AA MM CC CC 56 909 6.1136821798 GG MM AA MM CC CC 57 910 5.6204008657 GG MM AA MM CC CC 71 911 6.023447593 GG MM AA MM CC CC 49 912 5.6419070709 GG MI aA MM CC CC 59 913 5.6276211137 GG MM aA MM CC CC 76 914 6.0520891689 GG MM AA MM CC CC 64 915 5.8833223885 GG MM AA MM CC CC 79 918 5.910796644 GG MM AA MM CC CC 65 919 5.8051349689 GG MM AA MM CC CC 65 920 5.7899601709 GG MM AA MM CC CC 72 925 5.8141305318 GG MM AA MM CC CC 61 927 5.3082676974 GG MM aa MM CC CC 66 928 5.6240175062 GG MM AA MM CC CC 69 929 5.4071717715 GG MM aA MM CC CC 66 932 5.463831805 GG MM AA MM CC CC 57 934 5.7838251823 GG MM aa MM CC CC 51 935 5.730099783 GG MM AA MM CC CC 53 936 5.5093883366 GG MM AA MM CC CC 65 938 6.1923624895 GA MM AA MM CC CC 59 940 6.0210233493 GG MI AA MM CC CC 77 941 5.9080829382 GG MM aA MV CC CT 73 942 5.6419070709 GG MM aA MM CC CC 56 944 5.9964520886 GG MM AA MM CC CC 48 946 5.6021188209 GG MM AA MM CC CC 71 948 5.8749307309 GG MM AA MM CC CC 69 949 5.9427993751 GG MM aA MM CC CC 49 950 5.8464387751 GG MM AA MM CC CC 60 951 5.81711116 GG MM AA MM CC CC 74 952 5.4930614433 GG MM AA MM CC CC 67 953 6.0038870671 GG MM AA MM CC CC 68 954 5.6835797673 GG MM AA MM CC CC 49 955 5.9375362051 GA MM AA MM CC CC 75 956 5.4205349993 GG MM aA MM CC CC 73 958 6.023447593 GG MI aA MV CC CT 74 959 5.5333894887 GG MM aA MM CC CC 58 960 5.8550719222 GG MM AA MM CC CC 70 961 5.8579331545 GG MM aA MM CC CC 64 962 5.7807435158 GG MM aA MM CC CC 37 964 5.2882670307 GG MI AA MM CC CC 70 965 5.9532433343 GG MM AA MM CC CC 69 966 5.6383546693 GG MM aA MM CC CC 59 967 5.9375362051 GG MI AA MM CC CC 58 969 5.9427993751 GG MI AA MM CC CC 77 970 5.7589017739 GG MM AA MM CC CC 39 971 6.047372179 GG MM AA MM CC CC 72 972 5.6454468976 GG MM aa MM CC CC 67 979 5.7868973814 GG MM AA MM CC CC 77 980 5.9839362807 GG MM AA MM CC CC 60 981 5.9135030056 GG MM aA MM CC CC 66 982 6.0637852087 GG MM AA MM CC CC 71 983 5.7462031905 GG MM AA MM CC CC 51 984 5.5947113796 GG MM AA MM CC CC 52 986 5.8636311756 GG MM AA MM CC CC 41 987 5.5053315359 GG MM AA MM CC CC 68 989 5.7462031905 GG MM AA MM CC CC 64 990 5.5529595849 GG MM aA MM CC CC 69 991 6.1312264895 GG MM AA MM CC CC 64 993 5.730099783 GG MI AA MM CC CC 60 994 6.1569789856 GG MI AA MM CC CC 67 996 5.7037824747 GG MM AA MM CC CC 50 997 5.6835797673 GG MM AA MM CC CC 79 999 6.2747620212 GG MM AA MM CC CC 57 1001 5.5093883366 GG MM AA MM CC CC 58 1002 6.1717005974 GG MI AA MM CC CC 73 1003 5.80814249 GG MM AA MM CC CC 59 1004 6.1590953885 GG MM AA MM CC CC 43 1006 5.8833223885 GG MM AA MM CC CC 73 1008 6.0402547113 GG MM aA MM CC CC 71 1009 5.9532433343 GG MM AA MM CC CC 75 1010 5.7745515455 GG MI AA MM CC CC 65 1011 5.5012582105 GG MM AA MM CC CC 64 1014 5.429345629 GG MI aA MM CC CC 61 1015 5.7004435734 GG MM AA MM CC CC 58 1017 5.4722706737 GG MM aA MM CC CC 70 1019 5.6276211137 GG MM AA MM CC CC 63 1020 5.7071102647 GG MM AA MM CC CC 55 1021 5.6559918108 GG MM AA MM CC CC 60 1024 5.8916442118 GG MM AA MM CC CC 66 1026 5.5683445038 GG MM AA MM CC CC 70 1027 6.1841488909 GG MI AA MM CC CC 73 1028 5.6767538023 GG MM aA MM CC CC 71 1030 5.7333412769 GG MM AA MM CC CC 68 1031 6.0402547113 GG MM aA MM CC CC 71 1032 6.0844994131 GG MM AA MM CC CC 55 1033 5.7397929122 GG MM aa MM CC CC 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5.7557422136 GG MM AA MM CC CC 72 1113 5.537334267 GG MM AA MM CC CC 58 1114 5.4553211154 GA MM AA MM CC CC 68 1115 5.8260001074 GG MM aA MM CC CC 63 1116 5.7714411231 GG MM aA MM CC CC 72 1117 5.7170277014 GG MM AA MM CC CC 70 1118 5.1416635565 GG MM AA MM CC CC 56 1119 5.9026333334 GG MM aA MM CC CC 60 1120 5.4249500175 GG MM aa MV CC CT 50 1121 5.7493929859 GG MM aA MV CC CT 59 1122 6.2747620212 GG MM aA MM CC CC 57 1123 5.9162020626 GG MM AA MM CC CC 46 1124 5.5872486584 GG MM AA MM CC CC 67 1125 5.4380793089 GG MM aA MM CC CC 76 1126 5.9558373695 GG MM AA MM CC CC 63 1127 5.4889377262 GG MM aA MM CC CC 78 1128 5.8636311756 GG MM AA MM CC CC 52 1129 5.9712618398 GG MM aA MM CC CC 73 1130 5.6094717952 GG MM AA MM CC CC 74 1131 5.7557422136 GG MM AA MM CC CC 71 1132 5.7960577508 GG MI AA MM CC CC 70 1133 5.7037824747 GG MM AA MM CC CC 78 1134 5.7397929122 GG MM AA MM CC CC 71 1135 5.9506425526 GG MI AA MM CC CC 53 1136 5.3278761688 GG MM AA MM CC CC 47 1137 5.0998664278 GG MM aA MM CC CC 73 1138 5.6869753563 GG MM aA MV CC CT 41 1139 5.8721177895 GG MM AA MM CC CC 68 1140 5.8200829304 GG MM AA MM CC CC 69 1141 5.5490760849 GG MM AA MM CC CC 72 1142 5.3981627015 GG MM AA MM CC CC 67 1144 5.6419070709 GG MM aA MM CC CC 63 1145 5.6629604801 GG MM AA MM CC CC 70 1148 6.133398043 GA MM AA MM CC CC 70 1149 5.6559918108 GG MM AA MM CC CC 68 1150 5.8636311756 GG MM AA MM CC CC 63 1151 5.9532433343 GG MM aA MM CC CC 75 1152 5.9480349892 GG MM aA MM CC CC 60 1154 6.2441669007 GG MI AA MM CC CC 53 1155 5.5645204073 GG MM AA MM CC CC 59 1157 5.730099783 GG MM AA MM CC CC 72 1158 5.579729826 GG MM aA MV CC CT 55 1160 5.5053315359 GG MM aA MM CC CC 76 1161 5.7462031905 GG MM AA MM CC CC 55 1162 5.9242557974 GG MM aA MM CC CC 60 1163 6.2897155709 GA MM aA MM CC CC 59 1165 5.8406416574 GG MM aA MM CC CC 60 1168 5.6419070709 GG MI AA MM CC CC 72 1169 5.8944028343 GG MM AA MM CC CC 72 1172 6.3153580015 GG MI aA MM CC CC 69 1174 5.3612921657 GG MM aA MM CC CC 58 1176 5.7745515455 GG MM aa MM CC CC 58 1177 5.8636311756 GG MM aa MM CC CC 75 1178 5.6594822158 GG MI AA MM CC CC 64 1180 5.80814249 GA MM AA MM CC CC 58 1181 5.7004435734 GG MM AA MM CC CC 55 1182 5.958424693 GG MI AA MM CC CC 65 1183 5.7838251823 GG MM aA MM CC CC 71 1184 5.9939614273 GG MM AA MM CC CC 54 1185 6.100318952 GG MI AA MM CC CC 54 1186 5.7557422136 GG MM AA MM CC CC 78 1187 5.8377304472 GG MM aA MM CC CC 72 1188 6.1114673395 GG MM AA MM CC CC 48 1189 6.001414878 GG MM AA MM CC CC 63 1190 5.9375362051 GG MM AA MM CC CC 68 1192 6.047372179 GG MM AA MM CC CC 78 1193 5.7899601709 GG MM aA MM CC CC 59 1195 5.6094717952 GG MM AA MM CC CC 61 1196 5.680172609 GA MM AA MM CC CC 36 1926 5.843544417 GG MM AA MM CC CC 55 1927 6.1025585946 GG MM aA MM CC CC 40 1929 5.9053618481 GG MM AA MM CC CC 49 1930 6.0306852603 GG MM AA MM CC CC 57 1931 5.9215784196 GG MI AA MM CC CC 48 1932 5.8348107371 GG MM AA MM CC CC 50 1933 5.7170277014 GG MM AA MM CC CC 56 1934 5.680172609 GG MM aA MM CC CC 54 1935 5.7930136084 GG MM aA MM CC CC 55 1936 5.6058020663 GG MM aa MM CC CC 54 1937 5.7397929122 GG MM AA MM CC CC 56 1938 5.5451774445 GG MM AA MM CC CC 59 1939 5.7589017739 GG MM AA MM CT CC 52 1940 5.7137328055 GG MM AA MM CC CC 56 1941 5.843544417 GG MM aA MM CC CC 52 1942 5.730099783 GG MM AA MM CC CC 55 1943 5.4764635519 GG MM AA MM CC CC 53 1944 6.6066501862 GG MM AA MM CC CC 52 1945 6.154858094 GG MI AA MM CC CC 66 1946 5.811140993 GG MM AA MM CC CC 57 1947 5.910796644 GG MM aA MM CC CC 63 1948 5.7620513828 GG MI AA MM CC CC 76 1949 5.8377304472 GG MM aa MV CC CT 64 1951 5.6240175062 GG MI aA MM CC CC 59 1953 5.7620513828 GG MM AA MM CC CC 67 1954 5.8348107371 GG MM AA MM CC CC 64 1956 5.4680601411 GG MM aA MM CC CC 62 1957 5.7170277014 GG MM aa MM CC CC 72 1958 5.7899601709 GG MM AA MM CC CC 72 1959 5.9242557974 GG MM AA MM CC CC 67 1960 5.6021188209 GG MM aA MV CC CT 66 1961 5.9889614169 GG MM AA MM CC CC 50 1962 5.7430031878 GG MI aA MM CC CC 74 1963 5.6664266881 GG MM aA MM CC CC 65 1964 5.6094717952 GG MI AA MM CC CC 63 1966 5.8522024798 GG MM aA MM CC CC 76 1967 5.537334267 GG MM AA MM CC CC 79 1968 5.7745515455 GG MM AA MM CC CC 61 1969 5.7745515455 GG MM AA MM CC CC 67 1970 5.7899601709 GG MM AA MM CC CC 65 1971 6.1441856341 GG MM aA MM CC CC 67 1972 5.8464387751 GG MM AA MM CC CC 65 1973 6.023447593 GG MM AA MM CC CC 63 1974 6.013715156 GG MI AA MM CC CC 64 1975 5.8464387751 GG MM aA MM CC CC 68 1976 5.7397929122 GG MM AA MM CC CC 63 1977 5.5134287462 GG MM aA MM CC CC 63 1978 5.8579331545 GG MM AA MM CC CC 63 1979 5.9454206086 GG MM AA MM CC CC 65 1980 5.5254529391 GG MI aA MM CC CC 59 1981 5.8777357818 GG MM aA MM CC CC 65 1982 5.8607862235 GG MM AA MM CC CC 72 1983 5.6903594543 GG MM aA MM CC CC 62 1984 5.8200829304 GG MM aA MM CC CC 62 1985 6.0282785202 GG MI AA MM CC CC 55 1986 5.8916442118 GG MM AA MM CT CC 52 1988 5.6419070709 GG MM aA MM CC CC 57 1989 5.6937321388 GG MM AA MM CC CC 58 1990 5.8260001074 GG MM aa MM CC CC 62 1991 5.4680601411 GG MM aa MV CC CT 64 1993 5.9053618481 GG MI AA MM CC CC 76 1994 5.5214609179 GG MM AA MM CC CC 60 1995 5.1416635565 GG MM AA MM CC CC 54 1996 5.4889377262 GG MM AA MM CC CC 68 1997 5.3471075307 GG MM AA MM CC CC 53 1998 5.7960577508 GG MM AA MM CC CC 61 1999 5.8260001074 GG MM AA MM CC CC 61 2000 5.8260001074 GG MM AA MM CC CC 66 2001 6.3261494732 GG MM aA MM CC CC 54 2002 6.001414878 GG MM aA MM CC CC 53 2003 5.9135030056 GG MM aA MM CC CC 57 2004 5.5834963088 GG MM aA MM CC CC 60 2006 5.9558373695 GG MM AA MM CC CC 70 2007 5.7365722975 GG MM aA MM CC CC 61 2008 6.1355648911 GG MM AA MM CC CC 69 2009 5.9989365619 GG MM AA MM CC CC 60 2010 6.1224928095 GG MM AA MM CC CC 49 2011 5.8406416574 GG MM AA MM CC CC 59 2012 5.9135030056 GG MM AA MM CC CC 62 2013 5.8692969131 GG MM aA MM CC CC 60 2014 5.7776523232 GG MM AA MM CC CC 57 2015 5.910796644 GG MM AA MM CC CC 53 2016 5.8289456176 GG MM AA MM CC CC 60 2017 6.3885614055 GG MM AA MM CC CC 54 2018 6.1882641231 GG MI AA MM CC CC 69 2019 5.8021183754 GG MM aA MM CC CC 71 2020 5.5529595849 GA MM AA MM CC CC 61 2021 5.9348941956 GG MM AA MM CC CC 74 2022 5.6204008657 GG MM AA MM CC CC 76 2023 5.6240175062 GG MM AA MM CC CC 70 2024 5.7397929122 GG MM AA MM CC CC 67 2025 5.5529595849 GG MM AA MM CC CC 73 2026 5.9375362051 GG MM AA MM CC CC 71 2027 5.8406416574 GG MM AA MM CC CC 67 2028 6.013715156 GG MM AA MM CC CC 78 2029 5.4553211154 GA MM aA MM CC CC 67 2030 5.8805329864 GG MM aA MM CC CC 56 2031 5.7462031905 GG MI AA MM CC CC 69 2032 5.9053618481 GG MM AA MM CC CC 63 2033 5.8377304472 GG MM aA MM CC CC 69 2034 5.8289456176 GG MM AA MM CC CC 60 2035 6.0776422433 GG MM AA MM CC CC 54 2036 5.6383546693 GG MM aa MM CC CC 59 2037 6.0544393463 GG MM AA MM CC CC 65 2038 5.81711116 GG MM AA MM CC CC 61 2039 5.8260001074 GG MM AA MM CC CC 70 2040 5.9763509093 GG MI AA MM CC CC 69 2041 5.6733232672 GG MM AA MM CC CC 52 2042 6.200509174 GG MM AA MM CC CC 68 2043 5.8348107371 GG MM AA MM CC CC 62 2044 5.8348107371 GG MM AA MM CC 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MM AA MM CC CC 55 2072 6.0890448754 GG MM AA MM CC CC 57 2073 5.680172609 GG MM AA MM CC CC 62 2074 5.4971682253 GA MM AA MM CC CC 59 2075 5.4116460519 GG MM aA MM CC CC 59 2076 5.7960577508 GG MM AA MM CC CC 64 2077 5.811140993 GG MM aA MM CC CC 69 2078 5.5412635452 GG MM AA MM CC CC 60 2079 5.6347896032 GG MM aA MM CC CC 68 2080 5.8607862235 GG MM AA MM CC CC 65 2081 5.8377304472 GG MM AA MM CC CC 62 2082 6.280395839 GA MM AA MM CC CC 52 2083 5.7589017739 GG MM aA MM CC CC 58 2084 5.8550719222 GG MM AA MM CC CC 61 2085 5.9506425526 GG MM aa MM CC CC 64 2086 5.7776523232 GG MM AA MM CC CC 64 2087 5.6131281064 GG MI AA MM CC CC 62 2088 6.0637852087 GG MM AA MM CC CC 59 2089 5.8805329864 GG MM AA MM CC CC 64 2091 5.8406416574 GG MM aA MM CC CC 58 2092 5.8493247799 GG MM AA MM CC CC 53 2093 5.7037824747 GA MM AA MM CC CC 62 2094 5.170483995 GG MM aA MM CC CC 61 2095 6.2126060958 GG MM AA MM CC CC 66 2096 6.1312264895 GG MM AA MM CC CC 69 2097 5.7620513828 GA MM AA MM CC CC 60 2098 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12 11 12 10867 1 0 49 39.7361212916168 11 11 11 11 11 11 22 11 10906 1 0 50 39.8961195378072 22 11 22 0 11 11 11 22 10934 1 0 39 38.4940312213039 12 11 12 12 12 12 11 12 10969 0 0 26 36.8120631238362 11 11 11 22 11 22 11 11 11003 0 0 41 31.0204081632653 0 0 0 0 0 0 0 0 11006 1 0 62 39.5644410209726 12 12 11 11 11 12 12 11 11029 0 0 60 38.9473684210526 22 22 11 11 11 22 11 11 11033 1 0 60 32.605888429752 11 11 11 12 12 12 12 11 11102 0 0 51 39.8148148148148 22 22 11 11 11 22 11 11 11118 0 0 24 37.865649208 22 11 22 11 11 0 11 22 11182 0 0 23 39.1364726675924 11 11 11 22 22 22 11 11 11223 1 0 54 39.68253968254 0 0 0 0 0 0 0 0 11258 1 0 30 33.4251606978879 12 11 12 11 12 11 11 12 11309 1 0 53 36.81788297173 11 11 11 12 11 12 12 11 11373 1 0 20 38.1841165972635 11 11 11 12 12 12 12 11 11422 0 0 48 36.81788297173 22 11 22 22 22 22 11 11 11452 1 0 31 39.0392623438429 12 11 12 12 11 12 11 12 11514 1 0 68 39.3021120293847 12 11 12 12 11 12 11 12 11526 0 0 50 36.39315808628 11 11 11 11 11 11 22 11 11577 1 0 54 37.5776274672679 22 11 22 12 12 12 11 22 11606 1 0 45 38.9348025711662 22 12 12 11 11 12 11 12 11670 1 0 28 39.9337573864277 11 11 11 12 12 12 12 11 11771 1 0 66 38.828125 11 11 11 11 11 11 22 11 11801 1 0 45 39.3503337062613 12 11 12 11 11 11 12 12 11836 1 0 44 38.4849870446578 22 22 11 0 11 12 12 11 11867 1 0 37 39.79 11 0 11 11 11 11 22 11 11929 1 0 50 34.6809353943717 12 12 11 11 11 12 12 11 12017 0 0 53 37.8775510204081 11 11 11 11 11 11 22 11 12036 1 0 53 39.328231292517 11 11 11 12 12 12 12 11 12083 0 0 51 39.6813284087787 22 11 22 11 11 11 11 11 12090 0 0 72 39.57994190686 11 11 11 11 11 11 22 11 12106 0 0 38 38.9415557470714 11 11 11 11 11 11 22 11 12273 1 0 25 39.84375 22 11 22 12 12 12 11 12 12286 1 0 21 33.27 12 11 12 11 11 11 12 12 12306 1 0 39 37.6378486205728 11 11 11 22 12 22 11 11 12528 1 0 45 39.2139889196675 12 11 12 11 11 11 0 11 12542 1 0 41 37.29 12 11 12 11 11 11 12 12 12551 1 0 37 39.64 12 11 12 11 11 11 12 12 12571 0 0 39 31.29 22 11 22 22 22 22 11 11 12598 1 0 39 30.93 11 11 11 12 12 12 12 11 12644 1 0 57 39.12 12 11 12 12 12 12 12 11 12677 1 0 39 38.7 12 11 12 11 11 11 12 12 12717 1 0 46 36.9792422702859 11 11 11 12 12 12 12 11 12743 1 0 47 38.9348025711662 0 0 12 11 0 11 0 0 12747 0 0 58 38.0622837370242 11 11 11 11 11 11 11 22 12755 0 0 47 39.67 11 11 11 11 11 11 0 11 12775 0 0 53 38.12 11 11 11 11 11 11 22 11 12776 0 0 69 39.123149003112 22 22 11 11 11 22 0 11 12873 1 0 26 39.64 12 12 11 11 11 11 22 11 12951 1 0 29 35.12 11 11 11 12 12 12 12 11 1089 0 0 15 31.8 0 0 0 0 0 0 0 0 10128 1 0 65 43.62 11 11 11 11 11 11 22 11 10797 1 0 22 41.53 11 11 11 12 11 12 12 11 11406 0 0 41 33.94 11 11 11 11 11 11 22 11 thesias-3.1.1/java/000077500000000000000000000000001360777755100141175ustar00rootroot00000000000000thesias-3.1.1/java/ColumnHeaderListener.java000066400000000000000000000061161360777755100210420ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.*; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import javax.swing.JDialog; import java.io.*; import javax.swing.JMenuBar; import javax.swing.JMenu; import javax.swing.JMenuItem; public class ColumnHeaderListener extends MouseAdapter { public void mouseClicked(MouseEvent evt) { JTable table = ((JTableHeader)evt.getSource()).getTable(); TableColumnModel colModel = table.getColumnModel(); // The index of the column whose header was clicked int vColIndex = colModel.getColumnIndexAtX(evt.getX()); int mColIndex = table.convertColumnIndexToModel(vColIndex); TableColumn tm = table.getColumnModel().getColumn(0); tm.setCellRenderer(new ColorColumnRenderer(Color.lightGray, Color.blue)); // Return if not clicked on any column header if (vColIndex == -1) { return; } // Determine if mouse was clicked between column heads Rectangle headerRect = table.getTableHeader().getHeaderRect(vColIndex); if (vColIndex == 0) { headerRect.width -= 3; } else { headerRect.grow(-3, 0); } if (!headerRect.contains(evt.getX(), evt.getY())) { int vLeftColIndex = vColIndex; if (evt.getX() < headerRect.x) { vLeftColIndex--; } } } } class ColorColumnRenderer extends DefaultTableCellRenderer { Color bkgndColor, fgndColor; public ColorColumnRenderer(Color bkgnd, Color foregnd) { super(); bkgndColor = bkgnd; fgndColor = foregnd; } public Component getTableCellRendererComponent (JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) { Component cell = super.getTableCellRendererComponent( table, value, isSelected, hasFocus, row, column); cell.setBackground( bkgndColor ); cell.setForeground( fgndColor ); return cell; } } thesias-3.1.1/java/CustomDialog.java000066400000000000000000000115671360777755100173660ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import javax.swing.JOptionPane; import javax.swing.JDialog; import javax.swing.JTextField; import java.beans.*; import java.awt.*; import java.awt.event.*; import javax.swing.JLabel; import java.io.*; import javax.swing.*; import javax.swing.filechooser.*; class CustomDialog extends JFrame implements ActionListener, PropertyChangeListener { private String typedText = null; private JTextField textField; JFileChooser fc; private String magicWord; private JOptionPane optionPane; private String btnString1 = "Enter"; private String btnString2 = "Cancel"; private String sbtnClose = "Close"; private String sbtnAdvance = "Advance"; private String sbtnPrint = "Print"; private String sbtnSave = "Save"; JButton close; JButton advanceButton,printButton,saveButton; String sParam; Object covar[]; GraficT grafic; dataThesias datta; private String sPrint; String sSave; public String getValidatedText() { return typedText; } /** Creates the reusable dialog. */ public CustomDialog(dataThesias ddd,GraficT art,Frame aFrame, String aWord,StringBuffer s,String sParam,Object []covar,StringBuffer sbufTest) { super(); sSave = new String(s); sPrint = new String(sbufTest); grafic = art; datta = ddd; this.covar = covar; fc = new JFileChooser(); Color saumon = new Color( 255, 204, 153 ); setDefaultLookAndFeelDecorated(true); GridLayout grid = new GridLayout(2,0); getContentPane().setLayout(new BorderLayout()); JEditorPane a = new JEditorPane(); a.setContentType("text/html"); a.setEditable(false); a.setText(s.toString()); JScrollPane jscrol = new JScrollPane(a); getContentPane().add(jscrol,BorderLayout.CENTER); JPanel buttPanel = new JPanel(new GridLayout(1,2)); close = new JButton(sbtnClose); close.setBackground(saumon); close.setActionCommand(sbtnClose); close.addActionListener(this); buttPanel.add(close); this.sParam = sParam; if (sParam.length() != 0) { advanceButton = new JButton("Advance"); advanceButton.setBackground(saumon); advanceButton.setActionCommand(sbtnAdvance); advanceButton.addActionListener(this); buttPanel.add(advanceButton); } printButton = new JButton(sbtnPrint); printButton.setActionCommand(sbtnPrint); printButton.addActionListener(this); buttPanel.add(printButton); saveButton = new JButton(sbtnSave); saveButton.setActionCommand(sbtnSave); saveButton.addActionListener(this); buttPanel.add(saveButton); getContentPane().add(buttPanel,BorderLayout.SOUTH); Dimension dim = Toolkit.getDefaultToolkit().getScreenSize(); GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment(); GraphicsDevice[] gs = ge.getScreenDevices(); // Get size of each screen DisplayMode dm = gs[0].getDisplayMode(); int screenWidth = dm.getWidth(); int screenHeight = dm.getHeight(); this.setSize(dm.getWidth(),dm.getHeight()-80); printButton.setBackground(saumon); saveButton.setBackground(saumon); } public void actionPerformed(ActionEvent e) { if( sbtnClose.equals(e.getActionCommand()) ){ setVisible(false); } else if (sbtnAdvance.equals(e.getActionCommand()) ) { OptionDialog optDialog = new OptionDialog(datta,grafic,this,sParam,this.covar); optDialog.setVisible(true); } else if ( sbtnPrint.equals(e.getActionCommand()) ) { TextPrint t = new TextPrint(); t.runPrint(sPrint); } else if( sbtnSave.equals(e.getActionCommand()) ) { int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); String content; try { int i,j,tj = 0; FileWriter fwData; fwData = new FileWriter(file); fwData.write(sSave, 0 , sSave.length()); fwData.close(); fwData.close(); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } } } } public void propertyChange(PropertyChangeEvent e) { } public void clearAndHide() { textField.setText(null); setVisible(false); } } thesias-3.1.1/java/DocumentRenderer.java000066400000000000000000000140211360777755100202250ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Rectangle; import java.awt.Shape; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import javax.swing.JEditorPane; import javax.swing.text.Document; import javax.swing.text.PlainDocument; import javax.swing.text.View; import javax.swing.text.html.HTMLDocument; public class DocumentRenderer implements Printable { protected int currentPage = -1; protected JEditorPane jeditorPane; protected double pageEndY = 0; protected double pageStartY = 0; protected boolean scaleWidthToFit = true; protected PageFormat pFormat; protected PrinterJob pJob; public DocumentRenderer() { pFormat = new PageFormat(); pJob = PrinterJob.getPrinterJob(); } public Document getDocument() { if (jeditorPane != null) return jeditorPane.getDocument(); else return null; } public boolean getScaleWidthToFit() { return scaleWidthToFit; } public void pageDialog() { pFormat = pJob.pageDialog(pFormat); } public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) { double scale = 1; Graphics2D graphics2D; View rootView; graphics2D = (Graphics2D) graphics; jeditorPane.setSize((int) pageFormat.getImageableWidth(),Integer.MAX_VALUE); jeditorPane.validate(); rootView = jeditorPane.getUI().getRootView(jeditorPane); if ((scaleWidthToFit) && (jeditorPane.getMinimumSize().getWidth() > pageFormat.getImageableWidth())) { scale = pageFormat.getImageableWidth()/ jeditorPane.getMinimumSize().getWidth(); graphics2D.scale(scale,scale); } graphics2D.setClip((int) (pageFormat.getImageableX()/scale), (int) (pageFormat.getImageableY()/scale), (int) (pageFormat.getImageableWidth()/scale), (int) (pageFormat.getImageableHeight()/scale)); if (pageIndex > currentPage) { currentPage = pageIndex; pageStartY += pageEndY; pageEndY = graphics2D.getClipBounds().getHeight(); } graphics2D.translate(graphics2D.getClipBounds().getX(), graphics2D.getClipBounds().getY()); Rectangle allocation = new Rectangle(0, (int) -pageStartY, (int) (jeditorPane.getMinimumSize().getWidth()), (int) (jeditorPane.getPreferredSize().getHeight())); if (printView(graphics2D,allocation,rootView)) { return Printable.PAGE_EXISTS; } else { pageStartY = 0; pageEndY = 0; currentPage = -1; return Printable.NO_SUCH_PAGE; } } public void print(HTMLDocument htmlDocument) { setDocument(htmlDocument); printDialog(); } public void print(JEditorPane jedPane) { setDocument(jedPane); printDialog(); } public void print(PlainDocument plainDocument) { setDocument(plainDocument); printDialog(); } protected void printDialog() { if (pJob.printDialog()) { pJob.setPrintable(this,pFormat); try { pJob.print(); } catch (PrinterException printerException) { pageStartY = 0; pageEndY = 0; currentPage = -1; System.out.println("Error Printing Document"); } } } protected boolean printView(Graphics2D graphics2D, Shape allocation, View view) { boolean pageExists = false; Rectangle clipRectangle = graphics2D.getClipBounds(); Shape childAllocation; View childView; if (view.getViewCount() > 0) { for (int i = 0; i < view.getViewCount(); i++) { childAllocation = view.getChildAllocation(i,allocation); if (childAllocation != null) { childView = view.getView(i); if (printView(graphics2D,childAllocation,childView)) { pageExists = true; } } } } else { if (allocation.getBounds().getMaxY() >= clipRectangle.getY()) { pageExists = true; if ((allocation.getBounds().getHeight() > clipRectangle.getHeight()) && (allocation.intersects(clipRectangle))) { view.paint(graphics2D,allocation); } else { if (allocation.getBounds().getY() >= clipRectangle.getY()) { if (allocation.getBounds().getMaxY() <= clipRectangle.getMaxY()) { view.paint(graphics2D,allocation); } else { if (allocation.getBounds().getY() < pageEndY) { pageEndY = allocation.getBounds().getY(); } } } } } } return pageExists; } protected void setContentType(String type) { jeditorPane.setContentType(type); } public void setDocument(HTMLDocument htmlDocument) { jeditorPane = new JEditorPane(); setDocument("text/html",htmlDocument); } public void setDocument(JEditorPane jedPane) { jeditorPane = new JEditorPane(); setDocument(jedPane.getContentType(),jedPane.getDocument()); } public void setDocument(PlainDocument plainDocument) { jeditorPane = new JEditorPane(); setDocument("text/plain",plainDocument); } protected void setDocument(String type, Document document) { setContentType(type); jeditorPane.setDocument(document); } public void setScaleWidthToFit(boolean scaleWidth) { scaleWidthToFit = scaleWidth; } } thesias-3.1.1/java/GraficT.java000066400000000000000000001402511360777755100163040ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.*; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import javax.swing.JDialog; import java.io.*; import javax.swing.JMenuBar; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.filechooser.*; import java.util.regex.*; import java.awt.*; import java.awt.event.*; import javax.swing.table.*; public class GraficT extends JPanel implements ActionListener, ItemListener { final static boolean shouldFill = true; final static boolean shouldWeightX = true; final static boolean RIGHT_TO_LEFT = false; JFrame frame; JMenuBar menuBar; public JRadioButton v0Button, v1Button, v2Button, v3Button, v4Button, v5Button; ButtonGroup group; public JComboBox lpvCombo, idtimeCombo3_5, idtimeCombo4, numsxCombo, idoffsetCombo; JLabel l1,l2,l3; JButton runButton,advanceButton,exitButton; JCheckBox cbMissingGenotyp,cbPrintLDMatrix,cbEstimateHaplotypic,cbPrintR2,cbLink,cbOffset; JFileChooser fc; JTable table; MyTableModel tableModel; public boolean bMissingGenotyp, bPrintLDMatrix,bEstimateHaplotypic,bPrintR2,bLink,bOffset; public ListDemo lociChooser,covariables; public String rowstring,value; public Clipboard system; public StringSelection stsel; public int kindOfPhenotype; public boolean paramData; JScrollPane dataScrollPane; public ParamTable paramTable; public thesiaslib t; private Cursor hourglassCursor; private Cursor normalCursor; private static Pattern pat1; private static Pattern pat2; private static Matcher mat1; private static Matcher mat2; public Color saumon; public Color chair; public GraficT ( JFrame frame){ super(new GridLayout(1,1)); paramData = false; bMissingGenotyp = bPrintLDMatrix = bEstimateHaplotypic = bPrintR2 = bLink = bOffset = false; this.frame = frame; addComponentsToPane(); KeyStroke copy = KeyStroke.getKeyStroke(KeyEvent.VK_C,ActionEvent.CTRL_MASK,false); KeyStroke paste = KeyStroke.getKeyStroke(KeyEvent.VK_V,ActionEvent.CTRL_MASK,false); table.registerKeyboardAction(this,"Copy",copy,JComponent.WHEN_FOCUSED); table.registerKeyboardAction(this,"Paste",paste,JComponent.WHEN_FOCUSED); system = Toolkit.getDefaultToolkit().getSystemClipboard(); hourglassCursor = new Cursor(Cursor.WAIT_CURSOR); normalCursor = new Cursor(Cursor.DEFAULT_CURSOR); fc = new JFileChooser("./"); if (RIGHT_TO_LEFT) {setComponentOrientation(ComponentOrientation.RIGHT_TO_LEFT);} t = new thesiaslib(); Color chair = new Color( 249, 230, 196 ); frame.setBackground(chair); frame.setForeground(chair); } public void addComponentsToPane(){ Color chair = new Color( 249, 230, 196 ); Color saumon = new Color( 255, 204, 153 ); group = new ButtonGroup(); v0Button = new JRadioButton("Null");v0Button.setActionCommand("v0Button"); v0Button.setSelected(true); v0Button.setMnemonic(KeyEvent.VK_R); v1Button = new JRadioButton("Binary ");v1Button.setActionCommand("v1Button"); v2Button = new JRadioButton("Quantitative");v2Button.setActionCommand("v2Button"); v3Button = new JRadioButton("Survival");v3Button.setActionCommand("v3Button"); v4Button = new JRadioButton("Matched C-C"); v4Button.setActionCommand("v4Button"); v5Button = new JRadioButton("Categorical"); v5Button.setActionCommand("v5Button"); group.add(v0Button);group.add(v1Button); group.add(v2Button); group.add(v3Button);group.add(v4Button);group.add(v5Button); v0Button.addActionListener(this);v1Button.addActionListener(this); v2Button.addActionListener(this);v3Button.addActionListener(this); v4Button.addActionListener(this);v5Button.addActionListener(this); JSplitPane splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT); splitPane.setResizeWeight(0.0); add(splitPane, BorderLayout.CENTER); splitPane.setBackground(chair); splitPane.setForeground(chair); v0Button.setBackground(chair); v1Button.setBackground(chair); v2Button.setBackground(chair); v3Button.setBackground(chair); v4Button.setBackground(chair); v5Button.setBackground(chair); JPanel tableLayout = new JPanel(new GridLayout(1,1) ); tableLayout.setBorder(BorderFactory.createTitledBorder("Data table")); tableLayout.setBackground(chair); tableLayout.setForeground(chair); tableModel = new MyTableModel(7, 10); table = new JTable(tableModel); JTableHeader tHeader; tHeader = table.getTableHeader(); tHeader.setReorderingAllowed(false); tHeader.setResizingAllowed(true); tHeader.addMouseListener(new ColumnHeaderListener()); table.setPreferredScrollableViewportSize(new Dimension(100, 120)); table.setDragEnabled(true); table.setTableHeader(tHeader); tHeader.setBackground(saumon); table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); table.setColumnSelectionAllowed(false); table.setRowSelectionAllowed(true); dataScrollPane = new JScrollPane(table); dataScrollPane.setRowHeaderView(computeRowHeader(7)); tableLayout.add(dataScrollPane); splitPane.add(tableLayout); JPanel bottomLayout = new JPanel(); GridBagLayout gridBagLayout = new GridBagLayout(); GridBagConstraints cGridBag = new GridBagConstraints(); bottomLayout.setLayout(gridBagLayout); bottomLayout.setBackground(chair); bottomLayout.setForeground(chair); JPanel checkPanel = new JPanel(new GridLayout(6, 0)); checkPanel.setBorder(BorderFactory.createTitledBorder("Kind of phenotype") ); checkPanel.add(v0Button); checkPanel.add(v1Button); checkPanel.add(v2Button); checkPanel.add(v3Button); checkPanel.add(v4Button); checkPanel.add(v5Button); checkPanel.setBackground(saumon); JPanel paramVariables1 = new JPanel(new GridLayout(1,1)); paramVariables1 .setBorder(BorderFactory.createTitledBorder("Selection of Variables") ); paramVariables1.setBackground(saumon); paramVariables1.setForeground(saumon); JPanel paramVariables = new JPanel(new GridLayout(3, 2)); paramVariables.setBackground(chair); paramVariables.setForeground(chair); JPanel temp = new JPanel(new GridLayout(6,1)); temp.setBackground(saumon); temp.setForeground(saumon); cbMissingGenotyp = new JCheckBox("Deal with missing genotypic data"); cbMissingGenotyp.addItemListener(this); cbPrintR2 = new JCheckBox("Print R2 haplotypic information"); cbPrintR2 .addItemListener(this); cbPrintLDMatrix = new JCheckBox("Print LD Matrix"); cbPrintLDMatrix.addItemListener(this); cbEstimateHaplotypic = new JCheckBox("Estimation of haplotype effects"); cbEstimateHaplotypic.addItemListener(this); temp.add(cbMissingGenotyp); temp.add(cbPrintR2); temp.add(cbPrintLDMatrix); temp.add(cbEstimateHaplotypic); JPanel tempBis1 = new JPanel(new GridLayout(1,2)); JPanel tempBis2 = new JPanel(new GridLayout(1,2)); temp.add(tempBis1); temp.add(tempBis2); cbLink = new JCheckBox("X-Linked Analysis"); cbLink.addItemListener(this); cbOffset = new JCheckBox("Offset"); cbOffset.addItemListener(this); tempBis1.add(cbLink); tempBis2.add(cbOffset); cbMissingGenotyp.setBackground(chair); cbPrintR2.setBackground(chair); cbPrintLDMatrix.setBackground(chair); cbEstimateHaplotypic.setBackground(chair); cbLink.setBackground(chair); cbOffset.setBackground(chair); String[] textForColomns = {"no value"}; l1 = new JLabel("Phenotype variable"); l1.setOpaque(true); l1.setBackground(chair); lpvCombo = new JComboBox(textForColomns); l2 = new JLabel("Time variable"); l2.setOpaque(true); l2.setBackground(chair); idtimeCombo3_5 = new JComboBox(textForColomns); l3 = new JLabel("Matching variable"); l3.setOpaque(true); l3.setBackground(chair); idtimeCombo4 = new JComboBox(textForColomns); numsxCombo = new JComboBox(textForColomns); idoffsetCombo = new JComboBox(textForColomns); lpvCombo.setBackground(Color.white); idtimeCombo3_5.setBackground(Color.white); idtimeCombo4.setBackground(Color.white); numsxCombo.setBackground(Color.white); idoffsetCombo.setBackground(Color.white); paramVariables.add(l1); paramVariables.add(lpvCombo); paramVariables.add(l2); paramVariables.add(idtimeCombo3_5); paramVariables.add(l3); paramVariables.add(idtimeCombo4); tempBis1.add(numsxCombo); tempBis2.add(idoffsetCombo); JPanel kindPanel = new JPanel(new GridLayout(2,1)); kindPanel.setBackground(chair); kindPanel.add(checkPanel); kindPanel.add(paramVariables1); paramVariables1.add(paramVariables); cGridBag.gridx = 0; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 2; cGridBag.weightx =1.0; bottomLayout.add(kindPanel,cGridBag); cGridBag.gridx = 1; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 1; cGridBag.weightx =1.0; cGridBag.ipadx = 2; lociChooser = new ListDemo("Selection of Loci", this); bottomLayout.add(lociChooser,cGridBag); lociChooser.setBackground(saumon); cGridBag.gridx = 2; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 1; cGridBag.weightx =1.0; covariables = new ListDemo("Selection of Covariates",null); covariables.setBackground(saumon); paramTable = new ParamTable(); paramTable.setBackground(chair); cGridBag.gridx = 3; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 1; cGridBag.weightx =1.0; bottomLayout.add(paramTable,cGridBag); cGridBag.gridx = 1; cGridBag.gridy = 1; cGridBag.gridwidth = 2; cGridBag.gridheight = 1; bottomLayout.add(temp,cGridBag); cGridBag.gridx = 3; cGridBag.gridy = 1; cGridBag.gridwidth = 1; cGridBag.gridheight = 1; cGridBag.weightx = 0.001; cGridBag.weighty =.0; cGridBag.anchor = GridBagConstraints.SOUTH; JPanel butonPanel = new JPanel(new GridLayout(0,2)); runButton = new JButton("Run"); butonPanel.add(runButton); runButton.setActionCommand("runButton"); runButton.addActionListener(this); advanceButton = new JButton("Advance"); advanceButton.setActionCommand("advanceButton"); advanceButton.addActionListener(this); advanceButton.setVisible(false); exitButton = new JButton("Exit"); exitButton.setActionCommand("exitButton"); exitButton.addActionListener(this); butonPanel.add(exitButton); bottomLayout.add(butonPanel, cGridBag); exitButton.setBackground(saumon); runButton.setBackground(saumon); splitPane.add(bottomLayout); setEditableText(0); v1Button.setEnabled(false); v2Button.setEnabled(false); v3Button.setEnabled(false); v4Button.setEnabled(false); v5Button.setEnabled(false); } public JMenuBar addMenuBar(){ menuBar = new JMenuBar(); JMenu menu = new JMenu("Menu"); JMenuItem menuItem = new JMenuItem("Open File"); JMenuItem menuItem2 = new JMenuItem("About Thesias"); Color saumon = new Color( 255, 204, 153 ); menuBar.setBackground(saumon); menu.setBackground(saumon); menuItem.setBackground(saumon); menuItem2.setBackground(saumon); menuItem.setActionCommand("importMenu"); menuItem.addActionListener(this); menuItem2.addActionListener(this); menu.add(menuItem); menu.add(menuItem2); menuBar.add(menu); return menuBar; } public void itemStateChanged(ItemEvent e){ Object source = e.getItemSelectable(); if (source == cbMissingGenotyp){ bMissingGenotyp = ( bMissingGenotyp ) ? false : true; } else if ( source == cbPrintLDMatrix) { bPrintLDMatrix = ( bPrintLDMatrix ) ? false : true; } else if( source == cbEstimateHaplotypic ) { bEstimateHaplotypic = ( bEstimateHaplotypic ) ? false : true; if( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } else if( source == cbPrintR2 ){ bPrintR2 = ( bPrintR2 ) ? false : true; } else if(source == cbOffset){ bOffset =(bOffset)? false : true; if(bOffset){idoffsetCombo.setEnabled(true);} else{idoffsetCombo.setEnabled(false);} } else if(source == cbLink){ bLink =(bLink)? false : true; if(bLink){numsxCombo.setEnabled(true);} else{numsxCombo.setEnabled(false);} } } public void setEditableText(int i){ kindOfPhenotype = i; switch( i ) { case 0: lpvCombo.setEnabled(false); idtimeCombo3_5.setEnabled(false); idtimeCombo4.setEnabled(false); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); cbEstimateHaplotypic.setEnabled(false); cbLink.setEnabled(false); cbLink.setVisible(true); cbOffset.setEnabled(false); cbOffset.setVisible(true); paramTable.setVisible(true); paramTable.setParamTableEnabled(false); paramTable.reinitParamTable(); lociChooser.setEnabled(false); covariables.setEnabled(false); cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbPrintR2.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); lpvCombo.setSelectedIndex(0); idtimeCombo3_5.setSelectedIndex(0); idtimeCombo4.setSelectedIndex(0); numsxCombo.setSelectedIndex(0); idoffsetCombo.setSelectedIndex(0); break; case 1: lpvCombo.setEnabled(true); idtimeCombo3_5.setEnabled(false); idtimeCombo4.setEnabled(false); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); cbEstimateHaplotypic.setEnabled(true); cbLink.setVisible(true); cbLink.setEnabled(true); cbOffset.setVisible(true); cbOffset.setEnabled(true); paramTable.setVisible(true); paramTable.setParamTableEnabled(true); lociChooser.setEnabled(true); covariables.setEnabled(true); cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbPrintR2.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); lpvCombo.setSelectedIndex(0); idtimeCombo3_5.setSelectedIndex(0); idtimeCombo4.setSelectedIndex(0); numsxCombo.setSelectedIndex(0); idoffsetCombo.setSelectedIndex(0); break; case 2: lpvCombo.setEnabled(true); idtimeCombo3_5.setEnabled(false); idtimeCombo4.setEnabled(false); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); cbEstimateHaplotypic.setEnabled(true); cbLink.setVisible(true); cbLink.setEnabled(true); cbOffset.setVisible(true); cbOffset.setEnabled(false); paramTable.setVisible(true); paramTable.setParamTableEnabled(true); cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbPrintR2.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); lpvCombo.setSelectedIndex(0); idtimeCombo3_5.setSelectedIndex(0); idtimeCombo4.setSelectedIndex(0); numsxCombo.setSelectedIndex(0); idoffsetCombo.setSelectedIndex(0); break; case 3: lpvCombo.setEnabled(true); idtimeCombo3_5.setEnabled(true); idtimeCombo4.setEnabled(false); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); cbEstimateHaplotypic.setVisible(true); cbEstimateHaplotypic.setEnabled(true); cbLink.setEnabled(false); cbLink.setVisible(true); cbOffset.setEnabled(false); cbOffset.setVisible(true); paramTable.setVisible(true); paramTable.setParamTableEnabled(true); cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbPrintR2.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); lpvCombo.setSelectedIndex(0); idtimeCombo3_5.setSelectedIndex(0); idtimeCombo4.setSelectedIndex(0); numsxCombo.setSelectedIndex(0); idoffsetCombo.setSelectedIndex(0); break; case 4: lpvCombo.setEnabled(true); idtimeCombo3_5.setEnabled(false); idtimeCombo4.setEnabled(true); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); cbEstimateHaplotypic.setEnabled(true); cbLink.setEnabled(false); cbLink.setVisible(true); cbOffset.setEnabled(false); cbOffset.setVisible(true); paramTable.setVisible(true); paramTable.setParamTableEnabled(true); cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbPrintR2.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); lpvCombo.setSelectedIndex(0); idtimeCombo3_5.setSelectedIndex(0); idtimeCombo4.setSelectedIndex(0); numsxCombo.setSelectedIndex(0); idoffsetCombo.setSelectedIndex(0); break; case 5: lpvCombo.setEnabled(true); idtimeCombo3_5.setEnabled(false); idtimeCombo4.setEnabled(false); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); cbEstimateHaplotypic.setEnabled(true); cbLink.setEnabled(false); cbLink.setVisible(true); cbOffset.setEnabled(false); cbOffset.setVisible(true); paramTable.setVisible(true); paramTable.setParamTableEnabled(true); cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbPrintR2.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); lpvCombo.setSelectedIndex(0); idtimeCombo3_5.setSelectedIndex(0); idtimeCombo4.setSelectedIndex(0); numsxCombo.setSelectedIndex(0); idoffsetCombo.setSelectedIndex(0); break; } } public void actionPerformed(ActionEvent e) { if("About Thesias".equals(e.getActionCommand())){ java.net.URL imgURL = getClass().getResource("LogoThesias.png"); JOptionPane.showMessageDialog(this, "Testing Haplotype EffectS in Association Study (THESIAS)\nTHESIAS was developped by DA Tregouet,\nINSERM U525, Paris, France.\nFor any information, please contact DA Tregouet at\ndavid-alexandre.tregouet@inserm.fr", "About Thesias.", JOptionPane.INFORMATION_MESSAGE,new ImageIcon(imgURL)); } if( "v0Button".equals(e.getActionCommand()) ){ setEditableText(0); advanceButton.setEnabled(false); lociChooser.setEnabled(true); lociChooser.ReInit(); covariables.ReInit(); covariables.setEnabled(false); paramTable.reinitParamTable(); bMissingGenotyp = bPrintLDMatrix = bEstimateHaplotypic = bPrintR2 = bLink = bOffset = false; cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbPrintR2.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); } else if( "v1Button".equals(e.getActionCommand()) ){ setEditableText(1); covariables.setEnabled(true); if ( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } else if( "v2Button".equals(e.getActionCommand()) ) { setEditableText(2); covariables.setEnabled(true); if ( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } else if( "v3Button".equals(e.getActionCommand()) ){ setEditableText(3); covariables.setEnabled(true); if ( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } else if( "v4Button".equals(e.getActionCommand()) ){ setEditableText(4); covariables.setEnabled(true); if ( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } else if( "v5Button".equals(e.getActionCommand()) ){ setEditableText(5); covariables.setEnabled(true); if ( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } else if ( "importMenu".equals(e.getActionCommand()) ){ int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); lociChooser.setEnabled(true); t = null; t = new thesiaslib(); "v0Button".equals(e.getActionCommand()); StringBuffer sbuf = new StringBuffer(); String contentFile; int nbColumn=1; int nbLine=1; try{ FileReader fImported = new FileReader(file); BufferedReader buffR1 = new BufferedReader(fImported); contentFile = buffR1.readLine(); pat1 = Pattern.compile(" "); pat2 = Pattern.compile(";"); mat1 = pat1.matcher(contentFile); mat2 = pat2.matcher(contentFile); if (mat1.find()){contentFile = contentFile.replaceAll(" ", "\t");} if (mat2.find()){contentFile = contentFile.replaceAll(";", "\t");} StringTokenizer stTok = new StringTokenizer(contentFile,"\t"); nbColumn = stTok.countTokens(); int cpt; for (cpt = 0; buffR1.readLine() !=null;cpt++){ } nbLine =cpt+1; buffR1.close(); fImported.close(); fImported = null; buffR1 = null; stTok = null; } catch (IOException excIO){ System.out.println(excIO.toString()); } tableModel = null; tableModel = new MyTableModel(nbLine, nbColumn); table.setModel(tableModel); dataScrollPane.setRowHeaderView(computeRowHeader(nbLine)); String content; try { int i,j,tj = 0; Object d[][] = new Object[nbLine][nbColumn+1]; FileReader s; s = new FileReader(file); BufferedReader b = new BufferedReader(s); content = b.readLine(); pat1 = Pattern.compile(" "); pat2 = Pattern.compile(";"); mat1 = pat1.matcher(content); mat2 = pat2.matcher(content); if (mat1.find()){content = content.replaceAll(" ", "\t");} if (mat2.find()){content = content.replaceAll(";", "\t");} StringTokenizer st; i = 0; while( content != null ) { pat1 = Pattern.compile(" "); pat2 = Pattern.compile(";"); mat1 = pat1.matcher(content); mat2 = pat2.matcher(content); if (mat1.find()){content = content.replaceAll(" ", "\t");} if (mat2.find()){content = content.replaceAll(";", "\t");} st = new StringTokenizer(content); j = 0; while (st.hasMoreTokens()) d[i][j++] = st.nextToken(); tj = j; i++; content = b.readLine(); } b.close(); s.close(); b = null; s = null; st = null; tableModel.initData(d,i,tj); v1Button.setEnabled(false); v2Button.setEnabled(false); v3Button.setEnabled(false); v4Button.setEnabled(false); v5Button.setEnabled(false); lociChooser.ReInit(); lociChooser.setTextForColumn(nbColumn); covariables.ReInit(); paramTable.reinitParamTable(); covariables.setTextForColumn(nbColumn); lpvCombo.setEnabled(false); idtimeCombo3_5.setEnabled(false); idtimeCombo4.setEnabled(false); numsxCombo.setEnabled(false); idoffsetCombo.setEnabled(false); setTextForColumn(nbColumn); paramTable.setVisible(true); v0Button.setSelected(true); kindOfPhenotype = 0; cbMissingGenotyp.setSelected(false); cbPrintLDMatrix.setSelected(false); cbEstimateHaplotypic.setSelected(false); cbPrintR2.setSelected(false); cbLink.setSelected(false); cbOffset.setSelected(false); covariables.setEnabled(false); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } } } if ( e.getActionCommand().compareTo("exitButton") == 0 ) { System.exit(0); } if (e.getActionCommand().compareTo("advanceButton") == 0) {} if( e.getActionCommand().compareTo("runButton")==0 ) { if ( lociChooser.getsListSize() == 0) { return; } int i; int lpv = 0,ltv = 0,lmit = 0,lwv = 0, idoffset = 0, numx = 0; int idtime = 0; String paraFile = new String(); Object data[][]; if (v1Button.isSelected()) { if (!((String)lpvCombo.getSelectedItem()).equals("")) { lpv = Integer.parseInt( ((String)lpvCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } } if (v2Button.isSelected()) { if (!((String)lpvCombo.getSelectedItem()).equals("")) { lpv = Integer.parseInt( ((String)lpvCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for :Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } } if (v3Button.isSelected()) { if (!((String)lpvCombo.getSelectedItem()).equals("")) { lpv = Integer.parseInt( ((String)lpvCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } if (!((String)idtimeCombo3_5.getSelectedItem()).equals("")) { ltv = Integer.parseInt( ((String)idtimeCombo3_5.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } } if (v4Button.isSelected()) { if (!((String)lpvCombo.getSelectedItem()).equals("")) { lpv = Integer.parseInt( ((String)lpvCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } if (!((String)idtimeCombo4.getSelectedItem()).equals("")) { lmit = Integer.parseInt( ((String)idtimeCombo4.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } } if (v5Button.isSelected()) { if (!((String)lpvCombo.getSelectedItem()).equals("")) { lpv = Integer.parseInt( ((String)lpvCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Need some value for Selection of variable !","WARNING", JOptionPane.WARNING_MESSAGE); return; } } if (cbLink.isEnabled() && cbLink.isSelected()) { if (!((String)numsxCombo.getSelectedItem()).equals("")) { numx = Integer.parseInt( ((String)numsxCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Please select a gender variable!","WARNING", JOptionPane.WARNING_MESSAGE); return; } } if (cbOffset.isEnabled() && cbOffset.isSelected()) { if (!((String)idoffsetCombo.getSelectedItem()).equals("")) { idoffset = Integer.parseInt( ((String)idoffsetCombo.getSelectedItem()).substring(1) ); } else { JOptionPane.showMessageDialog(this, "Please select an offset variable!","WARNING", JOptionPane.WARNING_MESSAGE); return; } } else if( "v1Button".equals(e.getActionCommand()) ){ setEditableText(1); covariables.setEnabled(true); if ( bEstimateHaplotypic ) advanceButton.setEnabled(true); else advanceButton.setEnabled(false); } if( kindOfPhenotype == 3 ) idtime = ltv; else if (kindOfPhenotype == 4) idtime = lmit; if ( kindOfPhenotype > 0 ) { paraFile = paramTable.serializeData(); } Object objTemp[] = lociChooser.getElements(); int lociCols[] = new int [lociChooser.getElements().length]; for( int t = 0 ; t < lociCols.length ; t++ ) lociCols[t] = Integer.parseInt( ((String)objTemp[t]).substring(1) ); objTemp = covariables.getElements(); int covarCols[]; if (bLink) { covarCols = new int [covariables.getElements().length + 1]; covarCols[0] = numx; for( int t = 1 ; t < covarCols.length ; t++ ) { covarCols[t] = Integer.parseInt( ((String)objTemp[t-1]).substring(1) ); } } else { covarCols = new int [covariables.getElements().length]; for( int t = 0 ; t < covarCols.length ; t++ ) { covarCols[t] = Integer.parseInt( ((String)objTemp[t]).substring(1) ); } } int col; data = tableModel.data; if ( ((String) data[0][0]).length() == 0 ) return; v1Button.setEnabled(true); v2Button.setEnabled(true); v3Button.setEnabled(true); v4Button.setEnabled(true); v5Button.setEnabled(true); for(i = 0 ; i < data[0].length; i++) if ( ((String) data[0][i]).length() == 0 ) break; col = i; for(i = 0; i < data.length ; i++) { if( ((String) data[i][0]).length() == 0 ) break; } data = new Object[i][col]; for( i =0 ; i < data.length; i++) for(int j = 0 ; j < col ; j++) data[i][j] = tableModel.data[i][j]; writeDataToFile("datafile.txt", data, data.length, col); { FileWriter fwData; StringBuffer sBuf = new StringBuffer(); if( !bEstimateHaplotypic ) sBuf.append("n" + "\r\n" + "n" + "\r\n" + "n" + "\r\n" + "n" +"\r\n" +"n"); else sBuf.append("y" + "\r\n" + "n" + "\r\n" + "n" + "\r\n" + "n" +"\r\n" +"n"); try { fwData = new FileWriter("paramData.thi"); fwData.write(sBuf.toString(), 0 , sBuf.toString().length()); fwData.close(); } catch (IOException ee) { System.out.println(ee.toString()); } } dataThesias data3 = new dataThesias(); data3.lociColsLength = lociCols.length; data3.bPrintLDMatrix = bPrintLDMatrix; data3.bPrintR2 = bPrintR2; data3.bMissingGenotyp = bMissingGenotyp; data3.kindOfPhenotype = kindOfPhenotype; data3.lpv = lpv; data3.idtime= idtime; data3.lwv = idoffset; data3.covarColsLength = covarCols.length; data3.col = col; data3.initLoci(lociCols); data3.initCovar(covarCols); t.SetThesias( "datafile.txt", lociCols.length, lociCols, (bPrintLDMatrix) ? 1 : 0, (bMissingGenotyp) ? 1 : 0, (bPrintR2) ? 1 :0, kindOfPhenotype, lpv, idtime, (bOffset) ? 1 :0, idoffset, covarCols.length, covarCols, col, (bLink) ? 1 :0, numx); setCursor(hourglassCursor); t.run(); System.gc(); StringBuffer sbuf = new StringBuffer(); StringBuffer sbufTest = new StringBuffer(); String content; try { FileReader s; s = new FileReader("result.htm"); BufferedReader b = new BufferedReader(s); content = b.readLine(); while( content != null ) { sbuf.append(content); content = b.readLine(); } b.close(); s.close(); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } finally {} try { FileReader s; s = new FileReader("result.txt"); BufferedReader b = new BufferedReader(s); content = b.readLine(); while( content != null ) { sbufTest.append(content+"\r\n"); content = b.readLine(); } b.close(); s.close(); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } finally {} CustomDialog customDialog ; Object coaverCols2[] ; coaverCols2 = new Object[covarCols.length]; if ( covarCols.length > 0) { for( int k =0; k < covarCols.length ; k++ ) coaverCols2[k] = (new Integer(covarCols[k])).toString(); } if(bLink){ System.out.println(covarCols.length); } customDialog = new CustomDialog(data3,this,frame, "geisel",sbuf,new String(),coaverCols2,sbufTest); if( !bEstimateHaplotypic ) customDialog = new CustomDialog(data3,this,frame, "geisel",sbuf,new String(),coaverCols2,sbufTest); else customDialog = new CustomDialog(data3,this,frame, "geisel",sbuf,paraFile,coaverCols2,sbufTest); setCursor(normalCursor); customDialog.setVisible(true); paramTable.importData(); } if (e.getActionCommand().compareTo("Copy")==0) { StringBuffer sbf=new StringBuffer(); int numcols=table.getSelectedColumnCount(); int numrows=table.getSelectedRowCount(); int[] rowsselected=table.getSelectedRows(); int[] colsselected=table.getSelectedColumns(); if (!((numrows-1==rowsselected[rowsselected.length-1]-rowsselected[0] && numrows==rowsselected.length) && (numcols-1==colsselected[colsselected.length-1]-colsselected[0] && numcols==colsselected.length))) { JOptionPane.showMessageDialog(null, "Invalid Copy Selection", "Invalid Copy Selection", JOptionPane.ERROR_MESSAGE); return; } for (int i=0;i. */ import java.awt.*; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import javax.swing.JDialog; import java.io.*; class Hipothesis extends JPanel implements ActionListener { String left,right; String title; SimpleChooser sch[]; JTable tabel; AbstractTableModel dataModel; int nrRows; JButton addButton,removeButton; int visibleHypothesis; int tip; public Hipothesis(int maxRows,String firstEff,String secondEff,String mainTitle,String sButton,Object []left){ super(new GridBagLayout()); this.tip = 1; nrRows = maxRows; dataModel = new SimpleDataModel(left); makeAndDisplay(firstEff,secondEff,mainTitle,sButton,left,left); } public Hipothesis(int maxRows,String firstEff,String secondEff,String mainTitle,String sButton,int tip,Object []left,Object []right){ super(new GridBagLayout()); this.tip = 2; nrRows = maxRows; Object n[] = new Object[right.length]; for( int i = 0; i < right.length ; i++ ) { n[i] = new String( (i+1) + " " + "(V" + right[i].toString() + ")" ); } dataModel = new SimpleDataModel2D(left,n); makeAndDisplay(firstEff,secondEff,mainTitle,sButton,left,n); } private void makeAndDisplay(String firstEff,String secondEff,String mainTitle,String sButton,Object []left,Object []right) { visibleHypothesis = 0; GridBagConstraints cGridBag = new GridBagConstraints(); cGridBag.gridx = 0; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 2; cGridBag.weightx = 0.2; cGridBag.weighty = 1; cGridBag.fill = GridBagConstraints.BOTH; tabel = new JTable(dataModel); JTableHeader tHeader; tHeader = tabel.getTableHeader(); Color saumon = new Color( 255, 204, 153 ); tHeader.setBackground(saumon); JScrollPane scrollPane = new JScrollPane(tabel); add(scrollPane,cGridBag); cGridBag.gridx = 1; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 2; cGridBag.weightx = 0.3; cGridBag.weighty = 1; JPanel panel = new JPanel(new GridLayout(nrRows,1) ); sch = new SimpleChooser[nrRows]; for( int i =0 ; i < nrRows ; i++){ if( tip == 2) sch[i] = new SimpleChooser(firstEff,secondEff,mainTitle + " " +(i+1),left,right); else sch[i] = new SimpleChooser(firstEff,secondEff,mainTitle + " " +(i+1),left); sch[i].setVisible(false); panel.add(sch[i]); } JScrollPane scrollPane2 = new JScrollPane ( panel) ; add(scrollPane2,cGridBag); JPanel buttonsPan = new JPanel(new GridLayout(2,0) ); addButton = new JButton("Add " + sButton ); addButton.addActionListener(this); removeButton = new JButton("Remove " + sButton); removeButton.addActionListener(this); buttonsPan.add(addButton); buttonsPan.add(removeButton); Color chair = new Color( 249, 230, 196 ); tabel.setBackground(chair); panel.setBackground(chair); addButton.setBackground(saumon); removeButton.setBackground(saumon); scrollPane2.setBackground(saumon); scrollPane.setBackground(saumon); buttonsPan.setBackground(chair); buttonsPan.setForeground(chair); cGridBag.gridx = 3; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 1; cGridBag.weightx = 0; cGridBag.weighty = 0; cGridBag.fill = GridBagConstraints.NONE; add(buttonsPan,cGridBag); } public void actionPerformed(ActionEvent e) { if ( addButton == (JButton)e.getSource() ) { if ( visibleHypothesis == nrRows ) return ; sch[visibleHypothesis].setVisible(true); visibleHypothesis++; } else if ( removeButton == (JButton)e.getSource() ) { if ( visibleHypothesis-1 < 0 ) return ; visibleHypothesis--; sch[visibleHypothesis].setVisible(false); } } public String saveData() { StringBuffer buf = new StringBuffer(); if (visibleHypothesis == 0) { buf.append("n\r\n"); } else { buf.append("y\r\n"); buf.append(visibleHypothesis + "\r\n"); for( int i = 0 ; i < visibleHypothesis ; i++ ) { buf.append(sch[i].getItems() + "\r\n") ; } } return new String(buf); } }; thesias-3.1.1/java/Homogeneity.java000066400000000000000000000173521360777755100172610ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.*; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import javax.swing.JDialog; import java.io.*; class Homogeneity extends JPanel implements ActionListener { String left,right; String title; HomogenitySimpleChooser sch[]; JTable tabel; SimpleDataModel dataModel; int nrRows; JButton addButton,removeButton; int visibleHypothesis; private int tip; public Homogeneity(int maxRows,String firstEff,String secondEff,String mainTitle,String sButton,Object []left){ super(new GridBagLayout()); tip = 1; nrRows = maxRows; dataModel = new SimpleDataModel(left); makeAndDisplay(firstEff,secondEff,mainTitle,sButton,left); } private void makeAndDisplay(String firstEff,String secondEff,String mainTitle,String sButton,Object []left) { visibleHypothesis = 0; GridBagConstraints cGridBag = new GridBagConstraints(); cGridBag.gridx = 0; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 2; cGridBag.weightx = 0.2; cGridBag.weighty = 1; cGridBag.fill = GridBagConstraints.BOTH; tabel = new JTable(dataModel); JTableHeader tHeader; tHeader = tabel.getTableHeader(); Color saumon = new Color( 255, 204, 153 ); tHeader.setBackground(saumon); JScrollPane scrollPane = new JScrollPane(tabel); add(scrollPane,cGridBag); cGridBag.gridx = 1; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 2; cGridBag.weightx = 0.3; cGridBag.weighty = 1; JPanel panel = new JPanel(new GridLayout(nrRows,1) ); sch = new HomogenitySimpleChooser[nrRows]; for( int i =0 ; i < nrRows ; i++){ sch[i] = new HomogenitySimpleChooser(firstEff,secondEff,mainTitle + " " +(i+1),left); sch[i].setVisible(false); panel.add(sch[i]); } JScrollPane scrollPane2 = new JScrollPane ( panel) ; add(scrollPane2,cGridBag); JPanel buttonsPan = new JPanel(new GridLayout(2,0) ); addButton = new JButton("Add " + sButton ); addButton.addActionListener(this); removeButton = new JButton("Remove " + sButton); removeButton.addActionListener(this); buttonsPan.add(addButton); buttonsPan.add(removeButton); Color chair = new Color( 249, 230, 196 ); tabel.setBackground(chair); panel.setBackground(chair); addButton.setBackground(saumon); removeButton.setBackground(saumon); scrollPane2.setBackground(saumon); scrollPane.setBackground(saumon); buttonsPan.setBackground(chair); buttonsPan.setForeground(chair); cGridBag.gridx = 3; cGridBag.gridy = 0; cGridBag.gridwidth = 1; cGridBag.gridheight = 1; cGridBag.weightx = 0; cGridBag.weighty = 0; cGridBag.fill = GridBagConstraints.NONE; add(buttonsPan,cGridBag); } public void actionPerformed(ActionEvent e) { if ( addButton == (JButton)e.getSource() ) { if ( visibleHypothesis == nrRows ) return ; sch[visibleHypothesis].setVisible(true); visibleHypothesis++; } else if ( removeButton == (JButton)e.getSource() ) { if ( visibleHypothesis-1 < 0 ) return ; visibleHypothesis--; sch[visibleHypothesis].setVisible(false); } } public String saveData() { StringBuffer buf = new StringBuffer(); if(visibleHypothesis == 0) { buf.append("n" + "\r\n"); } else { buf.append("y" + "\r\n" + visibleHypothesis + "\r\n"); for( int k = 0 ; k < visibleHypothesis ; k++ ){ buf.append( sch[k].getNomber() + "\r\n"); } for( int k = 0 ; k < visibleHypothesis ; k++ ){ buf.append( sch[k].getPerechi() ); } } return new String(buf); } }; class HomogenitySimpleChooser extends JPanel implements ActionListener { JLabel lLeft,lRight,lTitle; JComboBox cLeft,cRight; VerySimpleChooser vsch[]; static int maxPairs = 8; JButton addPair,removePair; int visiblePair = 0; public HomogenitySimpleChooser(String l,String r,String t,Object []data){ GridBagLayout gridBagLayout = new GridBagLayout(); GridBagConstraints cGridBag = new GridBagConstraints(); this.setLayout(gridBagLayout); Color chair = new Color( 249, 230, 196 ); Color saumon = new Color( 255, 204, 153 ); this.setBackground(chair); visiblePair = 2; addPair = new JButton("Add"); removePair = new JButton("Remove"); addPair.addActionListener(this); removePair.addActionListener(this); JPanel butP = new JPanel(new GridLayout(1,2)); JPanel vschP = new JPanel( new GridLayout(4,2)); butP.add(addPair); butP.add(removePair); butP.setBackground(chair); vschP.setBackground(chair); addPair.setBackground(saumon); removePair.setBackground(saumon); vsch = new VerySimpleChooser[maxPairs]; setBorder(BorderFactory.createTitledBorder(t) ); vsch[0] = new VerySimpleChooser(1,l,r,t,data,data); vsch[1] = new VerySimpleChooser(2,l,r,t,data,data); vschP.add(vsch[0]); vschP.add(vsch[1]); for(int i = 2 ; i < maxPairs; i++){ vsch[i] = new VerySimpleChooser(i+1,l,r,t,data,data); vsch[i].setVisible(false); vschP.add(vsch[i]); } cGridBag.gridx = 0; cGridBag.gridy = 0; cGridBag.gridwidth = 2; cGridBag.gridheight = 1; cGridBag.fill = GridBagConstraints.HORIZONTAL; cGridBag.weightx = 1; cGridBag.weighty = 0.0; add(butP,cGridBag); cGridBag.gridx = 0; cGridBag.gridy = 1; cGridBag.gridwidth = 2; cGridBag.gridheight = 4; cGridBag.weightx = 1; cGridBag.weighty = 0.0; add(vschP,cGridBag); } public void actionPerformed(ActionEvent e) { if ( addPair == (JButton)e.getSource() ) { if ( visiblePair == maxPairs ) return ; vsch[visiblePair].setVisible(true); visiblePair++; } else if ( removePair == (JButton)e.getSource() ) { if ( visiblePair-1 < 2 ) return ; visiblePair--; vsch[visiblePair].setVisible(false); } } public String getNomber(){ return (new Integer(visiblePair)).toString(); } public String getPerechi() { StringBuffer buf = new StringBuffer(); for(int i =0 ; i < visiblePair ; i++){ buf.append(vsch[i].getData() + "\r\n"); } return new String(buf); } }; class VerySimpleChooser extends JPanel { JLabel lLeft,lRight,lTitle; JComboBox cLeft,cRight; public VerySimpleChooser(int i,String l,String r,String t,Object []dataLeft,Object []dataRight){ super ( new GridLayout(1,2) ); setBorder(BorderFactory.createTitledBorder("Pair " + i) ); cLeft = new JComboBox(dataLeft); cRight = new JComboBox(dataRight); add(cLeft); add(cRight); Color chair = new Color( 249, 230, 196 ); super.setBackground(chair); cLeft.setBackground(Color.white); cRight.setBackground(Color.white); } public String getData() { return new String( ((Integer)cLeft.getSelectedItem()).toString() + " " + ((Integer)cRight.getSelectedItem()).toString() ); } } thesias-3.1.1/java/OptionDialog.java000066400000000000000000000256501360777755100173620ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import javax.swing.JOptionPane; import javax.swing.JDialog; import javax.swing.JButton; import javax.swing.JRadioButton; import javax.swing.ButtonGroup; import javax.swing.JLabel; import javax.swing.ImageIcon; import javax.swing.BoxLayout; import javax.swing.Box; import javax.swing.BorderFactory; import javax.swing.border.Border; import javax.swing.JTabbedPane; import javax.swing.JPanel; import javax.swing.JFrame; import java.beans.*; import java.awt.*; import java.awt.event.*; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import java.io.*; import javax.swing.JComboBox; class OptionDialog extends JFrame implements ActionListener, PropertyChangeListener { private String magicWord; private JOptionPane optionPane; private String sbtnApply = "Run"; private String sbtnCancel = "Cancel"; private JButton jbtnApply,jbtnCancel; private String sHypothesis = "Hypothesis"; private String sHypothesisTip = "Do you want to test specific hypothesis on haplotypic effects"; private String sHomogeneity = "Homogeneity"; private String sHomogeneityTip = "Do you want to test for the homogeneity of some allelic effects"; private String sNonAdditivity = "Non-additivity"; private String sNonAdditivityTip ="Do you want to test the non-additivity of some haplotypic effects"; private String sEnvironmentInteractions = "Covariate interactions"; private String sEnvironmentInteractionsTip = "Do you want to test haplotype * environment interactions "; private Frame parent; Hipothesis hypothesis; private Hipothesis aditivity; Hipothesis interaction; Homogeneity homogeneity; GraficT grafic; dataThesias datta; private Cursor hourglassCursor; private Cursor normalCursor; public OptionDialog(dataThesias datta,GraficT art,Frame aFrame,String sParam,Object []covar) { super(); Color chair = new Color( 249, 230, 196 ); Color saumon = new Color( 255, 204, 153 ); super.setBackground(chair); hourglassCursor = new Cursor(Cursor.WAIT_CURSOR); normalCursor = new Cursor(Cursor.DEFAULT_CURSOR); parent = aFrame; this.datta = datta; grafic = art; int nkat = 1; if ( grafic.kindOfPhenotype == 5 ) { String content_prec = null; String content = null; try { FileReader s = new FileReader("para.txt"); BufferedReader b = new BufferedReader(s); while( (content = b.readLine())!= null ){content_prec = content;} b.close(); s.close(); } catch ( IOException eIO ){System.out.println(eIO.toString());} nkat = Integer.parseInt(content_prec); System.out.println("----------------------------"); System.out.println("nkat = "+nkat); System.out.println("sParam : " +sParam); } setBounds(10,10,100,30); StringTokenizer sTok = new StringTokenizer(sParam); Object dataTemp[] = new Object[1000]; Object dataBun[]; if ( sTok.hasMoreTokens() ) sTok.nextToken(); int i = 0, k =0; String a,b; while( sTok.hasMoreTokens() ) { i++; sTok.nextToken(); sTok.nextToken(); a = sTok.nextToken(); b = sTok.nextToken(); if( Double.parseDouble(a) > 0.5 || Double.parseDouble(b) > 0.5){ if ( grafic.kindOfPhenotype == 5 ){ dataTemp[i-1] = new Integer(i-1); } else { dataTemp[i-1] = new Integer(i); } k++; } } dataBun = new Object[k*nkat]; k =0 ; for( int j =0 ; j < i; j++){ if( dataTemp[j] != null){ dataBun[k++] = dataTemp[j]; } } if (nkat>1) { for( int j =k ; j < k*nkat; j++) { dataBun[j] = (Object)(new Integer(((Integer)dataBun[j-1]).intValue()+ 1)); } } dataTemp = null; hypothesis = new Hipothesis(15,"First effect","Second effect","Hypothesis","hypothesis",dataBun); aditivity = new Hipothesis(5,"First haplotype","Second haplotype","Deviation","deviation",dataBun); interaction = new Hipothesis(5,"Haplotype","Covariate","Interaction","interaction",2,dataBun,covar); homogeneity = new Homogeneity(5,"Haplotype","1231","Hypothesis","hypothesis",dataBun); Border padding = BorderFactory.createEmptyBorder(20,20,5,20); jbtnApply = new JButton(sbtnApply); jbtnCancel = new JButton(sbtnCancel); jbtnApply.setActionCommand(sbtnApply); jbtnApply.addActionListener(this); jbtnCancel.setActionCommand(sbtnCancel); jbtnCancel.addActionListener(this); JPanel butonsPanel = new JPanel(); butonsPanel.add(jbtnApply,BorderLayout.CENTER); butonsPanel.add(jbtnCancel,BorderLayout.CENTER); JTabbedPane tabbedPane = new JTabbedPane(); tabbedPane.addTab(sHypothesis, null, hypothesis, sHypothesisTip); tabbedPane.addTab( sHomogeneity, null, homogeneity,sHomogeneityTip); butonsPanel.setBackground(chair); butonsPanel.setForeground(chair); tabbedPane.setBackground(chair); jbtnApply.setBackground(saumon); jbtnCancel.setBackground(saumon); hypothesis.setBackground(chair); hypothesis.setForeground(chair); aditivity.setBackground(chair); interaction.setBackground(chair); homogeneity.setBackground(chair); tabbedPane.addTab(sNonAdditivity, null, aditivity, sNonAdditivityTip); if ( covar.length != 0) { tabbedPane.addTab(sEnvironmentInteractions, null, interaction, sEnvironmentInteractionsTip); } getContentPane().add(tabbedPane,BorderLayout.CENTER); getContentPane().add(butonsPanel,BorderLayout.SOUTH); this.setSize(600,500); this.setBackground(saumon); } public void actionPerformed(ActionEvent e) { if ( sbtnCancel.equals(e.getActionCommand()) ) { setVisible(false); } else if ( sbtnApply.equals(e.getActionCommand()) ) { saveDataToFile("paramData.thi"); setCursor(hourglassCursor); grafic.t.run(); StringBuffer sbuf = new StringBuffer(); StringBuffer sBufText = new StringBuffer(); String content; try { FileReader s; s = new FileReader("result.htm"); BufferedReader b = new BufferedReader(s); content = b.readLine(); while( content != null ) { sbuf.append(content); content = b.readLine(); } b.close(); s.close(); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } finally {} try { FileReader s; s = new FileReader("result.txt"); BufferedReader b = new BufferedReader(s); content = b.readLine(); while( content != null ) { sBufText.append(content+"\r\n"); content = b.readLine(); } b.close(); s.close(); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } finally {} CustomDialog customDialog ; Object coaverCols2[] ; coaverCols2 = new Object[0]; customDialog = new CustomDialog(datta,grafic,parent, "geisel",sbuf,new String(),coaverCols2,sBufText); setCursor(normalCursor); customDialog.setVisible(true); } } public void saveDataToFile(String fileName) { String CR = "\r\n"; StringBuffer sBuf = new StringBuffer(); sBuf.append("y" + CR); sBuf.append( hypothesis.saveData() ); sBuf.append (homogeneity.saveData()); sBuf.append( aditivity.saveData() ); sBuf.append( interaction.saveData() ); System.out.println(sBuf); FileWriter fwData; try { fwData = new FileWriter(fileName); fwData.write(sBuf.toString(), 0 , sBuf.toString().length()); fwData.close(); } catch (IOException e) { System.out.println(e.toString()); } } public void propertyChange(PropertyChangeEvent e) { } public void clearAndHide() { setVisible(false); } } class SimpleDataModel extends AbstractTableModel { private String[] columnNames = {"Possible Effect"}; private Object[][] data= {{new Integer(2)}}; public SimpleDataModel(){ } public SimpleDataModel(Object []left){ data = new Object[left.length][1]; for( int i =0 ; i < left.length; i++) data[i][0] = "Haplotype " + ((Integer) left[i] ).toString(); } public int getColumnCount() { return columnNames.length; } public int getRowCount() { return data.length; } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { return data[row][col]; } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { return false; } public void setValueAt(Object value, int row, int col) { data[row][col] = value; fireTableCellUpdated(row, col); } } class SimpleDataModel2D extends AbstractTableModel { private String[] columnNames = {"Possible Effect","Possible covariate"}; private Object[][] data = { {new Integer(1),"V5"}, {new Integer(2),"V6"}, {new Integer(3),""}, {new Integer(4),""}, }; public SimpleDataModel2D(){ } public SimpleDataModel2D(Object []left,Object []right){ int max; if ( left.length > right.length) max = left.length; else max = right.length; data = new Object[max][2]; for( int i =0 ; i< left.length; i++) data[i][0] = "Haplotype " + ((Integer) left[i] ).toString(); //left[i]; for( int i =0 ; i< right.length; i++) data[i][1] = right[i]; } public int getColumnCount() { return columnNames.length; } public int getRowCount() { return data.length; } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { return data[row][col]; } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { return false; } public void setValueAt(Object value, int row, int col) { data[row][col] = value; fireTableCellUpdated(row, col); } } thesias-3.1.1/java/ParamTable.java000066400000000000000000000135371360777755100170030ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.*; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JLabel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import javax.swing.JDialog; import java.io.*; import javax.swing.JMenuBar; import javax.swing.JMenu; import javax.swing.JMenuItem; import java.awt.Dimension; class ParamTable extends JPanel{ public JTable table; public ParamTableModel tableModel; int nMax; private JScrollPane paramScrollPane; public ParamTable() { super(new GridLayout(1,1)); tableModel = new ParamTableModel(1,4); table = new JTable(tableModel); table.setPreferredScrollableViewportSize(new Dimension(157, 97)); table.setDragEnabled(true); JTableHeader tHeader; tHeader = table.getTableHeader(); Color saumon = new Color( 255, 204, 153 ); tHeader.setBackground(saumon); Dimension dim = new Dimension( 157, 97); paramScrollPane = new JScrollPane(table); paramScrollPane.setSize(dim); nMax = 0; add(paramScrollPane); setBorder(BorderFactory.createEmptyBorder(13,0,0,0)); } public String serializeData(){ String fileName = "para.txt"; FileWriter fwData; StringBuffer sBuf = new StringBuffer(); try { int imax = 4; System.out.println(fileName); fwData = new FileWriter(fileName); sBuf.append(nMax + "\r\n"); for( int i = 0; i < nMax ; i++) { sBuf.append(tableModel.data[i][0] + " " + tableModel.data[i][1]); if( ((Boolean)tableModel.data[i][2]).booleanValue() ) sBuf.append(" 1"); else sBuf.append(" 0"); if( ((Boolean)tableModel.data[i][3]).booleanValue() ) sBuf.append(" 1"); else sBuf.append(" 0"); sBuf.append("\r\n"); } fwData.write(sBuf.toString(), 0 , sBuf.toString().length()); fwData.close(); } catch (IOException ee) { System.out.println(ee.toString()); } return sBuf.toString(); } public void importData(){ nMax = 0; String fileName = "para.txt"; try { FileReader s; int i = 0; s = new FileReader(fileName); BufferedReader b = new BufferedReader(s); String content; content = b.readLine(); int nbLine = Integer.parseInt(content); tableModel = null; tableModel = new ParamTableModel(nbLine,4); table.setModel(tableModel); double d; for( int k = 0 ; k < nMax ;k ++){ tableModel.data[k][0] = new String(); tableModel.data[k][1] = new String(); tableModel.data[k][2] = new Boolean(false); tableModel.data[k][3] = new Boolean(false); } while( content != null ) { content = b.readLine(); if ( content == null) break; StringTokenizer st = new StringTokenizer(content); if (st.countTokens() < 2) break; tableModel.data[i][0] = st.nextToken(); tableModel.data[i][1] = st.nextToken(); d = Double.parseDouble(st.nextToken() ); if ( d < 0.5 ) tableModel.data[i][2] = new Boolean(false); else tableModel.data[i][2] = new Boolean(true); d = Double.parseDouble(st.nextToken() ); if ( d < 0.5 ) tableModel.data[i][3] = new Boolean(false); else tableModel.data[i][3] = new Boolean(true); i++; } nMax = i; b.close(); s.close(); } catch ( IOException eIO ) { System.out.println(eIO.toString()); } } public void setParamTableEnabled(boolean state) { paramScrollPane.setEnabled(state); table.setEnabled(state); } public void reinitParamTable(){ tableModel = null; tableModel = new ParamTableModel(1,4); table.setModel(tableModel); } } class ParamTableModel extends AbstractTableModel { int rows, cols; private String[] columnNames = {"N","Freq","Effect"}; public Object[][] data; public ParamTableModel( int row, int col){ rows = row; cols = col; int i, j ; data = new Object[rows][cols]; for( i =0 ; i < rows ; i++){ for (j = 0 ; j < cols -2 ; j++ ) { data[i][j] = new String(); } for( ; j < cols ; j++) data[i][j] = new Boolean(false); } } public void resetData() { for( int i =0 ; i < rows ; i++) for (int j = 0 ; j < cols ; j++ ) { data[i][j] = new String(); } } public void initData(Object d[][], int a, int b) { for( int i = 0 ; i < a ; i++) for (int j = 0 ; j < b ; j++ ) { data[i][j] = (String)d[i][j]; } } public int getColumnCount() { return columnNames.length; } public int getRowCount() { return data.length; } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { if( data == null) return null; return data[row][col]; } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { if( col == 0 || col == 1 ) return false; return true; } public void setValueAt(Object value, int row, int col) { data[row][col] = value; fireTableCellUpdated(row, col); } }; thesias-3.1.1/java/PrintText.java000066400000000000000000000045211360777755100167250ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.*; import java.awt.font.*; import java.awt.geom.*; import java.awt.print.*; import java.text.*; public class PrintText implements Printable { private AttributedString mStyledText; private String mText; private String sPrint; public PrintText(String s) { sPrint = s; mStyledText = new AttributedString(s); } public void runPrint() { PrinterJob printerJob = PrinterJob.getPrinterJob(); Book book = new Book(); book.append(new PrintText(sPrint), new PageFormat()); printerJob.setPageable(book); boolean doPrint = printerJob.printDialog(); if (doPrint) { try { printerJob.print(); } catch (PrinterException exception) { System.err.println("Printing error: " + exception); } } } public int print(Graphics g, PageFormat format, int pageIndex) { Graphics2D g2d = (Graphics2D) g; g2d.translate(format.getImageableX(), format.getImageableY()); g2d.setPaint(Color.black); Point2D.Float pen = new Point2D.Float(); AttributedCharacterIterator charIterator = mStyledText.getIterator(); LineBreakMeasurer measurer = new LineBreakMeasurer(charIterator, g2d.getFontRenderContext()); float wrappingWidth = (float) format.getImageableWidth(); while (measurer.getPosition() < charIterator.getEndIndex()) { TextLayout layout = measurer.nextLayout(wrappingWidth); pen.y += layout.getAscent(); float dx = layout.isLeftToRight()? 0 : (wrappingWidth - layout.getAdvance()); layout.draw(g2d, pen.x + dx, pen.y); pen.y += layout.getDescent() + layout.getLeading(); } return Printable.PAGE_EXISTS; } } thesias-3.1.1/java/SimpleChooser.java000066400000000000000000000055451360777755100175470ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.*; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.table.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import java.awt.datatransfer.*; import java.util.*; import javax.swing.JDialog; import java.io.*; class SimpleChooser extends JPanel implements ActionListener { JLabel lLeft,lRight,lTitle; JComboBox cLeft,cRight; public SimpleChooser(String l,String r,String t,Object []dataLeft,Object []dataRight){ super ( new GridLayout(2,2) ); lLeft = new JLabel(l); lRight = new JLabel(r); cLeft = new JComboBox(dataLeft); cRight = new JComboBox(dataRight); setBorder(BorderFactory.createTitledBorder(t) ); add(lLeft); add(lRight); add(cLeft); add(cRight); cLeft.addActionListener(this); Color chair = new Color( 249, 230, 196 ); Color saumon = new Color( 255, 204, 153 ); lLeft.setBackground(chair); lRight.setBackground(chair); super.setBackground(chair); cLeft.setBackground(Color.white); cRight.setBackground(Color.white); } public SimpleChooser(String l,String r,String t,Object []data){ super ( new GridLayout(2,2) ); lLeft = new JLabel(l); lRight = new JLabel(r); cLeft = new JComboBox(data); cRight = new JComboBox(data); setBorder(BorderFactory.createTitledBorder(t) ); add(lLeft); add(lRight); add(cLeft); add(cRight); cLeft.addActionListener(this); Color chair = new Color( 249, 230, 196 ); Color saumon = new Color( 255, 204, 153 ); cLeft.setBackground(Color.white); cRight.setBackground(Color.white); super.setBackground(chair); } public String getItems() { String s = (cRight.getSelectedItem()).toString(); String t = (cRight.getSelectedItem()).toString(); if( s.indexOf("(") != -1 ){ t = s.substring(0,s.indexOf("(") ); } return new String( ((Integer)cLeft.getSelectedItem()).toString() + " " + t ); } public void actionPerformed(ActionEvent e) { } }; thesias-3.1.1/java/TextPrint.java000066400000000000000000000031311360777755100167210ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Rectangle; import java.awt.Shape; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import javax.swing.JEditorPane; import javax.swing.text.Document; import javax.swing.text.PlainDocument; import javax.swing.text.View; import javax.swing.text.html.HTMLDocument; import java.io.*; import java.awt.Font; public class TextPrint{ public void runPrint(String content ) { DocumentRenderer dc = new DocumentRenderer(); JEditorPane jeditorPane= new JEditorPane("text/plain",content); Font fnt = jeditorPane.getFont(); Font fntNou = fnt.deriveFont((float)8.0); System.out.println( "size" + fnt.getSize2D() ); jeditorPane.setFont(fntNou); dc.print(jeditorPane); } } thesias-3.1.1/java/thesiaslib.java000066400000000000000000000114661360777755100171210ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trégouët, Valérie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ public class thesiaslib { private String FileName; private int Nbloci; private int []Idloci; private int Ldmatrix; private int Msdata; private int R2; private int Chxt; private int Num0; private int Idtime; private int Idoffset; private int Ajust; private int [] Numajust; private int Maxvarfic; private int Offset; private int Xlnk; private int Numsx; public thesiaslib() { FileName = null; Nbloci = 0; Idloci = null; Ldmatrix = 0; Msdata = 0; R2 = 0; Chxt = 0; Num0 = 0; Idtime = 0; Offset = 0; Idoffset = 0; Ajust = 0; Numajust = null; Maxvarfic = 0; Xlnk = 0; Numsx = 0; } public thesiaslib(String sfilename, int nbloci, int [] idloci, int ldmatrix, int msdata, int pR2, int chxt, int num0, int idtime, int idoffset, int ajust, int [] numajust, int maxvarfic ) { FileName = sfilename; Nbloci = nbloci; Idloci = idloci; Ldmatrix = ldmatrix; Msdata = msdata; R2 = pR2; Chxt = chxt; Num0 = num0; Idtime = idtime; Idoffset = idoffset; Ajust = ajust; Numajust = numajust; Maxvarfic = maxvarfic; } public void SetThesias(String sfilename, int nbloci, int [] idloci, int ldmatrix, int msdata, int pR2, int chxt, int num0, int idtime, int offset, int idoffset, int ajust, int [] numajust, int maxvarfic, int xlnk, int numsx) { FileName = sfilename; Nbloci = nbloci; Idloci = idloci; Ldmatrix = ldmatrix; Msdata = msdata; R2 = pR2; Chxt = chxt; Num0 = num0; Idtime = idtime; Offset = offset; Idoffset = idoffset; Ajust = ajust; Numajust = numajust; Maxvarfic = maxvarfic; Xlnk = xlnk; Numsx = numsx; } public void SetThesias(String sfilename, int nbloci, int [] idloci, int ldmatrix, int msdata, int pR2, int chxt, int num0, int idtime, int idoffset, int ajust, int [] numajust, int maxvarfic) { FileName = sfilename; Nbloci = nbloci; Idloci = idloci; Ldmatrix = ldmatrix; Msdata = msdata; R2 = pR2; Chxt = chxt; Num0 = num0; Idtime = idtime; Idoffset = idoffset; Ajust = ajust; Numajust = numajust; Maxvarfic = maxvarfic; } public void run() { System.out.println(" FileName : " + FileName); System.out.println(" Maxvarfic: " + Maxvarfic); System.out.println(" Nbloci : " + Nbloci); for ( int j = 0; j < Nbloci; j++ ) { System.out.println(" Idloci ["+ j +"] : " + Idloci[j]); } System.out.println(" Ldmatrix : " + Ldmatrix); System.out.println(" Msdata : " + Msdata); System.out.println(" R2 : " + R2); System.out.println(" Chxt : " + Chxt); System.out.println(" Num0 : " + Num0); System.out.println(" Idtime : " + Idtime); System.out.println(" Offset : " + Offset); System.out.println(" Idoffset : " + Idoffset); System.out.println(" Ajust : " + Ajust); for ( int j = 0; j < Ajust; j++ ) { System.out.println(" Numajust ["+ j +"] : " + Numajust[j]); } System.out.println(" Xlnk : " + Xlnk); System.out.println(" Numsx : " + Numsx); int i = -222; try { i = thesiasRun( FileName, Maxvarfic, Nbloci, Idloci, Ldmatrix, Msdata, R2, Chxt, Num0, Idtime, Offset, Idoffset, Ajust, Numajust, Xlnk, Numsx); } catch(Exception e) { System.out.println(e.toString()); } } public native int thesiasRun(String sFileName, int maxvarfic, int nbloci, int [] idloci, int ldmatrix, int msdata, int R2, int chxt, int num0, int idtime, int offset, int idoffset, int ajust, int [] numajust, int xlnk, int numsx); static {System.loadLibrary("thesiaslib");} } thesias-3.1.1/misc/000077500000000000000000000000001360777755100141315ustar00rootroot00000000000000thesias-3.1.1/misc/LogoThesias.png000066400000000000000000000774051360777755100170750ustar00rootroot00000000000000PNG  IHDR`6sBIT|d IDATxܼy%yUy3s*梠(A*AiZـ(ˡ<3(,9*OiJ+3+;3'73oUY@_~+8c)y:T_vL(U/LPewqñn~c$&o{;+E>q䛾^E:%+,KʲX+)TJ Wo%]P/ ^xW|*DH%+R<LgsuMӡ,?O5QyStg?[?#Sc44(˜ v? 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This program is based on the maximum likelihood model described in Tregouet et al. 2002 (Hum Mol Genet 2002,11: 2015-2023) and is linked to the SEM algorithm (Tregouet et al. Ann Hum Genet 2004,68: 165-177). THESIAS allows one to simultaneous estimate haplotype frequencies and their associate effects on the phenotype of interest. In this new THESIAS release, quantitative, qualitative (logistic and matched-pair analysis), categorical and survival outcomes can be studied. X-linked haplotype analysis is also feasible. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can also be investigated. .SH AUTHOR THESIAS was written by David-Alexandre Trégouët. thesias-3.1.1/src/000077500000000000000000000000001360777755100137655ustar00rootroot00000000000000thesias-3.1.1/src/chdtr.c000066400000000000000000000066251360777755100152460ustar00rootroot00000000000000/* chdtr.c * * Chi-square distribution * * * * SYNOPSIS: * * double df, x, y, chdtr(); * * y = chdtr( df, x ); * * * * DESCRIPTION: * * Returns the area under the left hand tail (from 0 to x) * of the Chi square probability density function with * v degrees of freedom. * * * inf. * - * 1 | | v/2-1 -t/2 * P( x | v ) = ----------- | t e dt * v/2 - | | * 2 | (v/2) - * x * * where x is the Chi-square variable. * * The incomplete gamma integral is used, according to the * formula * * y = chdtr( v, x ) = igam( v/2.0, x/2.0 ). * * * The arguments must both be positive. * * * * ACCURACY: * * See igam(). * * ERROR MESSAGES: * * message condition value returned * chdtr domain x < 0 or v < 1 0.0 */ /* chdtrc() * * Complemented Chi-square distribution * * * * SYNOPSIS: * * double v, x, y, chdtrc(); * * y = chdtrc( v, x ); * * * * DESCRIPTION: * * Returns the area under the right hand tail (from x to * infinity) of the Chi square probability density function * with v degrees of freedom: * * * inf. * - * 1 | | v/2-1 -t/2 * P( x | v ) = ----------- | t e dt * v/2 - | | * 2 | (v/2) - * x * * where x is the Chi-square variable. * * The incomplete gamma integral is used, according to the * formula * * y = chdtr( v, x ) = igamc( v/2.0, x/2.0 ). * * * The arguments must both be positive. * * * * ACCURACY: * * See igamc(). * * ERROR MESSAGES: * * message condition value returned * chdtrc domain x < 0 or v < 1 0.0 */ /* chdtri() * * Inverse of complemented Chi-square distribution * * * * SYNOPSIS: * * double df, x, y, chdtri(); * * x = chdtri( df, y ); * * * * * DESCRIPTION: * * Finds the Chi-square argument x such that the integral * from x to infinity of the Chi-square density is equal * to the given cumulative probability y. * * This is accomplished using the inverse gamma integral * function and the relation * * x/2 = igami( df/2, y ); * * * * * ACCURACY: * * See igami.c. * * ERROR MESSAGES: * * message condition value returned * chdtri domain y < 0 or y > 1 0.0 * v < 1 * */ /* chdtr() */ /* Cephes Math Library Release 2.8: June, 2000 Copyright 1984, 1987, 2000 by Stephen L. Moshier */ #include "mconf.h" #ifdef ANSIPROT extern double igamc ( double, double ); extern double igam ( double, double ); extern double igami ( double, double ); #else double igamc(), igam(), igami(); #endif double chdtrc(df,x) double df, x; { if( (x < 0.0) || (df < 1.0) ) { mtherr( "chdtrc", DOMAIN ); return(0.0); } return( igamc( df/2.0, x/2.0 ) ); } double chdtr(df,x) double df, x; { if( (x < 0.0) || (df < 1.0) ) { mtherr( "chdtr", DOMAIN ); return(0.0); } return( igam( df/2.0, x/2.0 ) ); } double chdtri( df, y ) double df, y; { double x; if( (y < 0.0) || (y > 1.0) || (df < 1.0) ) { mtherr( "chdtri", DOMAIN ); return(0.0); } x = igami( 0.5 * df, y ); return( 2.0 * x ); } thesias-3.1.1/src/const.c000066400000000000000000000226531360777755100152670ustar00rootroot00000000000000/* const.c * * Globally declared constants * * * * SYNOPSIS: * * extern double nameofconstant; * * * * * DESCRIPTION: * * This file contains a number of mathematical constants and * also some needed size parameters of the computer arithmetic. * The values are supplied as arrays of hexadecimal integers * for IEEE arithmetic; arrays of octal constants for DEC * arithmetic; and in a normal decimal scientific notation for * other machines. The particular notation used is determined * by a symbol (DEC, IBMPC, or UNK) defined in the include file * mconf.h. * * The default size parameters are as follows. * * For DEC and UNK modes: * MACHEP = 1.38777878078144567553E-17 2**-56 * MAXLOG = 8.8029691931113054295988E1 log(2**127) * MINLOG = -8.872283911167299960540E1 log(2**-128) * MAXNUM = 1.701411834604692317316873e38 2**127 * * For IEEE arithmetic (IBMPC): * MACHEP = 1.11022302462515654042E-16 2**-53 * MAXLOG = 7.09782712893383996843E2 log(2**1024) * MINLOG = -7.08396418532264106224E2 log(2**-1022) * MAXNUM = 1.7976931348623158E308 2**1024 * * The global symbols for mathematical constants are * PI = 3.14159265358979323846 pi * PIO2 = 1.57079632679489661923 pi/2 * PIO4 = 7.85398163397448309616E-1 pi/4 * SQRT2 = 1.41421356237309504880 sqrt(2) * SQRTH = 7.07106781186547524401E-1 sqrt(2)/2 * LOG2E = 1.4426950408889634073599 1/log(2) * SQ2OPI = 7.9788456080286535587989E-1 sqrt( 2/pi ) * LOGE2 = 6.93147180559945309417E-1 log(2) * LOGSQ2 = 3.46573590279972654709E-1 log(2)/2 * THPIO4 = 2.35619449019234492885 3*pi/4 * TWOOPI = 6.36619772367581343075535E-1 2/pi * * These lists are subject to change. */ /* const.c */ /* Cephes Math Library Release 2.3: March, 1995 Copyright 1984, 1995 by Stephen L. Moshier */ #include "mconf.h" #ifdef UNK #if 1 double MACHEP = 1.11022302462515654042E-16; /* 2**-53 */ #else double MACHEP = 1.38777878078144567553E-17; /* 2**-56 */ #endif double UFLOWTHRESH = 2.22507385850720138309E-308; /* 2**-1022 */ #ifdef DENORMAL double MAXLOG = 7.09782712893383996732E2; /* log(MAXNUM) */ /* double MINLOG = -7.44440071921381262314E2; */ /* log(2**-1074) */ double MINLOG = -7.451332191019412076235E2; /* log(2**-1075) */ #else double MAXLOG = 7.08396418532264106224E2; /* log 2**1022 */ double MINLOG = -7.08396418532264106224E2; /* log 2**-1022 */ #endif double MAXNUM = 1.79769313486231570815E308; /* 2**1024*(1-MACHEP) */ double PI = 3.14159265358979323846; /* pi */ double PIO2 = 1.57079632679489661923; /* pi/2 */ double PIO4 = 7.85398163397448309616E-1; /* pi/4 */ double SQRT2 = 1.41421356237309504880; /* sqrt(2) */ double SQRTH = 7.07106781186547524401E-1; /* sqrt(2)/2 */ double LOG2E = 1.4426950408889634073599; /* 1/log(2) */ double SQ2OPI = 7.9788456080286535587989E-1; /* sqrt( 2/pi ) */ double LOGE2 = 6.93147180559945309417E-1; /* log(2) */ double LOGSQ2 = 3.46573590279972654709E-1; /* log(2)/2 */ double THPIO4 = 2.35619449019234492885; /* 3*pi/4 */ double TWOOPI = 6.36619772367581343075535E-1; /* 2/pi */ #ifdef INFINITIES //AICI //double INFINITY = 1.0/0.0; /* 99e999; */ double INFINITY = 1.79769313486231570815E308; #else double INFINITY = 1.79769313486231570815E308; /* 2**1024*(1-MACHEP) */ #endif #ifdef NANS //AICI double NAN = (1.0/0.0 - 1.0/0.0); //double NAN = 0.0; #else double NAN = 0.0; #endif #ifdef MINUSZERO double NEGZERO = -0.0; #else double NEGZERO = 0.0; #endif #endif #ifdef IBMPC /* 2**-53 = 1.11022302462515654042E-16 */ unsigned short MACHEP[4] = {0x0000,0x0000,0x0000,0x3ca0}; unsigned short UFLOWTHRESH[4] = {0x0000,0x0000,0x0000,0x0010}; #ifdef DENORMAL /* log(MAXNUM) = 7.09782712893383996732224E2 */ unsigned short MAXLOG[4] = {0x39ef,0xfefa,0x2e42,0x4086}; /* log(2**-1074) = - -7.44440071921381262314E2 */ /*unsigned short MINLOG[4] = {0x71c3,0x446d,0x4385,0xc087};*/ unsigned short MINLOG[4] = {0x3052,0xd52d,0x4910,0xc087}; #else /* log(2**1022) = 7.08396418532264106224E2 */ unsigned short MAXLOG[4] = {0xbcd2,0xdd7a,0x232b,0x4086}; /* log(2**-1022) = - 7.08396418532264106224E2 */ unsigned short MINLOG[4] = {0xbcd2,0xdd7a,0x232b,0xc086}; #endif /* 2**1024*(1-MACHEP) = 1.7976931348623158E308 */ unsigned short MAXNUM[4] = {0xffff,0xffff,0xffff,0x7fef}; unsigned short PI[4] = {0x2d18,0x5444,0x21fb,0x4009}; unsigned short PIO2[4] = {0x2d18,0x5444,0x21fb,0x3ff9}; unsigned short PIO4[4] = {0x2d18,0x5444,0x21fb,0x3fe9}; unsigned short SQRT2[4] = {0x3bcd,0x667f,0xa09e,0x3ff6}; unsigned short SQRTH[4] = {0x3bcd,0x667f,0xa09e,0x3fe6}; unsigned short LOG2E[4] = {0x82fe,0x652b,0x1547,0x3ff7}; unsigned short SQ2OPI[4] = {0x3651,0x33d4,0x8845,0x3fe9}; unsigned short LOGE2[4] = {0x39ef,0xfefa,0x2e42,0x3fe6}; unsigned short LOGSQ2[4] = {0x39ef,0xfefa,0x2e42,0x3fd6}; unsigned short THPIO4[4] = {0x21d2,0x7f33,0xd97c,0x4002}; unsigned short TWOOPI[4] = {0xc883,0x6dc9,0x5f30,0x3fe4}; #ifdef INFINITIES unsigned short INFINITY[4] = {0x0000,0x0000,0x0000,0x7ff0}; #else unsigned short INFINITY[4] = {0xffff,0xffff,0xffff,0x7fef}; #endif #ifdef NANS unsigned short NAN[4] = {0x0000,0x0000,0x0000,0x7ffc}; #else unsigned short NAN[4] = {0x0000,0x0000,0x0000,0x0000}; #endif #ifdef MINUSZERO unsigned short NEGZERO[4] = {0x0000,0x0000,0x0000,0x8000}; #else unsigned short NEGZERO[4] = {0x0000,0x0000,0x0000,0x0000}; #endif #endif #ifdef MIEEE /* 2**-53 = 1.11022302462515654042E-16 */ unsigned short MACHEP[4] = {0x3ca0,0x0000,0x0000,0x0000}; unsigned short UFLOWTHRESH[4] = {0x0010,0x0000,0x0000,0x0000}; #ifdef DENORMAL /* log(2**1024) = 7.09782712893383996843E2 */ unsigned short MAXLOG[4] = {0x4086,0x2e42,0xfefa,0x39ef}; /* log(2**-1074) = - -7.44440071921381262314E2 */ /* unsigned short MINLOG[4] = {0xc087,0x4385,0x446d,0x71c3}; */ unsigned short MINLOG[4] = {0xc087,0x4910,0xd52d,0x3052}; #else /* log(2**1022) = 7.08396418532264106224E2 */ unsigned short MAXLOG[4] = {0x4086,0x232b,0xdd7a,0xbcd2}; /* log(2**-1022) = - 7.08396418532264106224E2 */ unsigned short MINLOG[4] = {0xc086,0x232b,0xdd7a,0xbcd2}; #endif /* 2**1024*(1-MACHEP) = 1.7976931348623158E308 */ unsigned short MAXNUM[4] = {0x7fef,0xffff,0xffff,0xffff}; unsigned short PI[4] = {0x4009,0x21fb,0x5444,0x2d18}; unsigned short PIO2[4] = {0x3ff9,0x21fb,0x5444,0x2d18}; unsigned short PIO4[4] = {0x3fe9,0x21fb,0x5444,0x2d18}; unsigned short SQRT2[4] = {0x3ff6,0xa09e,0x667f,0x3bcd}; unsigned short SQRTH[4] = {0x3fe6,0xa09e,0x667f,0x3bcd}; unsigned short LOG2E[4] = {0x3ff7,0x1547,0x652b,0x82fe}; unsigned short SQ2OPI[4] = {0x3fe9,0x8845,0x33d4,0x3651}; unsigned short LOGE2[4] = {0x3fe6,0x2e42,0xfefa,0x39ef}; unsigned short LOGSQ2[4] = {0x3fd6,0x2e42,0xfefa,0x39ef}; unsigned short THPIO4[4] = {0x4002,0xd97c,0x7f33,0x21d2}; unsigned short TWOOPI[4] = {0x3fe4,0x5f30,0x6dc9,0xc883}; #ifdef INFINITIES unsigned short INFINITY[4] = {0x7ff0,0x0000,0x0000,0x0000}; #else unsigned short INFINITY[4] = {0x7fef,0xffff,0xffff,0xffff}; #endif #ifdef NANS unsigned short NAN[4] = {0x7ff8,0x0000,0x0000,0x0000}; #else unsigned short NAN[4] = {0x0000,0x0000,0x0000,0x0000}; #endif #ifdef MINUSZERO unsigned short NEGZERO[4] = {0x8000,0x0000,0x0000,0x0000}; #else unsigned short NEGZERO[4] = {0x0000,0x0000,0x0000,0x0000}; #endif #endif #ifdef DEC /* 2**-56 = 1.38777878078144567553E-17 */ unsigned short MACHEP[4] = {0022200,0000000,0000000,0000000}; unsigned short UFLOWTHRESH[4] = {0x0080,0x0000,0x0000,0x0000}; /* log 2**127 = 88.029691931113054295988 */ unsigned short MAXLOG[4] = {041660,007463,0143742,025733,}; /* log 2**-128 = -88.72283911167299960540 */ unsigned short MINLOG[4] = {0141661,071027,0173721,0147572,}; /* 2**127 = 1.701411834604692317316873e38 */ unsigned short MAXNUM[4] = {077777,0177777,0177777,0177777,}; unsigned short PI[4] = {040511,007732,0121041,064302,}; unsigned short PIO2[4] = {040311,007732,0121041,064302,}; unsigned short PIO4[4] = {040111,007732,0121041,064302,}; unsigned short SQRT2[4] = {040265,002363,031771,0157145,}; unsigned short SQRTH[4] = {040065,002363,031771,0157144,}; unsigned short LOG2E[4] = {040270,0125073,024534,013761,}; unsigned short SQ2OPI[4] = {040114,041051,0117241,0131204,}; unsigned short LOGE2[4] = {040061,071027,0173721,0147572,}; unsigned short LOGSQ2[4] = {037661,071027,0173721,0147572,}; unsigned short THPIO4[4] = {040426,0145743,0174631,007222,}; unsigned short TWOOPI[4] = {040042,0174603,067116,042025,}; /* Approximate infinity by MAXNUM. */ unsigned short INFINITY[4] = {077777,0177777,0177777,0177777,}; unsigned short NAN[4] = {0000000,0000000,0000000,0000000}; #ifdef MINUSZERO unsigned short NEGZERO[4] = {0000000,0000000,0000000,0100000}; #else unsigned short NEGZERO[4] = {0000000,0000000,0000000,0000000}; #endif #endif #ifndef UNK extern unsigned short MACHEP[]; extern unsigned short UFLOWTHRESH[]; extern unsigned short MAXLOG[]; extern unsigned short UNDLOG[]; extern unsigned short MINLOG[]; extern unsigned short MAXNUM[]; extern unsigned short PI[]; extern unsigned short PIO2[]; extern unsigned short PIO4[]; extern unsigned short SQRT2[]; extern unsigned short SQRTH[]; extern unsigned short LOG2E[]; extern unsigned short SQ2OPI[]; extern unsigned short LOGE2[]; extern unsigned short LOGSQ2[]; extern unsigned short THPIO4[]; extern unsigned short TWOOPI[]; extern unsigned short INFINITY[]; extern unsigned short NAN[]; extern unsigned short NEGZERO[]; #endif thesias-3.1.1/src/gamma.c000066400000000000000000000333451360777755100152230ustar00rootroot00000000000000/* gamma.c * * Gamma function * * * * SYNOPSIS: * * double x, y, gamma(); * extern int sgngam; * * y = gamma( x ); * * * * DESCRIPTION: * * Returns gamma function of the argument. The result is * correctly signed, and the sign (+1 or -1) is also * returned in a global (extern) variable named sgngam. * This variable is also filled in by the logarithmic gamma * function lgam(). * * Arguments |x| <= 34 are reduced by recurrence and the function * approximated by a rational function of degree 6/7 in the * interval (2,3). Large arguments are handled by Stirling's * formula. Large negative arguments are made positive using * a reflection formula. * * * ACCURACY: * * Relative error: * arithmetic domain # trials peak rms * DEC -34, 34 10000 1.3e-16 2.5e-17 * IEEE -170,-33 20000 2.3e-15 3.3e-16 * IEEE -33, 33 20000 9.4e-16 2.2e-16 * IEEE 33, 171.6 20000 2.3e-15 3.2e-16 * * Error for arguments outside the test range will be larger * owing to error amplification by the exponential function. * */ /* lgam() * * Natural logarithm of gamma function * * * * SYNOPSIS: * * double x, y, lgam(); * extern int sgngam; * * y = lgam( x ); * * * * DESCRIPTION: * * Returns the base e (2.718...) logarithm of the absolute * value of the gamma function of the argument. * The sign (+1 or -1) of the gamma function is returned in a * global (extern) variable named sgngam. * * For arguments greater than 13, the logarithm of the gamma * function is approximated by the logarithmic version of * Stirling's formula using a polynomial approximation of * degree 4. Arguments between -33 and +33 are reduced by * recurrence to the interval [2,3] of a rational approximation. * The cosecant reflection formula is employed for arguments * less than -33. * * Arguments greater than MAXLGM return MAXNUM and an error * message. MAXLGM = 2.035093e36 for DEC * arithmetic or 2.556348e305 for IEEE arithmetic. * * * * ACCURACY: * * * arithmetic domain # trials peak rms * DEC 0, 3 7000 5.2e-17 1.3e-17 * DEC 2.718, 2.035e36 5000 3.9e-17 9.9e-18 * IEEE 0, 3 28000 5.4e-16 1.1e-16 * IEEE 2.718, 2.556e305 40000 3.5e-16 8.3e-17 * The error criterion was relative when the function magnitude * was greater than one but absolute when it was less than one. * * The following test used the relative error criterion, though * at certain points the relative error could be much higher than * indicated. * IEEE -200, -4 10000 4.8e-16 1.3e-16 * */ /* gamma.c */ /* gamma function */ /* Cephes Math Library Release 2.8: June, 2000 Copyright 1984, 1987, 1989, 1992, 2000 by Stephen L. Moshier */ #include "mconf.h" #ifdef UNK static double P[] = { 1.60119522476751861407E-4, 1.19135147006586384913E-3, 1.04213797561761569935E-2, 4.76367800457137231464E-2, 2.07448227648435975150E-1, 4.94214826801497100753E-1, 9.99999999999999996796E-1 }; static double Q[] = { -2.31581873324120129819E-5, 5.39605580493303397842E-4, -4.45641913851797240494E-3, 1.18139785222060435552E-2, 3.58236398605498653373E-2, -2.34591795718243348568E-1, 7.14304917030273074085E-2, 1.00000000000000000320E0 }; #define MAXGAM 171.624376956302725 static double LOGPI = 1.14472988584940017414; #endif #ifdef DEC static unsigned short P[] = { 0035047,0162701,0146301,0005234, 0035634,0023437,0032065,0176530, 0036452,0137157,0047330,0122574, 0037103,0017310,0143041,0017232, 0037524,0066516,0162563,0164605, 0037775,0004671,0146237,0014222, 0040200,0000000,0000000,0000000 }; static unsigned short Q[] = { 0134302,0041724,0020006,0116565, 0035415,0072121,0044251,0025634, 0136222,0003447,0035205,0121114, 0036501,0107552,0154335,0104271, 0037022,0135717,0014776,0171471, 0137560,0034324,0165024,0037021, 0037222,0045046,0047151,0161213, 0040200,0000000,0000000,0000000 }; #define MAXGAM 34.84425627277176174 static unsigned short LPI[4] = { 0040222,0103202,0043475,0006750, }; #define LOGPI *(double *)LPI #endif #ifdef IBMPC static unsigned short P[] = { 0x2153,0x3998,0xfcb8,0x3f24, 0xbfab,0xe686,0x84e3,0x3f53, 0x14b0,0xe9db,0x57cd,0x3f85, 0x23d3,0x18c4,0x63d9,0x3fa8, 0x7d31,0xdcae,0x8da9,0x3fca, 0xe312,0x3993,0xa137,0x3fdf, 0x0000,0x0000,0x0000,0x3ff0 }; static unsigned short Q[] = { 0xd3af,0x8400,0x487a,0xbef8, 0x2573,0x2915,0xae8a,0x3f41, 0xb44a,0xe750,0x40e4,0xbf72, 0xb117,0x5b1b,0x31ed,0x3f88, 0xde67,0xe33f,0x5779,0x3fa2, 0x87c2,0x9d42,0x071a,0xbfce, 0x3c51,0xc9cd,0x4944,0x3fb2, 0x0000,0x0000,0x0000,0x3ff0 }; #define MAXGAM 171.624376956302725 static unsigned short LPI[4] = { 0xa1bd,0x48e7,0x50d0,0x3ff2, }; #define LOGPI *(double *)LPI #endif #ifdef MIEEE static unsigned short P[] = { 0x3f24,0xfcb8,0x3998,0x2153, 0x3f53,0x84e3,0xe686,0xbfab, 0x3f85,0x57cd,0xe9db,0x14b0, 0x3fa8,0x63d9,0x18c4,0x23d3, 0x3fca,0x8da9,0xdcae,0x7d31, 0x3fdf,0xa137,0x3993,0xe312, 0x3ff0,0x0000,0x0000,0x0000 }; static unsigned short Q[] = { 0xbef8,0x487a,0x8400,0xd3af, 0x3f41,0xae8a,0x2915,0x2573, 0xbf72,0x40e4,0xe750,0xb44a, 0x3f88,0x31ed,0x5b1b,0xb117, 0x3fa2,0x5779,0xe33f,0xde67, 0xbfce,0x071a,0x9d42,0x87c2, 0x3fb2,0x4944,0xc9cd,0x3c51, 0x3ff0,0x0000,0x0000,0x0000 }; #define MAXGAM 171.624376956302725 static unsigned short LPI[4] = { 0x3ff2,0x50d0,0x48e7,0xa1bd, }; #define LOGPI *(double *)LPI #endif /* Stirling's formula for the gamma function */ #if UNK static double STIR[5] = { 7.87311395793093628397E-4, -2.29549961613378126380E-4, -2.68132617805781232825E-3, 3.47222221605458667310E-3, 8.33333333333482257126E-2, }; #define MAXSTIR 143.01608 static double SQTPI = 2.50662827463100050242E0; #endif #if DEC static unsigned short STIR[20] = { 0035516,0061622,0144553,0112224, 0135160,0131531,0037460,0165740, 0136057,0134460,0037242,0077270, 0036143,0107070,0156306,0027751, 0037252,0125252,0125252,0146064, }; #define MAXSTIR 26.77 static unsigned short SQT[4] = { 0040440,0066230,0177661,0034055, }; #define SQTPI *(double *)SQT #endif #if IBMPC static unsigned short STIR[20] = { 0x7293,0x592d,0xcc72,0x3f49, 0x1d7c,0x27e6,0x166b,0xbf2e, 0x4fd7,0x07d4,0xf726,0xbf65, 0xc5fd,0x1b98,0x71c7,0x3f6c, 0x5986,0x5555,0x5555,0x3fb5, }; #define MAXSTIR 143.01608 static unsigned short SQT[4] = { 0x2706,0x1ff6,0x0d93,0x4004, }; #define SQTPI *(double *)SQT #endif #if MIEEE static unsigned short STIR[20] = { 0x3f49,0xcc72,0x592d,0x7293, 0xbf2e,0x166b,0x27e6,0x1d7c, 0xbf65,0xf726,0x07d4,0x4fd7, 0x3f6c,0x71c7,0x1b98,0xc5fd, 0x3fb5,0x5555,0x5555,0x5986, }; #define MAXSTIR 143.01608 static unsigned short SQT[4] = { 0x4004,0x0d93,0x1ff6,0x2706, }; #define SQTPI *(double *)SQT #endif int sgngam = 0; extern int sgngam; extern double MAXLOG, MAXNUM, PI; #ifdef ANSIPROT extern double pow ( double, double ); extern double log ( double ); extern double exp ( double ); extern double sin ( double ); extern double polevl ( double, void *, int ); extern double p1evl ( double, void *, int ); extern double floor ( double ); extern double fabs ( double ); extern int isnan ( double ); extern int isfinite ( double ); static double stirf ( double ); double lgam ( double ); #else double pow(), log(), exp(), sin(), polevl(), p1evl(), floor(), fabs(); int isnan(), isfinite(); static double stirf(); double lgam(); #endif #ifdef INFINITIES extern double INFINITY; #endif #ifdef NANS extern double NAN; #endif /* Gamma function computed by Stirling's formula. * The polynomial STIR is valid for 33 <= x <= 172. */ static double stirf(x) double x; { double y, w, v; w = 1.0/x; w = 1.0 + w * polevl( w, STIR, 4 ); y = exp(x); if( x > MAXSTIR ) { /* Avoid overflow in pow() */ v = pow( x, 0.5 * x - 0.25 ); y = v * (v / y); } else { y = pow( x, x - 0.5 ) / y; } y = SQTPI * y * w; return( y ); } double gamma(x) double x; { double p, q, z; int i; sgngam = 1; #ifdef NANS if( isnan(x) ) return(x); #endif #ifdef INFINITIES #ifdef NANS if( x == INFINITY ) return(x); if( x == -INFINITY ) return(NAN); #else if( !isfinite(x) ) return(x); #endif #endif q = fabs(x); if( q > 33.0 ) { if( x < 0.0 ) { p = floor(q); if( p == q ) { #ifdef NANS gamnan: mtherr( "gamma", DOMAIN ); return (NAN); #else goto goverf; #endif } i = p; if( (i & 1) == 0 ) sgngam = -1; z = q - p; if( z > 0.5 ) { p += 1.0; z = q - p; } z = q * sin( PI * z ); if( z == 0.0 ) { #ifdef INFINITIES return( sgngam * INFINITY); #else goverf: mtherr( "gamma", OVERFLOW ); return( sgngam * MAXNUM); #endif } z = fabs(z); z = PI/(z * stirf(q) ); } else { z = stirf(x); } return( sgngam * z ); } z = 1.0; while( x >= 3.0 ) { x -= 1.0; z *= x; } while( x < 0.0 ) { if( x > -1.E-9 ) goto small; z /= x; x += 1.0; } while( x < 2.0 ) { if( x < 1.e-9 ) goto small; z /= x; x += 1.0; } if( x == 2.0 ) return(z); x -= 2.0; p = polevl( x, P, 6 ); q = polevl( x, Q, 7 ); return( z * p / q ); small: if( x == 0.0 ) { #ifdef INFINITIES #ifdef NANS goto gamnan; #else return( INFINITY ); #endif #else mtherr( "gamma", SING ); return( MAXNUM ); #endif } else return( z/((1.0 + 0.5772156649015329 * x) * x) ); } /* A[]: Stirling's formula expansion of log gamma * B[], C[]: log gamma function between 2 and 3 */ #ifdef UNK static double A[] = { 8.11614167470508450300E-4, -5.95061904284301438324E-4, 7.93650340457716943945E-4, -2.77777777730099687205E-3, 8.33333333333331927722E-2 }; static double B[] = { -1.37825152569120859100E3, -3.88016315134637840924E4, -3.31612992738871184744E5, -1.16237097492762307383E6, -1.72173700820839662146E6, -8.53555664245765465627E5 }; static double C[] = { /* 1.00000000000000000000E0, */ -3.51815701436523470549E2, -1.70642106651881159223E4, -2.20528590553854454839E5, -1.13933444367982507207E6, -2.53252307177582951285E6, -2.01889141433532773231E6 }; /* log( sqrt( 2*pi ) ) */ static double LS2PI = 0.91893853320467274178; #define MAXLGM 2.556348e305 #endif #ifdef DEC static unsigned short A[] = { 0035524,0141201,0034633,0031405, 0135433,0176755,0126007,0045030, 0035520,0006371,0003342,0172730, 0136066,0005540,0132605,0026407, 0037252,0125252,0125252,0125132 }; static unsigned short B[] = { 0142654,0044014,0077633,0035410, 0144027,0110641,0125335,0144760, 0144641,0165637,0142204,0047447, 0145215,0162027,0146246,0155211, 0145322,0026110,0010317,0110130, 0145120,0061472,0120300,0025363 }; static unsigned short C[] = { /*0040200,0000000,0000000,0000000*/ 0142257,0164150,0163630,0112622, 0143605,0050153,0156116,0135272, 0144527,0056045,0145642,0062332, 0145213,0012063,0106250,0001025, 0145432,0111254,0044577,0115142, 0145366,0071133,0050217,0005122 }; /* log( sqrt( 2*pi ) ) */ static unsigned short LS2P[] = {040153,037616,041445,0172645,}; #define LS2PI *(double *)LS2P #define MAXLGM 2.035093e36 #endif #ifdef IBMPC static unsigned short A[] = { 0x6661,0x2733,0x9850,0x3f4a, 0xe943,0xb580,0x7fbd,0xbf43, 0x5ebb,0x20dc,0x019f,0x3f4a, 0xa5a1,0x16b0,0xc16c,0xbf66, 0x554b,0x5555,0x5555,0x3fb5 }; static unsigned short B[] = { 0x6761,0x8ff3,0x8901,0xc095, 0xb93e,0x355b,0xf234,0xc0e2, 0x89e5,0xf890,0x3d73,0xc114, 0xdb51,0xf994,0xbc82,0xc131, 0xf20b,0x0219,0x4589,0xc13a, 0x055e,0x5418,0x0c67,0xc12a }; static unsigned short C[] = { /*0x0000,0x0000,0x0000,0x3ff0,*/ 0x12b2,0x1cf3,0xfd0d,0xc075, 0xd757,0x7b89,0xaa0d,0xc0d0, 0x4c9b,0xb974,0xeb84,0xc10a, 0x0043,0x7195,0x6286,0xc131, 0xf34c,0x892f,0x5255,0xc143, 0xe14a,0x6a11,0xce4b,0xc13e }; /* log( sqrt( 2*pi ) ) */ static unsigned short LS2P[] = { 0xbeb5,0xc864,0x67f1,0x3fed }; #define LS2PI *(double *)LS2P #define MAXLGM 2.556348e305 #endif #ifdef MIEEE static unsigned short A[] = { 0x3f4a,0x9850,0x2733,0x6661, 0xbf43,0x7fbd,0xb580,0xe943, 0x3f4a,0x019f,0x20dc,0x5ebb, 0xbf66,0xc16c,0x16b0,0xa5a1, 0x3fb5,0x5555,0x5555,0x554b }; static unsigned short B[] = { 0xc095,0x8901,0x8ff3,0x6761, 0xc0e2,0xf234,0x355b,0xb93e, 0xc114,0x3d73,0xf890,0x89e5, 0xc131,0xbc82,0xf994,0xdb51, 0xc13a,0x4589,0x0219,0xf20b, 0xc12a,0x0c67,0x5418,0x055e }; static unsigned short C[] = { 0xc075,0xfd0d,0x1cf3,0x12b2, 0xc0d0,0xaa0d,0x7b89,0xd757, 0xc10a,0xeb84,0xb974,0x4c9b, 0xc131,0x6286,0x7195,0x0043, 0xc143,0x5255,0x892f,0xf34c, 0xc13e,0xce4b,0x6a11,0xe14a }; /* log( sqrt( 2*pi ) ) */ static unsigned short LS2P[] = { 0x3fed,0x67f1,0xc864,0xbeb5 }; #define LS2PI *(double *)LS2P #define MAXLGM 2.556348e305 #endif /* Logarithm of gamma function */ double lgam(x) double x; { double p, q, u, w, z; int i; sgngam = 1; #ifdef NANS if( isnan(x) ) return(x); #endif /* #ifdef INFINITIES if( !isfinite(x) ) return(INFINITY); #endif */ if( x < -34.0 ) { q = -x; w = lgam(q); /* note this modifies sgngam! */ p = floor(q); if( p == q ) { lgsing: #ifdef INFINITIES mtherr( "lgam", SING ); return (INFINITY); #else goto loverf; #endif } i = p; if( (i & 1) == 0 ) sgngam = -1; else sgngam = 1; z = q - p; if( z > 0.5 ) { p += 1.0; z = p - q; } z = q * sin( PI * z ); if( z == 0.0 ) goto lgsing; /* z = log(PI) - log( z ) - w;*/ z = LOGPI - log( z ) - w; return( z ); } if( x < 13.0 ) { z = 1.0; p = 0.0; u = x; while( u >= 3.0 ) { p -= 1.0; u = x + p; z *= u; } while( u < 2.0 ) { if( u == 0.0 ) goto lgsing; z /= u; p += 1.0; u = x + p; } if( z < 0.0 ) { sgngam = -1; z = -z; } else sgngam = 1; if( u == 2.0 ) return( log(z) ); p -= 2.0; x = x + p; p = x * polevl( x, B, 5 ) / p1evl( x, C, 6); return( log(z) + p ); } if( x > MAXLGM ) { #ifdef INFINITIES return( sgngam * INFINITY ); #else loverf: mtherr( "lgam", OVERFLOW ); return( sgngam * MAXNUM ); #endif } q = ( x - 0.5 ) * log(x) - x + LS2PI; if( x > 1.0e8 ) return( q ); p = 1.0/(x*x); if( x >= 1000.0 ) q += (( 7.9365079365079365079365e-4 * p - 2.7777777777777777777778e-3) *p + 0.0833333333333333333333) / x; else q += polevl( p, A, 4 ) / x; return( q ); } thesias-3.1.1/src/igam.c000066400000000000000000000075241360777755100150560ustar00rootroot00000000000000/* igam.c * * Incomplete gamma integral * * * * SYNOPSIS: * * double a, x, y, igam(); * * y = igam( a, x ); * * DESCRIPTION: * * The function is defined by * * x * - * 1 | | -t a-1 * igam(a,x) = ----- | e t dt. * - | | * | (a) - * 0 * * * In this implementation both arguments must be positive. * The integral is evaluated by either a power series or * continued fraction expansion, depending on the relative * values of a and x. * * ACCURACY: * * Relative error: * arithmetic domain # trials peak rms * IEEE 0,30 200000 3.6e-14 2.9e-15 * IEEE 0,100 300000 9.9e-14 1.5e-14 */ /* igamc() * * Complemented incomplete gamma integral * * * * SYNOPSIS: * * double a, x, y, igamc(); * * y = igamc( a, x ); * * DESCRIPTION: * * The function is defined by * * * igamc(a,x) = 1 - igam(a,x) * * inf. * - * 1 | | -t a-1 * = ----- | e t dt. * - | | * | (a) - * x * * * In this implementation both arguments must be positive. * The integral is evaluated by either a power series or * continued fraction expansion, depending on the relative * values of a and x. * * ACCURACY: * * Tested at random a, x. * a x Relative error: * arithmetic domain domain # trials peak rms * IEEE 0.5,100 0,100 200000 1.9e-14 1.7e-15 * IEEE 0.01,0.5 0,100 200000 1.4e-13 1.6e-15 */ /* Cephes Math Library Release 2.8: June, 2000 Copyright 1985, 1987, 2000 by Stephen L. Moshier */ #include "mconf.h" #ifdef ANSIPROT extern double lgam ( double ); extern double exp ( double ); extern double log ( double ); extern double fabs ( double ); extern double igam ( double, double ); extern double igamc ( double, double ); #else double lgam(), exp(), log(), fabs(), igam(), igamc(); #endif extern double MACHEP, MAXLOG; static double big = 4.503599627370496e15; static double biginv = 2.22044604925031308085e-16; double igamc( a, x ) double a, x; { double ans, ax, c, yc, r, t, y, z; double pk, pkm1, pkm2, qk, qkm1, qkm2; if( (x <= 0) || ( a <= 0) ) return( 1.0 ); if( (x < 1.0) || (x < a) ) return( 1.0 - igam(a,x) ); ax = a * log(x) - x - lgam(a); if( ax < -MAXLOG ) { mtherr( "igamc", UNDERFLOW ); return( 0.0 ); } ax = exp(ax); /* continued fraction */ y = 1.0 - a; z = x + y + 1.0; c = 0.0; pkm2 = 1.0; qkm2 = x; pkm1 = x + 1.0; qkm1 = z * x; ans = pkm1/qkm1; do { c += 1.0; y += 1.0; z += 2.0; yc = y * c; pk = pkm1 * z - pkm2 * yc; qk = qkm1 * z - qkm2 * yc; if( qk != 0 ) { r = pk/qk; t = fabs( (ans - r)/r ); ans = r; } else t = 1.0; pkm2 = pkm1; pkm1 = pk; qkm2 = qkm1; qkm1 = qk; if( fabs(pk) > big ) { pkm2 *= biginv; pkm1 *= biginv; qkm2 *= biginv; qkm1 *= biginv; } } while( t > MACHEP ); return( ans * ax ); } /* left tail of incomplete gamma function: * * inf. k * a -x - x * x e > ---------- * - - * k=0 | (a+k+1) * */ double igam( a, x ) double a, x; { double ans, ax, c, r; if( (x <= 0) || ( a <= 0) ) return( 0.0 ); if( (x > 1.0) && (x > a ) ) return( 1.0 - igamc(a,x) ); /* Compute x**a * exp(-x) / gamma(a) */ ax = a * log(x) - x - lgam(a); if( ax < -MAXLOG ) { mtherr( "igam", UNDERFLOW ); return( 0.0 ); } ax = exp(ax); /* power series */ r = a; c = 1.0; ans = 1.0; do { r += 1.0; c *= x/r; ans += c; } while( c/ans > MACHEP ); return( ans * ax/a ); } thesias-3.1.1/src/igami.c000066400000000000000000000061041360777755100152200ustar00rootroot00000000000000/* igami() * * Inverse of complemented imcomplete gamma integral * * * * SYNOPSIS: * * double a, x, p, igami(); * * x = igami( a, p ); * * DESCRIPTION: * * Given p, the function finds x such that * * igamc( a, x ) = p. * * Starting with the approximate value * * 3 * x = a t * * where * * t = 1 - d - ndtri(p) sqrt(d) * * and * * d = 1/9a, * * the routine performs up to 10 Newton iterations to find the * root of igamc(a,x) - p = 0. * * ACCURACY: * * Tested at random a, p in the intervals indicated. * * a p Relative error: * arithmetic domain domain # trials peak rms * IEEE 0.5,100 0,0.5 100000 1.0e-14 1.7e-15 * IEEE 0.01,0.5 0,0.5 100000 9.0e-14 3.4e-15 * IEEE 0.5,10000 0,0.5 20000 2.3e-13 3.8e-14 */ /* Cephes Math Library Release 2.8: June, 2000 Copyright 1984, 1987, 1995, 2000 by Stephen L. Moshier */ #include "mconf.h" extern double MACHEP, MAXNUM, MAXLOG, MINLOG; #ifdef ANSIPROT extern double igamc ( double, double ); extern double ndtri ( double ); extern double exp ( double ); extern double fabs ( double ); extern double log ( double ); extern double sqrt ( double ); extern double lgam ( double ); #else double igamc(), ndtri(), exp(), fabs(), log(), sqrt(), lgam(); #endif double igami( a, y0 ) double a, y0; { double x0, x1, x, yl, yh, y, d, lgm, dithresh; int i, dir; /* bound the solution */ x0 = MAXNUM; yl = 0; x1 = 0; yh = 1.0; dithresh = 5.0 * MACHEP; /* approximation to inverse function */ d = 1.0/(9.0*a); y = ( 1.0 - d - ndtri(y0) * sqrt(d) ); x = a * y * y * y; lgm = lgam(a); for( i=0; i<10; i++ ) { if( x > x0 || x < x1 ) goto ihalve; y = igamc(a,x); if( y < yl || y > yh ) goto ihalve; if( y < y0 ) { x0 = x; yl = y; } else { x1 = x; yh = y; } /* compute the derivative of the function at this point */ d = (a - 1.0) * log(x) - x - lgm; if( d < -MAXLOG ) goto ihalve; d = -exp(d); /* compute the step to the next approximation of x */ d = (y - y0)/d; if( fabs(d/x) < MACHEP ) goto done; x = x - d; } /* Resort to interval halving if Newton iteration did not converge. */ ihalve: d = 0.0625; if( x0 == MAXNUM ) { if( x <= 0.0 ) x = 1.0; while( x0 == MAXNUM ) { x = (1.0 + d) * x; y = igamc( a, x ); if( y < y0 ) { x0 = x; yl = y; break; } d = d + d; } } d = 0.5; dir = 0; for( i=0; i<400; i++ ) { x = x1 + d * (x0 - x1); y = igamc( a, x ); lgm = (x0 - x1)/(x1 + x0); if( fabs(lgm) < dithresh ) break; lgm = (y - y0)/y0; if( fabs(lgm) < dithresh ) break; if( x <= 0.0 ) break; if( y >= y0 ) { x1 = x; yh = y; if( dir < 0 ) { dir = 0; d = 0.5; } else if( dir > 1 ) d = 0.5 * d + 0.5; else d = (y0 - yl)/(yh - yl); dir += 1; } else { x0 = x; yl = y; if( dir > 0 ) { dir = 0; d = 0.5; } else if( dir < -1 ) d = 0.5 * d; else d = (y0 - yl)/(yh - yl); dir -= 1; } } if( x == 0.0 ) mtherr( "igami", UNDERFLOW ); done: return( x ); } thesias-3.1.1/src/isnan.c000066400000000000000000000075031360777755100152460ustar00rootroot00000000000000/* isnan() * signbit() * isfinite() * * Floating point numeric utilities * * * * SYNOPSIS: * * double ceil(), floor(), frexp(), ldexp(); * int signbit(), isnan(), isfinite(); * double x, y; * int expnt, n; * * y = floor(x); * y = ceil(x); * y = frexp( x, &expnt ); * y = ldexp( x, n ); * n = signbit(x); * n = isnan(x); * n = isfinite(x); * * * * DESCRIPTION: * * All four routines return a double precision floating point * result. * * floor() returns the largest integer less than or equal to x. * It truncates toward minus infinity. * * ceil() returns the smallest integer greater than or equal * to x. It truncates toward plus infinity. * * frexp() extracts the exponent from x. It returns an integer * power of two to expnt and the significand between 0.5 and 1 * to y. Thus x = y * 2**expn. * * ldexp() multiplies x by 2**n. * * signbit(x) returns 1 if the sign bit of x is 1, else 0. * * These functions are part of the standard C run time library * for many but not all C compilers. The ones supplied are * written in C for either DEC or IEEE arithmetic. They should * be used only if your compiler library does not already have * them. * * The IEEE versions assume that denormal numbers are implemented * in the arithmetic. Some modifications will be required if * the arithmetic has abrupt rather than gradual underflow. */ /* Cephes Math Library Release 2.3: March, 1995 Copyright 1984, 1995 by Stephen L. Moshier */ #include "mconf.h" #ifdef UNK /* ceil(), floor(), frexp(), ldexp() may need to be rewritten. */ #undef UNK #if BIGENDIAN #define MIEEE 1 #else #define IBMPC 1 #endif #endif /* Return 1 if the sign bit of x is 1, else 0. */ int signbit(x) double x; { union { double d; short s[4]; int i[2]; } u; u.d = x; if( sizeof(int) == 4 ) { #ifdef IBMPC return( u.i[1] < 0 ); #endif #ifdef DEC return( u.s[3] < 0 ); #endif #ifdef MIEEE return( u.i[0] < 0 ); #endif } else { #ifdef IBMPC return( u.s[3] < 0 ); #endif #ifdef DEC return( u.s[3] < 0 ); #endif #ifdef MIEEE return( u.s[0] < 0 ); #endif } } /* Return 1 if x is a number that is Not a Number, else return 0. */ int isnan(x) double x; { #ifdef NANS union { double d; unsigned short s[4]; unsigned int i[2]; } u; u.d = x; if( sizeof(int) == 4 ) { #ifdef IBMPC if( ((u.i[1] & 0x7ff00000) == 0x7ff00000) && (((u.i[1] & 0x000fffff) != 0) || (u.i[0] != 0))) return 1; #endif #ifdef DEC if( (u.s[1] & 0x7fff) == 0) { if( (u.s[2] | u.s[1] | u.s[0]) != 0 ) return(1); } #endif #ifdef MIEEE if( ((u.i[0] & 0x7ff00000) == 0x7ff00000) && (((u.i[0] & 0x000fffff) != 0) || (u.i[1] != 0))) return 1; #endif return(0); } else { /* size int not 4 */ #ifdef IBMPC if( (u.s[3] & 0x7ff0) == 0x7ff0) { if( ((u.s[3] & 0x000f) | u.s[2] | u.s[1] | u.s[0]) != 0 ) return(1); } #endif #ifdef DEC if( (u.s[3] & 0x7fff) == 0) { if( (u.s[2] | u.s[1] | u.s[0]) != 0 ) return(1); } #endif #ifdef MIEEE if( (u.s[0] & 0x7ff0) == 0x7ff0) { if( ((u.s[0] & 0x000f) | u.s[1] | u.s[2] | u.s[3]) != 0 ) return(1); } #endif return(0); } /* size int not 4 */ #else /* No NANS. */ return(0); #endif } /* Return 1 if x is not infinite and is not a NaN. */ int isfinite(x) double x; { #ifdef INFINITIES union { double d; unsigned short s[4]; unsigned int i[2]; } u; u.d = x; if( sizeof(int) == 4 ) { #ifdef IBMPC if( (u.i[1] & 0x7ff00000) != 0x7ff00000) return 1; #endif #ifdef DEC if( (u.s[3] & 0x7fff) != 0) return 1; #endif #ifdef MIEEE if( (u.i[0] & 0x7ff00000) != 0x7ff00000) return 1; #endif return(0); } else { #ifdef IBMPC if( (u.s[3] & 0x7ff0) != 0x7ff0) return 1; #endif #ifdef DEC if( (u.s[3] & 0x7fff) != 0) return 1; #endif #ifdef MIEEE if( (u.s[0] & 0x7ff0) != 0x7ff0) return 1; #endif return(0); } #else /* No INFINITY. */ return(1); #endif } thesias-3.1.1/src/mconf.h000066400000000000000000000125021360777755100152400ustar00rootroot00000000000000/* mconf.h * * Common include file for math routines * * * * SYNOPSIS: * * #include "mconf.h" * * * * DESCRIPTION: * * This file contains definitions for error codes that are * passed to the common error handling routine mtherr() * (which see). * * The file also includes a conditional assembly definition * for the type of computer arithmetic (IEEE, DEC, Motorola * IEEE, or UNKnown). * * For Digital Equipment PDP-11 and VAX computers, certain * IBM systems, and others that use numbers with a 56-bit * significand, the symbol DEC should be defined. In this * mode, most floating point constants are given as arrays * of octal integers to eliminate decimal to binary conversion * errors that might be introduced by the compiler. * * For little-endian computers, such as IBM PC, that follow the * IEEE Standard for Binary Floating Point Arithmetic (ANSI/IEEE * Std 754-1985), the symbol IBMPC should be defined. These * numbers have 53-bit significands. In this mode, constants * are provided as arrays of hexadecimal 16 bit integers. * * Big-endian IEEE format is denoted MIEEE. On some RISC * systems such as Sun SPARC, double precision constants * must be stored on 8-byte address boundaries. Since integer * arrays may be aligned differently, the MIEEE configuration * may fail on such machines. * * To accommodate other types of computer arithmetic, all * constants are also provided in a normal decimal radix * which one can hope are correctly converted to a suitable * format by the available C language compiler. To invoke * this mode, define the symbol UNK. * * An important difference among these modes is a predefined * set of machine arithmetic constants for each. The numbers * MACHEP (the machine roundoff error), MAXNUM (largest number * represented), and several other parameters are preset by * the configuration symbol. Check the file const.c to * ensure that these values are correct for your computer. * * Configurations NANS, INFINITIES, MINUSZERO, and DENORMAL * may fail on many systems. Verify that they are supposed * to work on your computer. */ /* Cephes Math Library Release 2.3: June, 1995 Copyright 1984, 1987, 1989, 1995 by Stephen L. Moshier */ /* Define if the `long double' type works. */ #define HAVE_LONG_DOUBLE 1 /* Define as the return type of signal handlers (int or void). */ #define RETSIGTYPE void /* Define if you have the ANSI C header files. */ #define STDC_HEADERS 1 /* Define if your processor stores words with the most significant byte first (like Motorola and SPARC, unlike Intel and VAX). */ /* #undef WORDS_BIGENDIAN */ /* Define if floating point words are bigendian. */ /* #undef FLOAT_WORDS_BIGENDIAN */ /* The number of bytes in a int. */ #define SIZEOF_INT 4 /* Define if you have the header file. */ #define HAVE_STRING_H 1 /* Name of package */ #define PACKAGE "cephes" /* Version number of package */ #define VERSION "2.7" /* Constant definitions for math error conditions */ #define DOMAIN 1 /* argument domain error */ #define SING 2 /* argument singularity */ #define OVERFLOW 3 /* overflow range error */ #define UNDERFLOW 4 /* underflow range error */ #define TLOSS 5 /* total loss of precision */ #define PLOSS 6 /* partial loss of precision */ #define EDOM 33 #define ERANGE 34 /* Complex numeral. */ typedef struct { double r; double i; } cmplx; #ifdef HAVE_LONG_DOUBLE /* Long double complex numeral. */ typedef struct { long double r; long double i; } cmplxl; #endif /* Type of computer arithmetic */ /* PDP-11, Pro350, VAX: */ /* #define DEC 1 */ /* Intel IEEE, low order words come first: */ /* #define IBMPC 1 */ /* Motorola IEEE, high order words come first * (Sun 680x0 workstation): */ /* #define MIEEE 1 */ /* UNKnown arithmetic, invokes coefficients given in * normal decimal format. Beware of range boundary * problems (MACHEP, MAXLOG, etc. in const.c) and * roundoff problems in pow.c: * (Sun SPARCstation) */ #define UNK 1 /* If you define UNK, then be sure to set BIGENDIAN properly. */ #ifdef FLOAT_WORDS_BIGENDIAN #define BIGENDIAN 1 #else #define BIGENDIAN 0 #endif /* Define this `volatile' if your compiler thinks * that floating point arithmetic obeys the associative * and distributive laws. It will defeat some optimizations * (but probably not enough of them). * * #define VOLATILE volatile */ #define VOLATILE /* For 12-byte long doubles on an i386, pad a 16-bit short 0 * to the end of real constants initialized by integer arrays. * * #define XPD 0, * * Otherwise, the type is 10 bytes long and XPD should be * defined blank (e.g., Microsoft C). * * #define XPD */ #define XPD 0, /* Define to support tiny denormal numbers, else undefine. */ #define DENORMAL 1 /* Define to ask for infinity support, else undefine. */ #define INFINITIES 1 /* Define to ask for support of numbers that are Not-a-Number, else undefine. This may automatically define INFINITIES in some files. */ #define NANS 1 /* Define to distinguish between -0.0 and +0.0. */ #define MINUSZERO 1 /* Define 1 for ANSI C atan2() function See atan.c and clog.c. */ #define ANSIC 1 /* Get ANSI function prototypes, if you want them. */ #if 1 /* #ifdef __STDC__ */ #define ANSIPROT 1 int mtherr ( char *, int ); #else int mtherr(); #endif /* Variable for error reporting. See mtherr.c. */ extern int merror; thesias-3.1.1/src/mtherr.c000066400000000000000000000045011360777755100154320ustar00rootroot00000000000000/* mtherr.c * * Library common error handling routine * * * * SYNOPSIS: * * char *fctnam; * int code; * int mtherr(); * * mtherr( fctnam, code ); * * * * DESCRIPTION: * * This routine may be called to report one of the following * error conditions (in the include file mconf.h). * * Mnemonic Value Significance * * DOMAIN 1 argument domain error * SING 2 function singularity * OVERFLOW 3 overflow range error * UNDERFLOW 4 underflow range error * TLOSS 5 total loss of precision * PLOSS 6 partial loss of precision * EDOM 33 Unix domain error code * ERANGE 34 Unix range error code * * The default version of the file prints the function name, * passed to it by the pointer fctnam, followed by the * error condition. The display is directed to the standard * output device. The routine then returns to the calling * program. Users may wish to modify the program to abort by * calling exit() under severe error conditions such as domain * errors. * * Since all error conditions pass control to this function, * the display may be easily changed, eliminated, or directed * to an error logging device. * * SEE ALSO: * * mconf.h * */ /* Cephes Math Library Release 2.0: April, 1987 Copyright 1984, 1987 by Stephen L. Moshier Direct inquiries to 30 Frost Street, Cambridge, MA 02140 */ #include #include "mconf.h" int merror = 0; /* Notice: the order of appearance of the following * messages is bound to the error codes defined * in mconf.h. */ static char *ermsg[7] = { "unknown", /* error code 0 */ "domain", /* error code 1 */ "singularity", /* et seq. */ "overflow", "underflow", "total loss of precision", "partial loss of precision" }; int mtherr( name, code ) char *name; int code; { /* Display string passed by calling program, * which is supposed to be the name of the * function in which the error occurred: */ printf( "\n%s ", name ); /* Set global error message word */ merror = code; /* Display error message defined * by the code argument. */ if( (code <= 0) || (code >= 7) ) code = 0; printf( "%s error\n", ermsg[code] ); /* Return to calling * program */ return( 0 ); } thesias-3.1.1/src/ndtri.c000066400000000000000000000235631360777755100152620ustar00rootroot00000000000000/* ndtri.c * * Inverse of Normal distribution function * * * * SYNOPSIS: * * double x, y, ndtri(); * * x = ndtri( y ); * * * * DESCRIPTION: * * Returns the argument, x, for which the area under the * Gaussian probability density function (integrated from * minus infinity to x) is equal to y. * * * For small arguments 0 < y < exp(-2), the program computes * z = sqrt( -2.0 * log(y) ); then the approximation is * x = z - log(z)/z - (1/z) P(1/z) / Q(1/z). * There are two rational functions P/Q, one for 0 < y < exp(-32) * and the other for y up to exp(-2). For larger arguments, * w = y - 0.5, and x/sqrt(2pi) = w + w**3 R(w**2)/S(w**2)). * * * ACCURACY: * * Relative error: * arithmetic domain # trials peak rms * DEC 0.125, 1 5500 9.5e-17 2.1e-17 * DEC 6e-39, 0.135 3500 5.7e-17 1.3e-17 * IEEE 0.125, 1 20000 7.2e-16 1.3e-16 * IEEE 3e-308, 0.135 50000 4.6e-16 9.8e-17 * * * ERROR MESSAGES: * * message condition value returned * ndtri domain x <= 0 -MAXNUM * ndtri domain x >= 1 MAXNUM * */ /* Cephes Math Library Release 2.8: June, 2000 Copyright 1984, 1987, 1989, 2000 by Stephen L. Moshier */ #include "mconf.h" extern double MAXNUM; #ifdef UNK /* sqrt(2pi) */ static double s2pi = 2.50662827463100050242E0; #endif #ifdef DEC static unsigned short s2p[] = {0040440,0066230,0177661,0034055}; #define s2pi *(double *)s2p #endif #ifdef IBMPC static unsigned short s2p[] = {0x2706,0x1ff6,0x0d93,0x4004}; #define s2pi *(double *)s2p #endif #ifdef MIEEE static unsigned short s2p[] = { 0x4004,0x0d93,0x1ff6,0x2706 }; #define s2pi *(double *)s2p #endif /* approximation for 0 <= |y - 0.5| <= 3/8 */ #ifdef UNK static double P0[5] = { -5.99633501014107895267E1, 9.80010754185999661536E1, -5.66762857469070293439E1, 1.39312609387279679503E1, -1.23916583867381258016E0, }; static double Q0[8] = { /* 1.00000000000000000000E0,*/ 1.95448858338141759834E0, 4.67627912898881538453E0, 8.63602421390890590575E1, -2.25462687854119370527E2, 2.00260212380060660359E2, -8.20372256168333339912E1, 1.59056225126211695515E1, -1.18331621121330003142E0, }; #endif #ifdef DEC static unsigned short P0[20] = { 0141557,0155170,0071360,0120550, 0041704,0000214,0172417,0067307, 0141542,0132204,0040066,0156723, 0041136,0163161,0157276,0007747, 0140236,0116374,0073666,0051764, }; static unsigned short Q0[32] = { /*0040200,0000000,0000000,0000000,*/ 0040372,0026256,0110403,0123707, 0040625,0122024,0020277,0026661, 0041654,0134161,0124134,0007244, 0142141,0073162,0133021,0131371, 0042110,0041235,0043516,0057767, 0141644,0011417,0036155,0137305, 0041176,0076556,0004043,0125430, 0140227,0073347,0152776,0067251, }; #endif #ifdef IBMPC static unsigned short P0[20] = { 0x142d,0x0e5e,0xfb4f,0xc04d, 0xedd9,0x9ea1,0x8011,0x4058, 0xdbba,0x8806,0x5690,0xc04c, 0xc1fd,0x3bd7,0xdcce,0x402b, 0xca7e,0x8ef6,0xd39f,0xbff3, }; static unsigned short Q0[36] = { /*0x0000,0x0000,0x0000,0x3ff0,*/ 0x74f9,0xd220,0x4595,0x3fff, 0xe5b6,0x8417,0xb482,0x4012, 0x81d4,0x350b,0x970e,0x4055, 0x365f,0x56c2,0x2ece,0xc06c, 0xcbff,0xa8e9,0x0853,0x4069, 0xb7d9,0xe78d,0x8261,0xc054, 0x7563,0xc104,0xcfad,0x402f, 0xcdd5,0xfabf,0xeedc,0xbff2, }; #endif #ifdef MIEEE static unsigned short P0[20] = { 0xc04d,0xfb4f,0x0e5e,0x142d, 0x4058,0x8011,0x9ea1,0xedd9, 0xc04c,0x5690,0x8806,0xdbba, 0x402b,0xdcce,0x3bd7,0xc1fd, 0xbff3,0xd39f,0x8ef6,0xca7e, }; static unsigned short Q0[32] = { /*0x3ff0,0x0000,0x0000,0x0000,*/ 0x3fff,0x4595,0xd220,0x74f9, 0x4012,0xb482,0x8417,0xe5b6, 0x4055,0x970e,0x350b,0x81d4, 0xc06c,0x2ece,0x56c2,0x365f, 0x4069,0x0853,0xa8e9,0xcbff, 0xc054,0x8261,0xe78d,0xb7d9, 0x402f,0xcfad,0xc104,0x7563, 0xbff2,0xeedc,0xfabf,0xcdd5, }; #endif /* Approximation for interval z = sqrt(-2 log y ) between 2 and 8 * i.e., y between exp(-2) = .135 and exp(-32) = 1.27e-14. */ #ifdef UNK static double P1[9] = { 4.05544892305962419923E0, 3.15251094599893866154E1, 5.71628192246421288162E1, 4.40805073893200834700E1, 1.46849561928858024014E1, 2.18663306850790267539E0, -1.40256079171354495875E-1, -3.50424626827848203418E-2, -8.57456785154685413611E-4, }; static double Q1[8] = { /* 1.00000000000000000000E0,*/ 1.57799883256466749731E1, 4.53907635128879210584E1, 4.13172038254672030440E1, 1.50425385692907503408E1, 2.50464946208309415979E0, -1.42182922854787788574E-1, -3.80806407691578277194E-2, -9.33259480895457427372E-4, }; #endif #ifdef DEC static unsigned short P1[36] = { 0040601,0143074,0150744,0073326, 0041374,0031554,0113253,0146016, 0041544,0123272,0012463,0176771, 0041460,0051160,0103560,0156511, 0041152,0172624,0117772,0030755, 0040413,0170713,0151545,0176413, 0137417,0117512,0022154,0131671, 0137017,0104257,0071432,0007072, 0135540,0143363,0063137,0036166, }; static unsigned short Q1[32] = { /*0040200,0000000,0000000,0000000,*/ 0041174,0075325,0004736,0120326, 0041465,0110044,0047561,0045567, 0041445,0042321,0012142,0030340, 0041160,0127074,0166076,0141051, 0040440,0046055,0040745,0150400, 0137421,0114146,0067330,0010621, 0137033,0175162,0025555,0114351, 0135564,0122773,0145750,0030357, }; #endif #ifdef IBMPC static unsigned short P1[36] = { 0x8edb,0x9a3c,0x38c7,0x4010, 0x7982,0x92d5,0x866d,0x403f, 0x7fbf,0x42a6,0x94d7,0x404c, 0x1ba9,0x10ee,0x0a4e,0x4046, 0x463e,0x93ff,0x5eb2,0x402d, 0xbfa1,0x7a6c,0x7e39,0x4001, 0x9677,0x448d,0xf3e9,0xbfc1, 0x41c7,0xee63,0xf115,0xbfa1, 0xe78f,0x6ccb,0x18de,0xbf4c, }; static unsigned short Q1[32] = { /*0x0000,0x0000,0x0000,0x3ff0,*/ 0xd41b,0xa13b,0x8f5a,0x402f, 0x296f,0x89ee,0xb204,0x4046, 0x461c,0x228c,0xa89a,0x4044, 0xd845,0x9d87,0x15c7,0x402e, 0xba20,0xa83c,0x0985,0x4004, 0x0232,0xcddb,0x330c,0xbfc2, 0xb31d,0x456d,0x7f4e,0xbfa3, 0x061e,0x797d,0x94bf,0xbf4e, }; #endif #ifdef MIEEE static unsigned short P1[36] = { 0x4010,0x38c7,0x9a3c,0x8edb, 0x403f,0x866d,0x92d5,0x7982, 0x404c,0x94d7,0x42a6,0x7fbf, 0x4046,0x0a4e,0x10ee,0x1ba9, 0x402d,0x5eb2,0x93ff,0x463e, 0x4001,0x7e39,0x7a6c,0xbfa1, 0xbfc1,0xf3e9,0x448d,0x9677, 0xbfa1,0xf115,0xee63,0x41c7, 0xbf4c,0x18de,0x6ccb,0xe78f, }; static unsigned short Q1[32] = { /*0x3ff0,0x0000,0x0000,0x0000,*/ 0x402f,0x8f5a,0xa13b,0xd41b, 0x4046,0xb204,0x89ee,0x296f, 0x4044,0xa89a,0x228c,0x461c, 0x402e,0x15c7,0x9d87,0xd845, 0x4004,0x0985,0xa83c,0xba20, 0xbfc2,0x330c,0xcddb,0x0232, 0xbfa3,0x7f4e,0x456d,0xb31d, 0xbf4e,0x94bf,0x797d,0x061e, }; #endif /* Approximation for interval z = sqrt(-2 log y ) between 8 and 64 * i.e., y between exp(-32) = 1.27e-14 and exp(-2048) = 3.67e-890. */ #ifdef UNK static double P2[9] = { 3.23774891776946035970E0, 6.91522889068984211695E0, 3.93881025292474443415E0, 1.33303460815807542389E0, 2.01485389549179081538E-1, 1.23716634817820021358E-2, 3.01581553508235416007E-4, 2.65806974686737550832E-6, 6.23974539184983293730E-9, }; static double Q2[8] = { /* 1.00000000000000000000E0,*/ 6.02427039364742014255E0, 3.67983563856160859403E0, 1.37702099489081330271E0, 2.16236993594496635890E-1, 1.34204006088543189037E-2, 3.28014464682127739104E-4, 2.89247864745380683936E-6, 6.79019408009981274425E-9, }; #endif #ifdef DEC static unsigned short P2[36] = { 0040517,0033507,0036236,0125641, 0040735,0044616,0014473,0140133, 0040574,0012567,0114535,0102541, 0040252,0120340,0143474,0150135, 0037516,0051057,0115361,0031211, 0036512,0131204,0101511,0125144, 0035236,0016627,0043160,0140216, 0033462,0060512,0060141,0010641, 0031326,0062541,0101304,0077706, }; static unsigned short Q2[32] = { /*0040200,0000000,0000000,0000000,*/ 0040700,0143322,0132137,0040501, 0040553,0101155,0053221,0140257, 0040260,0041071,0052573,0010004, 0037535,0066472,0177261,0162330, 0036533,0160475,0066666,0036132, 0035253,0174533,0027771,0044027, 0033502,0016147,0117666,0063671, 0031351,0047455,0141663,0054751, }; #endif #ifdef IBMPC static unsigned short P2[36] = { 0xd574,0xe793,0xe6e8,0x4009, 0x780b,0xc327,0xa931,0x401b, 0xb0ac,0xf32b,0x82ae,0x400f, 0x9a0c,0x18e7,0x541c,0x3ff5, 0x2651,0xf35e,0xca45,0x3fc9, 0x354d,0x9069,0x5650,0x3f89, 0x1812,0xe8ce,0xc3b2,0x3f33, 0x2234,0x4c0c,0x4c29,0x3ec6, 0x8ff9,0x3058,0xccac,0x3e3a, }; static unsigned short Q2[32] = { /*0x0000,0x0000,0x0000,0x3ff0,*/ 0xe828,0x568b,0x18da,0x4018, 0x3816,0xaad2,0x704d,0x400d, 0x6200,0x2aaf,0x0847,0x3ff6, 0x3c9b,0x5fd6,0xada7,0x3fcb, 0xc78b,0xadb6,0x7c27,0x3f8b, 0x2903,0x65ff,0x7f2b,0x3f35, 0xccf7,0xf3f6,0x438c,0x3ec8, 0x6b3d,0xb876,0x29e5,0x3e3d, }; #endif #ifdef MIEEE static unsigned short P2[36] = { 0x4009,0xe6e8,0xe793,0xd574, 0x401b,0xa931,0xc327,0x780b, 0x400f,0x82ae,0xf32b,0xb0ac, 0x3ff5,0x541c,0x18e7,0x9a0c, 0x3fc9,0xca45,0xf35e,0x2651, 0x3f89,0x5650,0x9069,0x354d, 0x3f33,0xc3b2,0xe8ce,0x1812, 0x3ec6,0x4c29,0x4c0c,0x2234, 0x3e3a,0xccac,0x3058,0x8ff9, }; static unsigned short Q2[32] = { /*0x3ff0,0x0000,0x0000,0x0000,*/ 0x4018,0x18da,0x568b,0xe828, 0x400d,0x704d,0xaad2,0x3816, 0x3ff6,0x0847,0x2aaf,0x6200, 0x3fcb,0xada7,0x5fd6,0x3c9b, 0x3f8b,0x7c27,0xadb6,0xc78b, 0x3f35,0x7f2b,0x65ff,0x2903, 0x3ec8,0x438c,0xf3f6,0xccf7, 0x3e3d,0x29e5,0xb876,0x6b3d, }; #endif #ifdef ANSIPROT extern double polevl ( double, double *, int ); extern double p1evl ( double, double *, int ); extern double log ( double ); extern double sqrt ( double ); #else double polevl(), p1evl(), log(), sqrt(); #endif double ndtri(y0) double y0; { double x, y, z, y2, x0, x1; int code; if( y0 <= 0.0 ) { mtherr( "ndtri", DOMAIN ); return( -MAXNUM ); } if( y0 >= 1.0 ) { mtherr( "ndtri", DOMAIN ); return( MAXNUM ); } code = 1; y = y0; if( y > (1.0 - 0.13533528323661269189) ) /* 0.135... = exp(-2) */ { y = 1.0 - y; code = 0; } if( y > 0.13533528323661269189 ) { y = y - 0.5; y2 = y * y; x = y + y * (y2 * polevl( y2, P0, 4)/p1evl( y2, Q0, 8 )); x = x * s2pi; return(x); } x = sqrt( -2.0 * log(y) ); x0 = x - log(x)/x; z = 1.0/x; if( x < 8.0 ) /* y > exp(-32) = 1.2664165549e-14 */ x1 = z * polevl( z, P1, 8 )/p1evl( z, Q1, 8 ); else x1 = z * polevl( z, P2, 8 )/p1evl( z, Q2, 8 ); x = x0 - x1; if( code != 0 ) x = -x; return( x ); } thesias-3.1.1/src/newthesias3d.c000066400000000000000000010573711360777755100165500ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trgout, Valrie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ // LA FONCTION INVERSION A ETE REMPLACEE PAR SYSL ET LES DOUBLE POINTEURS PAR DES TABLEAUX DE DIM 2 /* Tout se programme sera ralis pour des individus indpendants */ #include #include #include #include #include #include //#include "mconf.h" //#include "definition.h" //DEB debut de definition.h /*********************************************************************************************/ /* Dclarations des Constantes propres SEM */ /***************************************************************************************** ****/ #define mymaxit 2501/*2501*/ /*nb d'itration*/ #define nburn 1500/*1500*/ /*nb de burns*/ #define seuilfisher 0.0000001 /*seuil de convergence de l'algorithme de fisher*/ #define maxrun 20 /*nombre d'iteration de l'aglorithme de ' */ #define maxn 100 /*maximum nb of estimated parameters*/ #define pi 3.141592654 #define maxloc 25 /*nb maximum de loci */ #define locmq 2 /*nb de genotype manquant autoris < nbloci-locmq*/ #define maxcov 12 /*nb maximum de covariables and interaction*/ #define maxhypor 4 /*maximal number of different hypotheses on OR/differences */ #define maxor 8 /*maximal number of OR/differences to be tested within the same hypothesis*/ #define maxconst 15 /*maximal number of constraints to be set */ #define maxadd 7 /*maximal number of additivity constraints to be set */ #define maxhypint 6 #define maxclass 4 #define TINY 1.0e-20; // Fin definition.h extern double igam ( double, double ); extern double igami ( double, double ); extern double polevl ( double, double *, int ); extern double ndtri (double); extern double gamma (double); extern double chdtrc(double, double); extern int mtherr(char *, int ); // VG //extern void affichage(FILE *,double , double ),affichage2(FILE *,double , double ),affich3(FILE *,double , double ); //extern void fisherscoring(), Xfisherscoring(); //extern void fishem(double *, double *, matrixp ),Xfishem(double *, double *, matrixp ); //extern double likelihood(double *, double *) , Xlikelihood(double *, double *); //extern double condlike(double *), Xcondlike(double *); //extern void phenomean(FILE *,FILE *,matrixp); //extern void tritime(),tripair(),coxtempo(); //extern void initlist(); //extern void coxrubin(double **); //extern void likematchpair(double *,double *,double *); //extern void breslow1(double *,double *,double *); //extern void matchpair(); //extern void fishpair(double *, double *,matrixp); //extern int ipow(int ,int); //extern double residuel(double *, double *); //extern void presence(),hapopres(),recodage(),distrmq(); //extern double sysl(double **, long ); //extern int coding(double); //extern void rsquare(double *,FILE *,FILE *); //extern void Xfishnull(double *,matrixp),fishnull(double *,matrixp); //extern void ludcmp(double **,int, int *, double *),lubksb(double **,int,int *, double *), inversion(double **,int ); //FIN VG //VG //extern void pairedfish(double **); // FIN VG // DEB definition.h /*********************************************************************************************/ /* Dclarations des Types */ /*********************************************************************************************/ typedef int vectgen[maxloc][2]; typedef double vectdon[maxcov]; typedef struct dhaplotype { /* Definition d'un haplotype */ int numnew,identif; /* Verifier comment est utilise identif */ short present, listall[maxloc]; /* Verifier si "present" est utilis */ char code[maxloc][2]; /* Verifier si code est utilis qu' la fin. Si oui,on pourrait ne pas le dfinir en global.*/ double frqle; struct dhaplotype *down; } dhaplotype; typedef struct dindividu { /* Definition d'un individu */ int tnbhapo,nblm; /* nb de paires haplotypiques possibles + nb de loci manquants */ int **idnb;/* ensemble des paires haplotypiques possibles*/ int hapest[2]; /* paire haplotypique attribuee */ vectgen marq; /* vecteur des genotypes*/ double phen[2],wgt; /*vecteur phenotypique */ vectdon z; /* vecteur des covariables */ //int gender; struct dindividu *next; } dindividu; typedef struct combgeno {double fquence; int settab[maxloc],place; int **sethap,nbcomb; struct combgeno *apres; } combgeno; typedef struct dliste { double *compo; double pival; struct dliste *proch; } dliste; /*FISHER SCORING*/ typedef double vectp[maxn]; typedef vectp matrixp[maxn]; /*********************************************************************************************/ /* Dclarations des variables */ /*********************************************************************************************/ double **tablo,*tabpi,*dmat2,*mdvs2,*modif2,mdvd2[maxn][maxn]; double *tabres; //dliste *listbase,*listp,*listold; dhaplotype *tnbhnew,*tnbhbase,*vect1,*vect2; dindividu *base,*suiv; int nbtotused; int nbhhypo; /* nb potentiel d'haplotypes*/ int nbloci; /* nb de loci tudies */ int maxhapair=0;/* maximum nb de paires haplotypiques possibles observees */ int nnt; /* nb of regression parameters to be estimated */ int *nbor; int ***tabinter,**tabhypo,**tadd,**tabint,**tabhypint; short *fcoda1; /*Indicateur d' eventuelle presence (1/0) des haplotypes */ int *fcoda2; /*Tableau de renumerotation des haplotypes eventuellement presents */ short msdata; /* indicateur de prise en compte des donnees manquantes*/ short ldmatrix; short letcod; /* indicateur de prise en compte de code pour les alleles*/ short chxt,offset; /* type of phenotype: binary or quantitative or survival */ int ajust; /* nb de variables d'ajustement */ short rsq,wald; int numajust[maxcov],idoffset; short nbcas,nbcasm,nbtem,nbtot,nbused; /* nb de cas avec et sans missing data, total de sujets */ short nbhf[2][3]; short haplozero; /* indicateur d'estimation des effets haplotypiques */ //int interor,hypoth,nbhypor,nbadd=0,hypint=0,intercov=0,xlnk=0; //VG 09112006 int interor=0,hypoth=0,nbhypor=0,nbadd=0,hypint=0,intercov=0,xlnk=0; double *alfreq,*hafreq; /*tableau des fqces allliques et haplotypiques sous independances*/ double *freqest, *tempfreq; /*tableau des fqces haplotypiques estimes et courantes*/ double **freqdist, **tempdist; /*tableau des fqces haplotypiques estimes et courantes chez les temoins/cas*/ int *tabmq; /* tableau des donnees manquantes */ char letter[maxloc][2]; /* tableau du codage des alleles */ double *moyeff,*effest,**vecbeta,**vecbetat,*moyfreq; double tempx; short *inclus; int *numhap,nbhest=0; double mean,ste,ste0,steres,meanste=0; double llambdaval,wbgama,wblamda; int nbcatego,nkat; int *nbsujktgo; FILE *parafile; enum {go, quit, restart} conti; int *itp,*nitp,*itptp,*nitptp; int nall, n; //FIN definition.h /*********************************************************************************************/ /* Dclarations des fonctions */ /*********************************************************************************************/ //void lecture(); void determhapo(); void nbhapo1(vectgen); void nbhapo0(vectgen); void initfreq(); void lecteffe(); void generhap(); double probatot(); double probacond(int); double Xprobatot(); double Xprobacond(int); double llambda(double ); double somdelai(); void polytomous(); void categorie(); void vpolyto(double **); double likepoly(double *,double *); //deb foncgener void ludcmp(double **a,int n,int *indx,double *d) { int i, imax,j,k; double big,dum,sum,temp; double *vv; vv=(double *)malloc((size_t) (n*sizeof(double))); *d=1.0; for (i=0;ibig) big=temp; if (big==0.0) printf("Singular matrix in routine LUDCMP\n"); vv[i]=1.0/big; } for (j=0;j=big) {big=dum;imax=i;} } if (j!=imax) {for (k=0;k=1;i--) {sum=b[i-1]; for (j=i+1;j<=n;j++) sum-=a[i-1][j-1]*b[j-1]; b[i-1]=sum/a[i-1][i-1]; } } void inversion(double **a,int n) {int *indx,i,j; double d,*col,**y; indx=(int *) malloc((size_t) (n*sizeof(int))); col=(double *) malloc((size_t) (n*sizeof(double ))); y=(double **) malloc((size_t) (n*sizeof(double *))); for (i=0;ipresent=0;vect1->identif=-1; if (fcoda1[vect1->numnew]==1) {vect1->present=1;vect1->identif=nbhhypo; fcoda2[vect1->numnew]=nbhhypo; nbhhypo+=1; } vect1=vect1->down; } vect1=NULL; } /*******************Renumerote les haplotypes des individus**********************************/ void recodage() {int i; suiv=base; do {for (i=0;itnbhapo;i++) {suiv->idnb[i][0]=fcoda2[suiv->idnb[i][0]]; suiv->idnb[i][1]=fcoda2[suiv->idnb[i][1]]; } suiv=suiv->next; }while ((suiv!=NULL) && (suiv->next!=NULL)); suiv= NULL; } /**********************************Calculs du nombre de donnees manquantes********************/ void distrmq() {int i,j; double stdd=0; for (i=0;i<2;i++) for (j=0;j<3;j++) nbhf[i][j]=0; mean=0; nbused=0; nbcas=0;nbtot=0;nbcasm=0; tabmq=(int *) malloc((size_t) ((nbloci+1)*sizeof(int))); for (i=0;inblm]+=1; if ((chxt==1) || (chxt==3) || (chxt==4) || (chxt==6)) {nbcas+=(suiv->phen[0]==1)*((msdata==0)*(suiv->nblm==0)+(msdata==1)*(suiv->nblmphen[0]==1)*(suiv->nblm==0); } if (chxt==2) {mean+=(suiv->phen[0])*((msdata==1)*(suiv->nblmnblm==0)); stdd+=(suiv->phen[0])*(suiv->phen[0])*((msdata==1)*(suiv->nblmnblm==0)); } nbused+=1*((msdata==1)*(suiv->nblmnblm==0)); nbtot+=1; suiv=suiv->next; } while ((suiv!=NULL) && (suiv->next!=NULL)); } else if (xlnk==1) {do {if (suiv->nblm==0) nbhf[(int) suiv->z[0]][0]++; tabmq[suiv->nblm]+=1; if ((chxt==1) || (chxt==3) || (chxt==4) || (chxt==6)) {nbcas+=(suiv->phen[0]==1)*((msdata==0)*(suiv->nblm==0)+(msdata==1)*(suiv->nblmphen[0]==1)*(suiv->nblm==0); /* ATTENTION QUAND IL Y AURA DES DONNES MANQUANTES AVEC CETTE OPTION*/ if (suiv->nblm==0) nbhf[(int) suiv->z[0]][1+(int) suiv->phen[0]]++; } if (chxt==2) {mean+=(suiv->phen[0])*((msdata==1)*(suiv->nblmnblm==0)); stdd+=(suiv->phen[0])*(suiv->phen[0])*((msdata==1)*(suiv->nblmnblm==0)); } nbused+=1*((msdata==1)*(suiv->nblmnblm==0)); nbtot+=1; suiv=suiv->next; }while ((suiv!=NULL) && (suiv->next!=NULL)); } suiv=NULL; if ((chxt==1) || (chxt==3) || (chxt==4) || (chxt==6)) {nbtem=nbused-nbcas;} ste=sqrt((stdd-mean*mean/nbused)/(nbused-1)); ste0=ste; mean/=nbused; } int coding(double val) {int i,j; short trouve=0; j=0;i=-1; while ((j%f%f\n",valse,valt); if ( (chxt==1) || (chxt==4)) {fprintf(outf,"OR = %.5f [%.5f - %.5f] ",exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse)); } else if (chxt==2) {fprintf(outf,"Diff = %.5f [%.5f - %.5f] ",valef,valef-1.96*valse,valef+1.96*valse); } else if ((chxt==3) || (chxt==5)) {fprintf(outf,"HRR = %.5f [%.5f - %.5f] ",exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse)); } if (valp>0) {fprintf(outf,"p=%f \n\n",chdtrc(1.0,valp)); } else fprintf(outf,"p is undefined \n\n"); } void affichage2(FILE *outf,double valef,double valse) {double valt, valp; valt=(valef/valse); valp=valt*valt; fprintf(outf,"%f\t%f\n",valse,valt); if ( (chxt==1) || (chxt==4)) { //fprintf(outf,"\t\t\tOR = %.5f [%.5f - %.5f] ",exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse)); fprintf(outf,"\t\tOR = %.5f [%.5f - %.5f] ",exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse));// } else if (chxt==2) { //fprintf(outf,"\t\t\tDiff = %.5f [%.5f - %.5f] ",valef,valef-1.96*valse,valef+1.96*valse); fprintf(outf,"\t\tDiff = %.5f [%.5f - %.5f] ",valef,valef-1.96*valse,valef+1.96*valse);// } else if ((chxt==3) || (chxt==5)) { //fprintf(outf,"\t\t\tHRR = %.5f [%.5f - %.5f] ",exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse)); fprintf(outf,"\t\tHRR = %.5f [%.5f - %.5f] ",exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse));// } if (valp>0) {fprintf(outf," p=%f\n\n",chdtrc(1.0,valp)); } else fprintf(outf," p is undefined \n\n"); } void affich3(FILE *outf,double valef, double valse) {double valt, valp; valt=(valef/valse); valp=valt*valt; if ((valef==0) && ( (valse==1) || (valse==0))) {if ( (chxt==1) || (chxt==4)) {fprintf(outf,"OR = 1 ");} else if (chxt==2) {fprintf(outf,"Diff = 0 ");} } else if (valse>0) {if ( (chxt==1) || (chxt==4)) {fprintf(outf,"OR = %.5f [%.5f - %.5f] ", exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse));} else if (chxt==2) {fprintf(outf,"Diff = %.5f [%.5f - %.5f] ",valef,valef-1.96*valse,valef+1.96*valse);} else if ((chxt==3) || (chxt==5)) {fprintf(outf,"HRR = %.5f [%.5f - %.5f] ", exp(valef),exp(valef-1.96*valse),exp(valef+1.96*valse));} if (valp>0) {fprintf(outf," p=%f\n",chdtrc(1.0,valp));} else fprintf(outf," p is undefined \n"); } else if (valef!=0) {if ( (chxt==1) || (chxt==4)) {fprintf(outf,"OR = %.5f ", exp(valef));} else if (chxt==2) {fprintf(outf,"Diff = %.5f ",valef); } } } void presence() {int i; suiv = base; for (i=0;itnbhapo>0) {inclus[suiv->hapest[0]]=1; inclus[suiv->hapest[1]]=1; } suiv = suiv->next; } while ((suiv!=NULL) && (suiv->next!=NULL)); } double sysl(double a[maxn][maxn], long nn) {/* Inversion et calcul du determinant d'une matrice */ long ia[maxn]; long i, j,kk, ii; double cf, d,val; int su1, su2; /*sysl*/ val = 1; kk = 1; while (kk <= nn) {ia[kk - 1] = 0; i = 1; su1 = 1; while ((i <= nn) && (su1==1)) {j = 1; su2 = 1; while ((j <= kk) && (su2==1)) {if (i == ia[j - 1]) {su2 = 0;} j++; } ii = i; i++; if (su2==1) {if (a[ii - 1][ii - 1] != 0.0) {ia[kk - 1] = ii; d = a[ii - 1][ii - 1]; su1 = 0; } } } if (su1==1) {printf("Matrice non inversible\n"); val=0; exit(0); } for (i = 0; i < nn; i++) {if (i + 1 != ii) {cf = a[i][ii - 1] / d; for (j = 0; j < nn; j++) {if (j + 1 != ii) a[i][j] -= a[ii - 1][j] * cf; } } } for (j = 0; j < nn; j++) {if (j + 1 != ii) {a[ii - 1][j] /= d; a[j][ii - 1] = -(a[j][ii - 1] / d); } } a[ii - 1][ii - 1] = 1.0 / d; val *= d; kk++; } return(val); } void frqcomb(combgeno *genotb,double *moyfreq) {int i,nbhet,hetero[maxloc],h0,h00,tnbh1,backha,numh,idp,idx; /*int **listhap;*/ short iref; double answ; tnbh1=0; nbhet=0; for (i=0;isettab[i]==1) {hetero[nbhet]=i+1;nbhet+=1;} } if (nbhet<2) {tnbh1=1; h0=0;h00=0; for (i=1;i<=nbloci;i++) {h0+=(genotb->settab[i-1]==2)*ipow(2,nbloci-i); h00+=(genotb->settab[i-1]>0)*ipow(2,nbloci-i); } h0=fcoda2[h0]; h00=fcoda2[h00]; answ=moyfreq[h0]*moyfreq[h00]*(2-(h0==h00)); genotb->sethap= (int **) malloc((size_t) (1*sizeof(int *))); for (i=0;isethap[i]=(int *)malloc((size_t) (2*sizeof(int))); genotb->sethap[0][0]=h0; genotb->sethap[0][1]=h00; } else {tnbh1=ipow(2,nbhet-1); genotb->sethap= (int **) malloc((size_t) (tnbh1*sizeof(int *))); for (i=0;isethap[i]=(int *)malloc((size_t) (2*sizeof(int))); //listhap=(int **)malloc((size_t) (tnbh1*sizeof(int *))); //for (i=0;isettab[i-1]!=1) {backha+=(genotb->settab[i-1]==2)*ipow(2,nbloci-i);} } for (i=0;isethap[i][0]=backha; genotb->sethap[i][1]=backha+ipow(2,nbloci-hetero[0]); } for (i=1;i<=nbhet-1;i++) {numh=0;idx=ipow(2,nbhet-1-i);iref=1;idp=1; do {genotb->sethap[numh][0]+=(iref==2)*ipow(2,nbloci-hetero[i]); genotb->sethap[numh][1]+=(iref==1)*ipow(2,nbloci-hetero[i]); idp++; if (idp>idx) {if (iref==1) {iref=2;} else {iref=1;} idp=1; } numh++; }while (numhsethap[i][0]=fcoda2[genotb->sethap[i][0]]; genotb->sethap[i][1]=fcoda2[genotb->sethap[i][1]]; h0=genotb->sethap[i][0];h00=genotb->sethap[i][1]; answ+=moyfreq[h0]*moyfreq[h00]*(2-(h0==h00)); } // listhap=NULL; // free (listhap); } genotb->nbcomb=tnbh1; genotb->fquence=answ; } void rsquare(double *moyfreq,FILE *outfile,FILE *outres) {int ixpar,i,trouve,nctab=0,ll,j,h0,h00; combgeno *genotabase,*genotab1,*genotab2; double *expect,numera,denomi; char l; genotabase=(combgeno *)malloc((size_t) (sizeof(combgeno))); /* ATTENTION AU DONNES MAQNAUTENS Pour l'instant supposant qu'il n'y en a pas*/ ixpar=0; genotab1=genotabase; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) {if (suiv->nblm==0) {if (ixpar==0) {for (i=0;isettab[i]=(suiv->marq[i][0]+suiv->marq[i][1]-2); genotab1->place=nctab; frqcomb(genotab1,moyfreq); genotab1->apres=(combgeno *)malloc((size_t) (sizeof(combgeno))); genotab1=genotab1->apres; ixpar=1; nctab++; } else {genotab2=genotabase; trouve=0; while ((genotab2!=genotab1) && (trouve==0)) {i=0;while ((genotab2->settab[i]==(suiv->marq[i][0]+suiv->marq[i][1]-2)) && (iapres; } if (trouve==0) {for (i=0;isettab[i]=(suiv->marq[i][0]+suiv->marq[i][1]-2); genotab1->place=nctab; frqcomb(genotab1,moyfreq); genotab1->apres=(combgeno *)malloc((size_t) (sizeof(combgeno))); genotab1=genotab1->apres; nctab++; } } } suiv = suiv->next; } genotab1->apres=NULL; genotab1=NULL; expect=(double *)malloc((size_t) (nbhhypo*sizeof(double))); for (i=0;i\n"); fprintf(outfile,"\n"); fprintf(outfile,"\nHaplotypic R2 information\n\n"); fprintf(outfile,"\n"); fprintf(outfile," FrequencyR Square\n"); fprintf(outfile," \n\n"); fprintf(outres,"\t\tHaplotypic R2 information\n\n"); vect1=tnbhbase;i=0; while (vect1!=NULL) {if (vect1->present==1) {ll=fcoda2[vect1->numnew]; if (moyfreq[ll]>0) {//printf("I=%d Fq=%lf\t",ll,moyfreq[ll]); expect[ll]=0.0; genotab1=genotabase; while (genotab1->apres!=NULL) {numera=0.0;denomi=0.0; for (j=0;jnbcomb;j++) {h0=genotab1->sethap[j][0];h00=genotab1->sethap[j][1]; denomi+=moyfreq[h0]*moyfreq[h00]; numera+=moyfreq[h0]*moyfreq[h00]*((ll==h0)+(ll==h00)); } expect[ll]+=genotab1->fquence*(numera/denomi)*(numera/denomi); genotab1=genotab1->apres; } genotab1=NULL; expect[ll]-=4*moyfreq[ll]*moyfreq[ll]; expect[ll]/=2*moyfreq[ll]*(1-moyfreq[ll]); //printf("R2 =%lf\n",expect[ll]); fprintf(outfile,"Haplotype [%d] \n",i); fprintf(outfile,""); fprintf(outres,"Haplotype [%d] \t",i); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l); fprintf(outres,"%c",l); } fprintf(outfile,""); fprintf(outfile,"%f",moyfreq[ll]); fprintf(outres," %f\t",moyfreq[ll]); fprintf(outfile,"R2 = %f \n",expect[ll]); fprintf(outres,"R2 = %f\t\n",expect[ll]); } } i++; vect1=vect1->down; } /* NEW DAVID */ free (genotabase);genotabase=NULL; free (genotab1);genotab1=NULL; free (genotab2);genotab2=NULL; free (expect);expect=NULL; } void fishnull(double *frqsem,matrixp sfisher) {int i,j,dimf,dimf2; double h1,h2,like,likeli,val3; double *derivfrq,*deriv;int *place; double fisher[maxn][maxn]; printf("Running Variance Estimation\n"); place=(int *) malloc((size_t) (nbhhypo*sizeof(int))); for (i=0;i0) {place[i]=j;j++;} dimf=j-1;dimf2=j; //fisher=(double **) malloc((size_t) (dimf*sizeof(double *))); //for (i=0;inext!=NULL)) {for (i=0;itnbhapo;i++) {like=0; h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {like=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); /*Calcul des drivees premieres par rapport aux frequences */ if (suiv->idnb[i][0]==suiv->idnb[i][1]) {derivfrq[place[suiv->idnb[i][0]]]+=2*frqsem[suiv->idnb[i][0]];} else {derivfrq[place[suiv->idnb[i][0]]]+=2*frqsem[suiv->idnb[i][1]]; derivfrq[place[suiv->idnb[i][1]]]+=2*frqsem[suiv->idnb[i][0]]; } likeli+=like; }/* if */ }/* for i*/ /* ATTENTION A LA PREMIERE FREQUENCE D'OU LE -1 */ if (likeli>0) {for (i=0;inext; }/* while */ printf("Inverting Variance Matrix....\n"); sysl(fisher,dimf); for (i=0;i0) {place[i]=j;j++;} dimf=j-1;dimf2=j; //fisher=(double **) malloc((size_t) (dimf*sizeof(double *))); //for (i=0;inext!=NULL)) {for (i=0;iz[0]==1) {for (i=0;itnbhapo;i++) {like=0; h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {like=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); /*Calcul des drivees premieres par rapport aux frequences */ if (suiv->idnb[i][0]==suiv->idnb[i][1]) {derivfrq[place[suiv->idnb[i][0]]]+=2*frqsem[suiv->idnb[i][0]];} else {derivfrq[place[suiv->idnb[i][0]]]+=2*frqsem[suiv->idnb[i][1]]; derivfrq[place[suiv->idnb[i][1]]]+=2*frqsem[suiv->idnb[i][0]]; } likeli+=like; } /* if */ }/* for i*/ /* ATTENTION A LA PREMIERE FREQUENCE D'OU LE -1 */ } else if ((int) suiv->z[0]==0) {for (i=0;itnbhapo;i++) {like=0; h1=frqsem[suiv->idnb[i][0]]; if (h1>0) {like=h1; /*Calcul des drivees premieres par rapport aux frequences */ derivfrq[place[suiv->idnb[i][0]]]+=1; likeli+=like; } /* if */ } } if (likeli>0) {for (i=0;inext; }/* while */ printf("Inverting Variance Matrix....\n"); sysl(fisher,dimf); for (i=0;inext!=NULL)) { trouve=0; parcour=base; while ( (parcour!=NULL) && (parcour!=suiv) && (trouve==0)) {if (suiv->phen[1]>=parcour->phen[1]) {trouve=1;break;} parcour=parcour->next; } if (trouve==1) {newsui=base; proch=suiv->next; if (parcour==base) {newsui=base; while (newsui->next!=suiv) {newsui=newsui->next;} newsui->next=proch; base=suiv; suiv->next=parcour; } else {newsui=base; while (newsui->next!=parcour) {newsui=newsui->next;} newsui->next=suiv; newsui=parcour; while (newsui->next!=suiv) {newsui=newsui->next;} newsui->next=proch; suiv->next=parcour; } suiv=proch; } else suiv=suiv->next; } suiv= NULL; proch= NULL; parcour=NULL; newsui=NULL; free (newsui);free (proch);free(parcour); } void tripair() {dindividu *parcour,*newsui,*proch; int trouve; suiv=base; while ((suiv!=NULL) && (suiv->next!=NULL)) { trouve=0; parcour=base; while ( (parcour!=NULL) && (parcour!=suiv) && (trouve==0)) {if (suiv->phen[1]==parcour->phen[1]) {trouve=1;break;} parcour=parcour->next; } if (trouve==1) {newsui=base; proch=suiv->next; if (parcour==base) {newsui=base; while (newsui->next!=suiv) {newsui=newsui->next;} newsui->next=proch; base=suiv; suiv->next=parcour; } else {newsui=base; while (newsui->next!=parcour) {newsui=newsui->next;} newsui->next=suiv; newsui=parcour; while (newsui->next!=suiv) {newsui=newsui->next;} newsui->next=proch; suiv->next=parcour; } suiv=proch; } else suiv=suiv->next; } suiv= NULL; proch= NULL; parcour=NULL; newsui=NULL; free (newsui);free (proch);free(parcour); } /* vraisemblance Cox partielle avec tableau*/ void coxtablo() {double val1,val2,val3,varest,det,pibeta,expos; int hh1,hh2,h1,h2,v1,v2,nused=0,i,j,nls; for (i=0;itnbhapo>0) {if (nls==0) {for (i=0;iz[j]; if (haplozero==0) {h1=suiv->hapest[0];h2=suiv->hapest[1];hh1=coding(h1);hh2=coding(h2); if (hh1>0) {val1+=effest[hh1];} if (hh2>0) {val1+=effest[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*effest[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1));} } expos=exp(val1); for (i=0;iz[i];} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {tablo[nls][nitptp[hh1]]+=expos;} if ((hh2>0) && (itptp[hh2]==1)) {tablo[nls][nitptp[hh2]]+=expos;} if (hypoth>0) {for (i=0;i-1)) {tablo[nls][nitptp[hh1]]+=expos;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {tablo[nls][nitptp[hh2]]+=expos;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos; tablo[nls][nitptp[tabinter[j][i][0]-1]]+=expos; } if (hh2==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos; tablo[nls][nitptp[tabinter[j][i][0]-1]]+=expos; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos; tablo[nls][nitptp[tabinter[j][0][0]-1]]-=expos; } if (hh2==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos; tablo[nls][nitptp[tabinter[j][0][0]-1]]-=expos; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos;} if (hh2==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos;} } else {if (hh1==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos; tablo[nls][nitptp[tabinter[j][i][0]-1]]+=expos; tablo[nls][nitptp[tabinter[j][0][0]-1]]-=expos; } if (hh2==tabinter[j][i][1]-1) {tablo[nls][nitptp[tabinter[j][0][1]-1]]+=expos; tablo[nls][nitptp[tabinter[j][i][0]-1]]+=expos; tablo[nls][nitptp[tabinter[j][0][0]-1]]-=expos; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } tabpi[nls]+=expos; nls++; if (suiv->phen[0]==1.0) {for (i=0;iz[i];} if (haplozero==0) {hh1=coding(suiv->hapest[0]); hh2=coding(suiv->hapest[1]); if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=1;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=1;} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=1;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } /*ATTENTION L'INTERCEPT PEUT NE PAS ETRE CALCULE D'OU (N-1) */ for (i=0;inext; } while ( (suiv!=NULL) && (suiv->next!=NULL)) ; suiv=NULL; /*ATTENTION L'INTERCEPT PEUT NE PAS ETRE CALCULE D'OU (N-1) */ sysl(mdvd2,n-1); for (i=0;i-1) {effest[i]+=modif2[nitptp[i]-1];} if (hypoth>0) {for (i=0;i1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]-effest[tabinter[j][0][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]; } else {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]-effest[tabinter[j][0][0]-1]; } } } } if (hypint>0) {for (i=0;inext!=NULL)) {nused+=1-((suiv->tnbhapo>0) && (suiv->phen[0]==1.0)); if ( (suiv->tnbhapo>0) && (suiv->phen[0]==1.0)) {for (i=0;inext!=NULL) && (parcour->phen[1]>=suiv->phen[1])) {if ((parcour->tnbhapo>0)) {val1=0; for (j=0;jz[j]; if (haplozero==0) {h1=parcour->hapest[0]; h2=parcour->hapest[1]; hh1=coding(h1); hh2=coding(h2); if (hh1>0) {val1+=effest[hh1];} if (hh2>0) {val1+=effest[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*effest[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } expos=exp(val1); for (i=0;iz[i];} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=expos;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=expos;} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=expos;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=expos;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } pibeta+=expos; } parcour=parcour->next; }/* FIN DE PARCOUR*/ parcour=NULL; for (i=0;iz[i];} if (haplozero==0) {hh1=coding(suiv->hapest[0]); hh2=coding(suiv->hapest[1]); if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=1;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=1;} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=1;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } /*ATTENTION L'INTERCEPT PEUT NE PAS ETRE CALCULE D'OU (N-1) */ for (i=0;inext; } sysl(mdvd2,n-1); for (i=1;i-1) && (nitptp[j]>-1)) vintra[i][j]+=mdvd2[nitptp[i]-1][nitptp[j]-1]; /* NEW DAVID*/ free(parcour);parcour=NULL; } void breslow1(double *frqsem,double *lgoddsem,double *vtabres) {double val1,v1,vrais,h1,h2,like,p1,p2,vraisfa=0,vv2,pib2=0,pib0=0,pib1=0,expos1,expos2; int hh1,hh2/*,idx*/,i,j; dindividu *parcour; for (i=0;i<3;i++) {tabres[i]=0;vtabres[i]=0;} suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) /*ATTENTION AU PB EVENTUEL DES DONNES MANQUANTES*/ {if ( (suiv->tnbhapo>0) && (suiv->phen[0]==1.0)) {parcour=base; pib2=0;pib0=0;pib1=0; while ((parcour!=NULL) && (parcour->next!=NULL) && (parcour->phen[1]>=suiv->phen[1])) {if ( /*(parcour->phen[1]>=suiv->phen[1]) &&*/ (parcour->tnbhapo>0) ) {expos1=0; pib0+=1; val1=0; for (j=0;jz[j]; expos1=exp(val1);expos2=0.0; if (haplozero==0) {p2=0.0; for (i=0;itnbhapo;i++) {h1=frqsem[parcour->idnb[i][0]];h2=frqsem[parcour->idnb[i][1]]; v1=0;p1=0.0; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(parcour->idnb[i][0]==parcour->idnb[i][1])); hh1=coding(parcour->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(parcour->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } expos2+=p1*exp(v1); p2+=p1; } expos2/=p2; } else {expos2=1.0;} pib2+=expos1*expos2; pib1+=expos1; } parcour=parcour->next; } p2=0.0; v1=0;for (j=0;jz[j]; expos2=0.0; tabres[1]=exp(v1); if (haplozero==0) {p2=0.0; for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; v1=0;p1=0.0; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } expos2+=p1*exp(v1); p2+=p1; } expos2/=p2; } else expos2=1.0; tabres[2]=tabres[1]*=expos2; /* BRESLOW SANS AUCUN EFFET*/ tabres[0]=1/pib0; vtabres[0]-=log(tabres[0]); if (tabres[1]>0) {vtabres[1]-=log(tabres[1]/pib1);} if (tabres[2]>0) {vtabres[2]-=log(tabres[2]/pib2);} //if (vrais>0) {vraisfa -= log(vrais/pib2);} } suiv= suiv->next; } //tabres=NULL;free (tabres); //return(vtabres); parcour=NULL; free (parcour); } void likematchpair(double *frqsem,double *lgoddsem,double *vtabres) {double val1,v1,vrais,h1,h2,like,p1,p2,vraisfa=0,vv2,pib2=0,pib0=0,pib1=0,expos1,expos2; int hh1,hh2/*,idx*/,i,j; dindividu *parcour; for (i=0;i<3;i++) {tabres[i]=0;vtabres[i]=0;} suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) /*ATTENTION AU PB EVENTUEL DES DONNES MANQUANTES*/ {if ( (suiv->tnbhapo>0) && (suiv->phen[0]==1.0)) {parcour=base; pib2=0;pib0=0;pib1=0; while ((parcour!=NULL) && (parcour->next!=NULL) && (parcour->phen[1]<=suiv->phen[1])) {if ((parcour->tnbhapo>0) && (parcour->phen[1]==suiv->phen[1])) {expos1=0; pib0+=1; val1=0; for (j=0;jz[j]; expos1=exp(val1);expos2=0.0; if (haplozero==0) {p2=0.0; for (i=0;itnbhapo;i++) {h1=frqsem[parcour->idnb[i][0]];h2=frqsem[parcour->idnb[i][1]]; v1=0;p1=0.0; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(parcour->idnb[i][0]==parcour->idnb[i][1])); hh1=coding(parcour->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(parcour->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } expos2+=p1*exp(v1); p2+=p1; } expos2/=p2; } else {expos2=1.0;} pib2+=expos1*expos2; pib1+=expos1; } parcour=parcour->next; } p2=0.0; v1=0;for (j=0;jz[j]; expos2=0.0; tabres[1]=exp(v1); if (haplozero==0) {p2=0.0; for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; v1=0;p1=0.0; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } expos2+=p1*exp(v1); p2+=p1; } expos2/=p2; } else expos2=1.0; tabres[2]=tabres[1]*=expos2; /* BRESLOW SANS AUCUN EFFET*/ tabres[0]=1/pib0; vtabres[0]-=log(tabres[0]); if (tabres[1]>0) {vtabres[1]-=log(tabres[1]/pib1);} if (tabres[2]>0) {vtabres[2]-=log(tabres[2]/pib2);} } suiv= suiv->next; } //tabres=NULL; free (tabres); parcour=NULL; free (parcour); } /*Algorithme NR pour vraisemblance Cox partielle*/ void matchpair() {double val1,val2,val3,varest,det,pibeta,expos; int hh1,hh2,h1,h2,v1,v2,nused=0,i,j; dindividu *parcour; for (i=0;inext!=NULL)) {nused+=1-((suiv->tnbhapo>0) && (suiv->phen[0]==1.0)); if ( (suiv->tnbhapo>0) && (suiv->phen[0]==1.0)) {for (i=0;inext!=NULL) && (parcour->phen[1]<=suiv->phen[1])) {if ((parcour->tnbhapo>0) && (parcour->phen[1]==suiv->phen[1])) { val1=0; //val1=2*effest[0]; for (j=0;jz[j]; if (haplozero==0) {h1=parcour->hapest[0]; h2=parcour->hapest[1]; hh1=coding(h1); hh2=coding(h2); if (hh1>0) {val1+=effest[hh1];} if (hh2>0) {val1+=effest[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*effest[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } expos=exp(val1); for (i=0;iz[i];} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=expos;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=expos;} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=expos;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=expos;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=expos; dmat2[nitptp[tabinter[j][i][0]-1]]+=expos; dmat2[nitptp[tabinter[j][0][0]-1]]-=expos; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } pibeta+=expos; } parcour=parcour->next; }/* FIN DE PARCOUR*/ for (i=0;iz[i];} if (haplozero==0) {hh1=coding(suiv->hapest[0]); hh2=coding(suiv->hapest[1]); if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=1;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=1;} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=1;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } /*ATTENTION L'INTERCEPT PEUT NE PAS ETRE CALCULE D'OU (N-1) */ for (i=0;inext; } /*ATTENTION L'INTERCEPT PEUT NE PAS ETRE CALCULE D'OU (N-1) */ sysl(mdvd2,n-1); for (i=0;i-1) {effest[i]+=modif2[nitptp[i]-1];} if (hypoth>0) {for (i=0;i1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]-effest[tabinter[j][0][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]; } else {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]-effest[tabinter[j][0][0]-1]; } } } } if (hypint>0) {for (i=0;i0) {place2[i]=j;j++;} tempfq=(double **) malloc((size_t) (nbhest*sizeof(double *))); for (i=0;inext!=NULL)) {if ((suiv->tnbhapo>0) && (suiv->phen[0]==1.0)) {for (i=0;inext!=NULL) && (parcour->phen[1]<=suiv->phen[1])) {if ((parcour->tnbhapo>0) && (parcour->phen[1]==suiv->phen[1])) { val1=0; for (j=0;jz[j]; expos1=exp(val1); for (j=0;jz[j];} pibet+=expos1; } else {p2=0.0;expos2=0.0; for (i=0;itnbhapo;i++) {h1=frqsem[parcour->idnb[i][0]];h2=frqsem[parcour->idnb[i][1]]; p1=0.0;v1=0; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(parcour->idnb[i][0]==parcour->idnb[i][1])); hh1=coding(parcour->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(parcour->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } val1=exp(v1); if (parcour->idnb[i][0]==parcour->idnb[i][1]) {tempfq[place2[parcour->idnb[i][0]]][0]+=2*frqsem[parcour->idnb[i][0]]*val1; tempfq[place2[parcour->idnb[i][0]]][1]+=2*frqsem[parcour->idnb[i][0]]; } else {tempfq[place2[parcour->idnb[i][0]]][0]+=2*frqsem[parcour->idnb[i][1]]*val1; tempfq[place2[parcour->idnb[i][1]]][0]+=2*frqsem[parcour->idnb[i][0]]*val1; tempfq[place2[parcour->idnb[i][0]]][1]+=2*frqsem[parcour->idnb[i][1]]; tempfq[place2[parcour->idnb[i][1]]][1]+=2*frqsem[parcour->idnb[i][0]]; } val1=p1*exp(v1); p2+=p1; expos2+=val1; if ((hh1>0) && (itp[hh1]==1)) {tempod[nitp[hh1]]+=val1;} if ((hh2>0) && (itp[hh2]==1)) {tempod[nitp[hh2]]+=val1;} if (hypoth>0) {for (j=0;j-1) ) {tempod[nitp[hh1]]+=val1;} if ( (hh2==v2-1) && (nitp[hh2]>-1) ) {tempod[nitp[hh2]]+=val1;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][k][0]-1]]+=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][k][0]-1]]+=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;} if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;} } else {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;tempod[nitp[tabinter[j][k][0]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;tempod[nitp[tabinter[j][k][0]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } } } } } for (j=0;jz[tabint[j][1]-1]*((hh1==(tabint[j][0]-1))+(hh2==(tabint[j][0]-1))); } } } for (i=0;initp[nbhest+ajust-1])) {derivodd[i]+=tempod[i]*expos1/p2;} } expos2/=p2; for (j=0;jz[j];} pibet+=(expos1*expos2); } } parcour=parcour->next; } for (i=0;iz[i]; for (i=0;itnbhapo;i++) {hh1=coding(suiv->idnb[i][0]);hh2=coding(suiv->idnb[i][1]); h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {p1=0.0;v1=0; p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); p2+=p1; if (hh1>0) {v1+=lgoddsem[hh1];} if (hh2>0) {v1+=lgoddsem[hh2];} for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } val1=exp(v1); if (suiv->idnb[i][0]==suiv->idnb[i][1]) {tempfq[place2[suiv->idnb[i][0]]][0]+=2*frqsem[suiv->idnb[i][0]]*val1; tempfq[place2[suiv->idnb[i][0]]][1]+=2*frqsem[suiv->idnb[i][0]]; } else {tempfq[place2[suiv->idnb[i][0]]][0]+=2*frqsem[suiv->idnb[i][1]]*val1; tempfq[place2[suiv->idnb[i][1]]][0]+=2*frqsem[suiv->idnb[i][0]]*val1; tempfq[place2[suiv->idnb[i][0]]][1]+=2*frqsem[suiv->idnb[i][1]]; tempfq[place2[suiv->idnb[i][1]]][1]+=2*frqsem[suiv->idnb[i][0]]; } val1=p1*exp(v1); expos2+=val1; if ((hh1>0) && (itp[hh1]==1)) {tempod[nitp[hh1]]+=val1;} if ((hh2>0) && (itp[hh2]==1)) {tempod[nitp[hh2]]+=val1;} if (hypoth>0) {for (j=0;j-1) ) {tempod[nitp[hh1]]+=val1;} if ( (hh2==v2-1) && (nitp[hh2]>-1) ) {tempod[nitp[hh2]]+=val1;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][k][0]-1]]+=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][k][0]-1]]+=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;} if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;} } else {if (hh1==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;tempod[nitp[tabinter[j][k][0]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitp[tabinter[j][0][1]-1]]+=val1;tempod[nitp[tabinter[j][k][0]-1]]+=val1; tempod[nitp[tabinter[j][0][0]-1]]-=val1; } } } } } for (j=0;jz[tabint[j][1]-1]*((hh1==(tabint[j][0]-1))+(hh2==(tabint[j][0]-1))); } } } for (i=0;initp[nbhest+ajust-1])) {derivodd[i]+=(tempod[i]/expos2);} } for (i=0;inext; } //help=(double **) malloc((size_t) ((n-1)*sizeof(double *))); //for (i=0;inext!=NULL)) {if ((suiv->tnbhapo>0) && (suiv->phen[0]==1.0)) {for (i=0;inext!=NULL) && (parcour->phen[1]<=suiv->phen[1])) {if ((parcour->tnbhapo>0) && (parcour->phen[1]==suiv->phen[1])) {val1=0; for (j=0;jz[j]; expos1=exp(val1); for (j=0;jz[j];} pibet+=expos1; } else {p2=0.0;expos2=0.0;v1=0.0; hh1=coding(parcour->hapest[0]);if (hh1>0) {v1+=effest[hh1];} hh2=coding(parcour->hapest[1]);if (hh2>0) {v1+=effest[hh2];} for (j=0;jz[tabint[j][1]-1]*effest[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } val1=exp(v1); p2=1.0; expos2+=val1; if ((hh1>0) && (itptp[hh1]==1)) {tempod[nitptp[hh1]]+=val1;} if ((hh2>0) && (itptp[hh2]==1)) {tempod[nitptp[hh2]]+=val1;} for (j=0;j-1) ) {tempod[nitptp[hh1]]+=val1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1) ) {tempod[nitptp[hh2]]+=val1;} } for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][k][0]-1]]+=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][k][0]-1]]+=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;} if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;} } else {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][k][0]-1]]+=val1; tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][k][0]-1]]+=val1; tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } } } } for (j=0;jz[tabint[j][1]-1]*((hh1==(tabint[j][0]-1))+(hh2==(tabint[j][0]-1))); } for (i=0;initptp[nbhest+ajust-1])) {dmat2[i]+=tempod[i]*expos1/p2;} } expos2/=p2; for (j=0;jz[j];} pibet+=(expos1*expos2); } } parcour=parcour->next; } for (i=0;iz[i]; for (i=0;ihapest[0]);hh2=coding(suiv->hapest[1]); v1=0;p2=1; if (hh1>0) {v1+=effest[hh1];} if (hh2>0) {v1+=effest[hh2];} for (j=0;jz[tabint[j][1]-1]*effest[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } val1=exp(v1); expos2+=val1; if ((hh1>0) && (itptp[hh1]==1)) {tempod[nitptp[hh1]]+=val1;} if ((hh2>0) && (itptp[hh2]==1)) {tempod[nitptp[hh2]]+=val1;} for (j=0;j-1) ) {tempod[nitptp[hh1]]+=val1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1) ) {tempod[nitptp[hh2]]+=val1;} } for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1; tempod[nitptp[tabinter[j][k][0]-1]]+=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1; tempod[nitptp[tabinter[j][k][0]-1]]+=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1; tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1; tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } } else if ((tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;} if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;} } else {if (hh1==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][k][0]-1]]+=val1; tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][k][1]-1) {tempod[nitptp[tabinter[j][0][1]-1]]+=val1;tempod[nitptp[tabinter[j][k][0]-1]]+=val1; tempod[nitptp[tabinter[j][0][0]-1]]-=val1; } } } } for (j=0;jz[tabint[j][1]-1]*((hh1==(tabint[j][0]-1))+(hh2==(tabint[j][0]-1))); } for (i=0;initptp[nbhest+ajust-1])) {dmat2[i]+=(tempod[i]/expos2);} } } for (i=0;inext; } /*ATTENTION L'INTERCEPT PEUT NE PAS ETRE CALCULE D'OU (N-1) */ sysl(mdvd2,n-1); for (i=1;i-1) && (nitptp[j]>-1)) vintra[i][j]+=mdvd2[nitptp[i]-1][nitptp[j]-1]; parcour=NULL;free (parcour); } void fisherscoring() /* NEW ONE CORRIGEE POUR LE BUG DE PLP*/ {double val1,val2,val3,varest,det; int hh1,hh2,v1,v2,nused=0,i,j; char rep; for (i=0;inext!=NULL)) {if (suiv->tnbhapo>0) {for (i=0;iphen[0]; val2=2*effest[0]; for (i=0;iz[i]; if ((chxt==1) && (offset==1)) val2+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(suiv->hapest[0]);if (hh1>0) {val2+=effest[hh1];} hh2=coding(suiv->hapest[1]);if (hh2>0) {val2+=effest[hh2];} for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1));} } if ((int) chxt==1) {val3=exp(val2)/(1+exp(val2)); val1=-val3;varest=val1; dmat2[0]+=2*val1; for (i=0;iz[i]*val1;} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=val1;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=val1;} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=val1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=val1;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1; dmat2[nitptp[tabinter[j][i][0]-1]]+=val1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1; dmat2[nitptp[tabinter[j][i][0]-1]]+=val1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1; dmat2[nitptp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1; dmat2[nitptp[tabinter[j][0][0]-1]]-=val1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1; dmat2[nitptp[tabinter[j][i][0]-1]]+=val1; dmat2[nitptp[tabinter[j][0][0]-1]]-=val1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=val1; dmat2[nitptp[tabinter[j][i][0]-1]]+=val1; dmat2[nitptp[tabinter[j][0][0]-1]]-=val1; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } if ((int) suiv->phen[0]==1) {dmat2[0]+=2; for (i=0;iz[i];} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=1;} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=1;} for (i=0;i-1)) {dmat2[nitptp[hh1]]+=1;} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=1;} } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1;} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=1; dmat2[nitptp[tabinter[j][i][0]-1]]+=1; dmat2[nitptp[tabinter[j][0][0]-1]]-=1; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } } for (i=0;iz[i]; if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=dmat2[0];} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=dmat2[0];} for (i=0;i-1)) {dmat2[nitptp[hh1]]+=dmat2[0];} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=dmat2[0];} } for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=dmat2[0]; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=dmat2[0]; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=dmat2[0]; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=dmat2[0]; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0];} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0];} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=dmat2[0]; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=dmat2[0]; } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1));} } for (i=0;inext; } sysl(mdvd2,n); for (i=0;i-1) {effest[i]+=modif2[nitptp[i]];j++;} if (hypoth>0) {for (i=0;i1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]-effest[tabinter[j][0][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]; } else {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]-effest[tabinter[j][0][0]-1]; } } } } if (hypint>0) {for (i=0;inext!=NULL)) {if (suiv->tnbhapo>0) {val1=suiv->phen[0];val2=2*effest[0]; for (i=0;iz[i]; if (haplozero==0) {hh1=coding(suiv->hapest[0]);if (hh1>0) {val2+=effest[hh1];} hh2=coding(suiv->hapest[1]);if (hh2>0) {val2+=effest[hh2];} if (nbadd>0) {for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } steres+=(val1-val2)*(val1-val2); nused+=1; } suiv=suiv->next; } ste=sqrt(steres/(nused-1)); } for (i=0;inext!=NULL)) {if (suiv->tnbhapo>0) {if ((int) suiv->z[0]==1) {for (i=0;iphen[0]; val2=effest[0]; for (i=0;iz[i]; if (offset==1) val2+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(suiv->hapest[0]);if (hh1>0) {val2+=0.5*effest[hh1];} hh2=coding(suiv->hapest[1]);if (hh2>0) {val2+=0.5*effest[hh2];} if (nbadd>0) {for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } if (chxt==1) {val3=exp(val2)/(1+exp(val2));val1-=val3;varest=val3*(1-val3);} else if (chxt==2) {val1-=val2;varest=1;} dmat2[0]=varest; for (i=0;iz[i];} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=0.5*dmat2[0];} if ((hh2>0) && (itptp[hh2]==1)) {dmat2[nitptp[hh2]]+=0.5*dmat2[0];} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=0.5*dmat2[0];} if ( (hh2==v2-1) && (nitptp[hh2]>-1)) {dmat2[nitptp[hh2]]+=0.5*dmat2[0];} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=0.5*dmat2[0]; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=0.5*dmat2[0]; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=0.5*dmat2[0]; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=0.5*dmat2[0]; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0];} if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0];} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=0.5*dmat2[0]; } if (hh2==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=0.5*dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=0.5*dmat2[0]; } } } } } for (i=0;iz[tabint[i][1]-1]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } } else if ((int) suiv->z[0]==0) {for (i=0;iphen[0]; val2=effest[0]; for (i=0;iz[i]; if (offset==1) val2+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(suiv->hapest[0]);if (hh1>0) {val2+=effest[hh1];} for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*(hh1==tabint[i][0]-1); } } if (chxt==1) {val3=exp(val2)/(1+exp(val2));val1-=val3;varest=val3*(1-val3);} else if (chxt==2) {val1-=val2;varest=1;} dmat2[0]=varest; for (i=0;iz[i];} if (haplozero==0) {if ((hh1>0) && (itptp[hh1]==1)) {dmat2[nitptp[hh1]]+=dmat2[0];} if (hypoth>0) {for (i=0;i-1)) {dmat2[nitptp[hh1]]+=dmat2[0];} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=dmat2[0]; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=dmat2[0]; } } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0];} } else {if (hh1==tabinter[j][i][1]-1) {dmat2[nitptp[tabinter[j][0][1]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][i][0]-1]]+=dmat2[0]; dmat2[nitptp[tabinter[j][0][0]-1]]-=dmat2[0]; } } } } } for (i=0;iz[tabint[i][1]-1]*(hh1==tabint[i][0]-1); } } } for (i=0;inext; } sysl(mdvd2,n); for (i=0;i-1) {effest[i]+=modif2[nitptp[i]];j++;} if (hypoth>0) {for (i=0;i1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]-effest[tabinter[j][0][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]; } else {effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]-effest[tabinter[j][0][0]-1]; } } } } if (hypint>0) {for (i=0;inext!=NULL)) {if (suiv->tnbhapo>0) {val1=suiv->phen[0]; val2=effest[0]; for (i=0;iz[i]; if (haplozero==0) {if ((int) suiv->z[0]==0) {hh1=coding(suiv->hapest[0]);if (hh1>0) {val2+=effest[hh1];} for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*(hh1==tabint[i][0]-1); } } else if ((int) suiv->z[0]==1) {hh1=coding(suiv->hapest[0]);if (hh1>0) {val2+=0.5*effest[hh1];} hh2=coding(suiv->hapest[1]);if (hh2>0) {val2+=0.5*effest[hh2];} if (nbadd>0) {for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } } steres+=(val1-val2)*(val1-val2); nused+=1; } suiv=suiv->next; } ste=sqrt(steres/(nused-1)); } for (i=0;i0) {place[i]=j;j++;} //fisher=(double **) malloc((size_t) (nnt*sizeof(double *))); //for (i=0;inext!=NULL)) {for (i=0;iphen[0]; likeli=0; for (i=0;itnbhapo;i++) {like=0; h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); v1=2*lgoddsem[0]; for (j=0;jz[j]; if ( (chxt==1) && (offset==1)) v1+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } if (chxt==1) {like=exp(v1*val1)/(1+exp(v1));} else if (chxt==2) {v2=-0.5*(val1-v1)*(val1-v1)/(ste*ste);like=exp(v2)/(ste*sqrt(2.0*pi));} if (suiv->idnb[i][0]==suiv->idnb[i][1]) {derivfrq[place[suiv->idnb[i][0]]]+=2*like*frqsem[suiv->idnb[i][0]];} else {derivfrq[place[suiv->idnb[i][0]]]+=2*like*frqsem[suiv->idnb[i][1]]; derivfrq[place[suiv->idnb[i][1]]]+=2*like*frqsem[suiv->idnb[i][0]]; } if (chxt==1) {val2=like*(1-like)*p1*((val1==1)-(val1==0));} else if (chxt==2) {val2=p1*like*(val1-v1)/(ste*ste);} derivodd[0]+=2*val2; for (k=0;kz[k]*val2;} if (haplozero==0) {if ((hh1>0) && (itp[hh1]==1)) {derivodd[nitp[hh1]]+=val2;} if ((hh2>0) && (itp[hh2]==1)) {derivodd[nitp[hh2]]+=val2;} if (hypoth>0) {for (k=0;k-1)) {derivodd[nitp[hh1]]+=val2;} if ((hh2==vv2-1) && (nitp[hh2]>-1)) {derivodd[nitp[hh2]]+=val2;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][k][0]-1]]+=val2; } if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][k][0]-1]]+=val2; } } else if ( (tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][0][0]-1]]-=val2; } if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][0][0]-1]]-=val2; } } else if ( (tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2;} if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2;} } else {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][k][0]-1]]+=val2; derivodd[nitp[tabinter[j][0][0]-1]]-=val2; } if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][k][0]-1]]+=val2; derivodd[nitp[tabinter[j][0][0]-1]]-=val2; } } } } } for (k=0;kz[tabint[k][1]-1]*((hh1==tabint[k][0]-1)+(hh2==tabint[k][0]-1)); } }/* if haplozero*/ likeli+=p1*like; }/* if */ }/* for i*/ /* ATTENTION A LA PREMIERE FREQUENCE D'OU LE -1 */ if (likeli>0) {for (i=0;inext; }/* while */ printf("Inverting Variance Matrix....\n"); sysl(fisher,nnt); for (i=0;i0) {place[i]=j;j++;} //fisher=(double **) malloc((size_t) (nnt*sizeof(double *))); //for (i=0;inext!=NULL)) {for (i=0;iz[0]==1) {/*CALCUL DE P(Y,G)*/ val1=suiv->phen[0]; likeli=0; for (i=0;itnbhapo;i++) {like=0; h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); v1=lgoddsem[0]; for (j=0;jz[j]; if ( (chxt==1) && (offset==1)) v1+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=0.5*lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=0.5*lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } if (chxt==1) {like=exp(v1*val1)/(1+exp(v1));} else if (chxt==2) {v2=-0.5*(val1-v1)*(val1-v1)/(ste*ste);like=exp(v2)/(ste*sqrt(2.0*pi));} if (suiv->idnb[i][0]==suiv->idnb[i][1]) {derivfrq[place[suiv->idnb[i][0]]]+=2*like*frqsem[suiv->idnb[i][0]];} else {derivfrq[place[suiv->idnb[i][0]]]+=2*like*frqsem[suiv->idnb[i][1]]; derivfrq[place[suiv->idnb[i][1]]]+=2*like*frqsem[suiv->idnb[i][0]]; } /*Calcul des drivees premieres par rapport aux parametres de regression */ if (chxt==1) {val2=like*(1-like)*p1*((val1==1)-(val1==0));} else if (chxt==2) {val2=p1*like*(val1-v1)/(ste*ste);} derivodd[0]+=val2; for (k=0;kz[k]*val2;} if (haplozero==0) {if ((hh1>0) && (itp[hh1]==1)) {derivodd[nitp[hh1]]+=0.5*val2;} if ((hh2>0) && (itp[hh2]==1)) {derivodd[nitp[hh2]]+=0.5*val2;} if (hypoth>0) {for (k=0;k-1)) {derivodd[nitp[hh1]]+=0.5*val2;} if ((hh2==vv2-1) && (nitp[hh2]>-1)) {derivodd[nitp[hh2]]+=0.5*val2;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][k][0]-1]]+=0.5*val2; } if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][k][0]-1]]+=0.5*val2; } } else if ( (tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][0][0]-1]]-=0.5*val2; } if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][0][0]-1]]-=0.5*val2; } } else if ( (tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2;} if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2;} } else {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][k][0]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][0][0]-1]]-=0.5*val2; } if (hh2==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][k][0]-1]]+=0.5*val2; derivodd[nitp[tabinter[j][0][0]-1]]-=0.5*val2; } } } } } for (k=0;kz[tabint[k][1]-1]*((hh1==tabint[k][0]-1)+(hh2==tabint[k][0]-1)); } }/* if haplozero*/ likeli+=p1*like; }/* if */ }/* for i*/ /* ATTENTION A LA PREMIERE FREQUENCE D'OU LE -1 */ } else if ((int) suiv->z[0]==0) { val1=suiv->phen[0]; likeli=0; for (i=0;itnbhapo;i++) {like=0; h1=frqsem[suiv->idnb[i][0]]; if (h1>0) {p1=h1; v1=lgoddsem[0]; for (j=0;jz[j]; if ( (chxt==1) && (offset==1)) v1+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*(hh1==tabint[j][0]-1); } } if (chxt==1) {like=exp(v1*val1)/(1+exp(v1));} else if (chxt==2) {v2=-0.5*(val1-v1)*(val1-v1)/(ste*ste);like=exp(v2)/(ste*sqrt(2.0*pi));} derivfrq[place[suiv->idnb[i][0]]]+=like; if (chxt==1) {val2=like*(1-like)*p1*((val1==1)-(val1==0));} else if (chxt==2) {val2=p1*like*(val1-v1)/(ste*ste);} derivodd[0]+=val2; for (k=0;kz[k]*val2;} if (haplozero==0) {if ((hh1>0) && (itp[hh1]==1)) {derivodd[nitp[hh1]]+=val2;} if (hypoth>0) {for (k=0;k-1)) {derivodd[nitp[hh1]]+=val2;} } } if (interor==1) {for (j=0;j1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][k][0]-1]]+=val2; } } else if ( (tabinter[j][k][0]==1) && (tabinter[j][0][0]>1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][0][0]-1]]-=val2; } } else if ( (tabinter[j][k][0]==1) && (tabinter[j][0][0]==1)) {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2;} } else {if (hh1==tabinter[j][k][1]-1) {derivodd[nitp[tabinter[j][0][1]-1]]+=val2; derivodd[nitp[tabinter[j][k][0]-1]]+=val2; derivodd[nitp[tabinter[j][0][0]-1]]-=val2; } } } } } for (k=0;kz[tabint[k][1]-1]*(hh1==tabint[k][0]-1); } }/* if haplozero*/ likeli+=p1*like; }/* if */ }/* for i*/ } if (likeli>0) {for (i=0;inext; }/* while */ printf("Inverting Variance Matrix....\n"); sysl(fisher,nnt); for (i=0;inext!=NULL)) /*ATTENTION AU PB EVENTUEL DES DONNES MANQUANTES*/ {val1=suiv->phen[0]; if (suiv->tnbhapo>0) {vrais=0; for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; v1=2*lgoddsem[0]; for (j=0;jz[j]; if ( (chxt==1) && (offset==1)) v1+=suiv->z[ajust]; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); if (haplozero==0) {hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } if (chxt==1) {like=exp(v1*val1)/(1+exp(v1));} else if (chxt==2) {vv2=-0.5*(val1-v1)*(val1-v1)/(ste*ste); like=exp(vv2)/(ste*sqrt(2.0*pi)); } vrais+=p1*like; } } if (vrais>0) {vraisfa -= log(vrais);} } suiv= suiv->next; } return(-vraisfa); } /*********************CALCUL DE LA VRAISEMBLANCE TOTALE ******************************************/ double Xlikelihood(double *frqsem, double *lgoddsem) {double val1,v1,vrais,h1,h2,like,p1,vraisfa=0,vv2; int hh1,hh2/*,idx*/,i,j; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) /*ATTENTION AU PB EVENTUEL DES DONNES MANQUANTES*/ {val1=suiv->phen[0]; vrais=0; if ((suiv->tnbhapo>0) && ((int) suiv->z[0]==1)) {for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; v1=lgoddsem[0]; for (j=0;jz[j]; if ( (chxt==1) && (offset==1)) v1+=suiv->z[ajust]; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); if (haplozero==0) {hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=0.5*lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=0.5*lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } if (chxt==1) {like=exp(v1*val1)/(1+exp(v1));} else if (chxt==2) {vv2=-0.5*(val1-v1)*(val1-v1)/(ste*ste); like=exp(vv2)/(ste*sqrt(2.0*pi)); } vrais+=p1*like; } } } else if ((suiv->tnbhapo==1) && ((int) suiv->z[0]==0)) {h1=frqsem[suiv->idnb[0][0]]; v1=lgoddsem[0]; for (j=0;jz[j]; if ( (chxt==1) && (offset==1)) v1+=suiv->z[ajust]; if (h1>0) {p1=h1; if (haplozero==0) {hh1=coding(suiv->idnb[0][0]);if (hh1>0) {v1+=lgoddsem[hh1];} for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*(hh1==tabint[j][0]-1); } } if (chxt==1) {like=exp(v1*val1)/(1+exp(v1));} else if (chxt==2) {vv2=-0.5*(val1-v1)*(val1-v1)/(ste*ste); like=exp(vv2)/(ste*sqrt(2.0*pi)); } vrais+=p1*like; } } if (vrais>0) {vraisfa -= log(vrais);} suiv= suiv->next; } return(-vraisfa); } /*********************CALCUL DE LA VRAISEMBLANCE CONDITIONNELLE ******************************************/ double condlike(double *frqsem) {double denume,pgeno,p1,h1,h2; int i; denume= 0.0; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) {p1=0;pgeno=1.0; for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]]; h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {p1+=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); } } pgeno*=p1; if (pgeno>0) {denume+=log(pgeno);} suiv = suiv->next; } return(denume); } double Xcondlike(double *frqsem) {double denume,pgeno,p1,h1,h2; int i; denume= 0.0; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) {p1=0;pgeno=1.0; if ((int) suiv->z[0]==1) {for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]]; h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {p1+=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); } } } else if ((int) suiv->z[0]==0) {if (suiv->tnbhapo>1) {printf("Male individuals must be unambiguous!\n");exit(0);} for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]]; if (h1>0) p1+=h1; } } pgeno*=p1; if (pgeno>0) {denume+=log(pgeno);} suiv = suiv->next; } return(denume); } void phenomean(FILE *outf1,FILE *outf2,matrixp matse) {dhaplotype *vect1; int i,j,k,kk; char l; double mean,valef,valf; fprintf(outf1,"\n\nExpected Phenotypic Mean [95%% CI] According to Estimated Haplotypes\n\n"); fprintf(outf2,"

"); fprintf(outf2,"\n"); fprintf(outf2,"\n"); fprintf(outf2,"\n"); fprintf(outf2,"\n"); for (i=0;inumnew]!=numhap[i])) {vect1=vect1->down;} fprintf(outf2,"",mean); if (i==0) {valef=sqrt(matse[nbhest-1][nbhest-1]);} else {valf=matse[nbhest-1][nbhest-1]+matse[nbhest-1+nitp[i]][nbhest-1+nitp[i]]; valf+=2*matse[nbhest-1][nbhest-1+nitp[i]]; valef=sqrt(valf); } fprintf(outf1,"[%.5f - %.5f]\n",mean-1.96*valef,mean+1.96*valef); fprintf(outf2,"",mean-1.96*valef,mean+1.96*valef); vect1=NULL; } } fprintf(outf2,"
Expected Phenotypic Mean [95%% CI] According to Estimated Haplotypes
"); if ((itp[i]==1) || ( (itp[i]==0) && (effest[i]!=0)) || ( (itp[i]==0) && (nitp[i]==-2)) ) {for (kk=0;kklistall[kk]==1)+letter[kk][1]*(vect1->listall[kk]==2); fprintf(outf1,"%c",l);fprintf(outf2,"%c",l); } mean=effest[0]+effest[i]*(i>0); fprintf(outf1,"\t%.5f ",mean); fprintf(outf2,"%.5f[%.5f - %.5f]
\n"); /* NEW DAVID*/ free (vect1);vect1=NULL; } double residuel(double *frqsem, double *lgoddsem) {double residu=0,val1,v1,h1,h2,p1; int hh1,hh2,i,j,nuse=0; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) {val1=suiv->phen[0]-2*lgoddsem[0]; for (j=0;jz[j]; if (suiv->tnbhapo>0) {nuse+=1; for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; p1=0; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); v1=0; if (haplozero==0) {hh1=coding(suiv->idnb[i][0]);if (hh1>0) {v1+=lgoddsem[hh1];} hh2=coding(suiv->idnb[i][1]);if (hh2>0) {v1+=lgoddsem[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*lgoddsem[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } val1-=p1*v1; } } residu+=val1*val1; } suiv= suiv->next; } residu/=(nuse-1); return(residu); } double somdelai() {double somd=0.0; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) {if (suiv->tnbhapo>0) // && (suiv->phen[0]==1.0)) {somd+=suiv->phen[1]; } suiv=suiv->next; } return(somd); } //fin fonc12.c int lecture( char *fileName, int pMaxvarfic, int pNbloci, int *pIdloci, int pLdmatrix, int pMsdata, int pR2, int pChxt, int pNum0, int pIdtime, int pOffset, int pIdoffset, int pAjust, int *pNumajust, int pXlnk, int pNumsx); /**********************************Lecture du fichier de donnees*****************************/ int lecture( char *fileName, // 1 ok int pMaxvarfic, // 2 ok int pNbloci, // 3 ok int *pIdloci, // 4 ok int pLdmatrix, // 5 ok int pMsdata, // 6 ok int pR2, // 7 ok int pChxt, // 8 ok int pNum0, // 9 ok int pIdtime, // 10 ok int pOffset, // 16 int pIdoffset, // 11 ok int pAjust, // 12 ok int *pNumajust, // 13 ok int pXlnk, // 14 int pNumsx) // 15 { char flec[30],rep,cha; int maxvarfic,mxvfic=0,i,idp,idx,numh,numsx,num0,dtmq,a=0,cpt_tab=0,l; int *idloc,iref,idtime,idwgt; double res; vectgen geno; FILE *fildo /* *fillet*/; int *taille,*idlet; char **tempo; int kel = 0; printf("No loci : %d\n",pNbloci); for( kel = 0 ; kel < pNbloci ; kel++) { printf("loc[%d] = %d", kel+1, pIdloci[kel]); } for( kel = 0 ; kel < pAjust ; kel++) { printf("pNumajust[%d] = %d", kel+1, pNumajust[kel]); } printf("DataFile name :\n"); //-------------------- 1 -----------------------// strcpy(flec,fileName); //-------------------- fin 1 -----------------------// if ((fildo=fopen(flec,"r"))==NULL) { return -1; } //-------------------- 2 -----------------------// maxvarfic = pMaxvarfic; //-------------------- fin 2 -----------------------// printf("Number of di-allelic loci to be studied :\n"); //-------------------- 3 -----------------------// nbloci = pNbloci; //-------------------- fin 3 -----------------------// idloc =(int *)malloc((size_t) (nbloci*sizeof(int))); //-------------------- 4 -----------------------// for (i=0;ilistall[i-1]=iref; if (i==1) { tnbhnew->numnew=numh; tnbhnew->present=0; if (numh==ipow(2,nbloci)-1) {tnbhnew->down=NULL;} else {tnbhnew->down=(dhaplotype *) malloc((size_t) (sizeof(dhaplotype)));} } idp++; if (idp>idx) { if (iref==1) {iref=2;} else {iref=1;} idp=1; } numh++; tnbhnew=tnbhnew->down; } while (numh0) { //-------------------- 9 -----------------------// num0 = pNum0; //-------------------- fin 9 -----------------------// //-------------------- 10 -----------------------// if ((chxt==3) || (chxt==4)) { idtime = pIdtime; } //-------------------- fin 10 -----------------------// // GT 04-10-06 ce mecanisme est implement dans GraficT.. /* if (xlnk==0) { //-------------------- 12 -----------------------// ajust=pAjust; //-------------------- fin 12 -----------------------// if(ajust > 0) { //-------------------- 13 -----------------------// for (i=0;i 1) { //-------------------- 13 -----------------------// for (i=0;i 0) { //-------------------- 13 -----------------------// for (i=0;imaxcov) { printf("With such an offset and so many covaraites, the analysis can not be performed.\n"); printf("Please contact D.Tregouet for further information\n"); exit(0); } } do { cha=fgetc(fildo); if ( (cha=='\t') || (cha==32) || (cha==';')) { mxvfic++; } }while (cha!='\n'); mxvfic++; rewind (fildo); if (mxvfic!=maxvarfic) { printf("Error in number of variables in Datafile\n"); exit(0); } cpt_tab=0; taille =(int *)malloc((size_t) (10 * maxvarfic*sizeof(int))); tempo =(char **) malloc((size_t) (10 * maxvarfic*sizeof(char *))); for (i=0;iz[i]=res; } if (chxt>0) { strncpy(flec,tempo[num0-1],taille[num0-1]); flec[taille[num0-1]]='\0'; res=atof(flec); suiv->phen[0]=res; suiv->phen[1]=-1; if ( (chxt==1) && (offset==1)) { strncpy(flec,tempo[idoffset-1],taille[idoffset-1]); flec[taille[idoffset-1]]='\0'; res=atof(flec); suiv->z[ajust]=res; } if ( (chxt==3) || (chxt==4)) { strncpy(flec,tempo[idtime-1],taille[idtime-1]); flec[taille[idtime-1]]='\0'; res=atof(flec); suiv->phen[1]=res; } } for (i=0;imarq[i][0]=geno[i][0]; suiv->marq[i][1]=geno[i][1]; } suiv->nblm=dtmq; suiv->next=(dindividu *)malloc((size_t) (sizeof(dindividu))); /* on alloue pour un individu de plus */ suiv=suiv->next; suiv->next=NULL; /* on decale la liste d un cran */ } } suiv=NULL; if (fildo !=NULL) fclose(fildo); fildo=NULL; idlet=NULL; taille=NULL; tempo=NULL; idloc=NULL; free (idloc); free (tempo); free (taille); free (idlet); return 0; } /*****************Determine les haplotypes de chaque individu: corps de la procedure***********/ void determhapo() {int i ,nls=0; nbtotused=0; vectgen xg; printf("Running identification of haplotypes....\n"); if (msdata==1) {suiv=base; printf("(It can take quite a long time since you are dealing with missing data...\n"); while ((suiv!=NULL) && (suiv->next!=NULL)) {for (i=0;imarq[i][0];xg[i][1]=suiv->marq[i][1];} suiv->tnbhapo=0; nbhapo1(xg); if (suiv->tnbhapo>0) nbtotused+=1; suiv=suiv->next; } } else { suiv=base; do {for (i=0;imarq[i][0];xg[i][1]=suiv->marq[i][1];} suiv->tnbhapo=0; nbhapo0(xg); if (suiv->tnbhapo>0) nbtotused+=1; suiv=suiv->next; } while ((suiv!=NULL) && (suiv->next!=NULL)); } suiv=NULL; } /******Determine les haplotypes de chaque individu: sous procedure avec donnees manquantes*****/ void nbhapo1(vectgen xg) {int i,tnbh1; short keepon,h0,h00,l0,l00; tnbh1=0; if (suiv->nblmlistall[i];l00=vect2->listall[i]; if ( (((h0==l0) || (h0==0)) && ((h00==l00) || (h00==0))) || (((h0==l00) || (h0==0)) && ((h00==l0) || (h00==0))) ) {i+=1;keepon=1;} else {keepon=0;} } while ((keepon==1) && (i!=nbloci)); if ((keepon==1) && (i==nbloci)) {tnbh1+=1;} vect2=vect2->down; } vect1=vect1->down; } } suiv->idnb=(int **)malloc((size_t) (tnbh1*sizeof(int *))); for (i=0;iidnb[i]=(int *)malloc((size_t) (2*sizeof(int))); if (tnbh1>maxhapair) {maxhapair=tnbh1;} suiv->tnbhapo=tnbh1; tnbh1=0; if (suiv->nblmlistall[i];l00=vect2->listall[i]; if ( (((h0==l0) || (h0==0)) && ((h00==l00) || (h00==0))) || (((h0==l00) || (h0==0)) && ((h00==l0) || (h00==0))) ) {i+=1;keepon=1;} else {keepon=0;} } while ((keepon==1) && (i!=nbloci)); if ((keepon==1) && (i==nbloci)) {tnbh1+=1; suiv->idnb[tnbh1-1][0]=vect1->numnew; suiv->idnb[tnbh1-1][1]=vect2->numnew; } vect2=vect2->down; } vect1=vect1->down; } } for (i=0;iidnb[i][0]]=1;fcoda1[suiv->idnb[i][1]]=1;} } /******Determine les haplotypes de chaque individu: sous procedure sans donnees manquantes*****/ void nbhapo0(vectgen xg) {int i,nbhet,numh,h0,h00,backha,idp,idx,tnbh1; int hetero[maxloc]; short iref;char rep; tnbh1=0;nbhet=0; if (suiv->nblm==0) {for (i=0;i0) {suiv->idnb=(int **)malloc((size_t) (tnbh1*sizeof(int *))); for (i=0;iidnb[i]=(int *)malloc((size_t) (2*sizeof(int))); } if (tnbh1>maxhapair) {maxhapair=tnbh1;} suiv->tnbhapo=tnbh1; nbhet=0; if (suiv->nblm==0) {for (i=0;i0) && (xlnk==1) && ((int) suiv->z[0]==0)) { printf("One male individual heterozygotes at %d loci\n",nbhet); printf("In this current version, the individual must be deleted\n"); exit(0); printf("Do you want to continue (y/n) ?"); scanf("%c",&rep); if ((rep=='N') || (rep=='n')) {exit(0);} } if (nbhet<2) {h0=0;h00=0; for (i=1;i<=nbloci;i++) {h0+=(xg[i-1][0]==2)*ipow(2,nbloci-i); h00+=(xg[i-1][1]==2)*ipow(2,nbloci-i); } suiv->idnb[0][0]=h0; suiv->idnb[0][1]=h00; fcoda1[h0]=1;fcoda1[h00]=1; } else {backha=0; for (i=1;i<=nbloci;i++) {if (xg[i-1][0]==xg[i-1][1]) {backha+=(xg[i-1][0]==2)*ipow(2,nbloci-i);} } for (i=0;iidnb[i][0]=backha; suiv->idnb[i][1]=backha+ipow(2,nbloci-hetero[0]); } for (i=1;i<=nbhet-1;i++) {numh=0;idx=ipow(2,nbhet-1-i);iref=1;idp=1; do {suiv->idnb[numh][0]+=(iref==2)*ipow(2,nbloci-hetero[i]); suiv->idnb[numh][1]+=(iref==1)*ipow(2,nbloci-hetero[i]); idp++; if (idp>idx) {if (iref==1) {iref=2;} else {iref=1;} idp=1; } numh++; }while (numhidnb[i][0]]=1;fcoda1[suiv->idnb[i][1]]=1;} } } } /**********************Calcul des frequences alleliques et haplotypiques sans LD***************/ void initfreq(double *hw) {int i,l; int **ngeno,*nl,**ngenoh,**ngenof,nh,nf; double fi1,fi2; ngeno=(int **) malloc ((size_t) (nbloci*sizeof(int *))); for (i=0;inext!=NULL)) {if (suiv->nblm==0) {l++; for (i=0;imarq[i][0]==1)+(suiv->marq[i][1]==1); ngeno[i][0]+=( (suiv->marq[i][0]==1) && (suiv->marq[i][1]==1) ); ngeno[i][2]+=( (suiv->marq[i][0]==2) && (suiv->marq[i][1]==2) ); ngeno[i][1]+=( ((suiv->marq[i][0]==1) && (suiv->marq[i][1]==2)) || ((suiv->marq[i][0]==2) && (suiv->marq[i][1]==1))); } } suiv=suiv->next; } for (i=0;inext!=NULL)) {if (suiv->nblmmarq[i][0]==1) || (suiv->marq[i][1]==2)) {nl[i]+=1; alfreq[i]+=(suiv->marq[i][0]==1)+(suiv->marq[i][1]==1); ngeno[i][0]+=( (suiv->marq[i][0]==1) && (suiv->marq[i][1]==1) ); ngeno[i][2]+=( (suiv->marq[i][0]==2) && (suiv->marq[i][1]==2) ); ngeno[i][1]+=( ((suiv->marq[i][0]==1) && (suiv->marq[i][1]==2)) || ((suiv->marq[i][0]==2) && (suiv->marq[i][1]==1))); } } } suiv=suiv->next; } for (i=0;inext!=NULL)) {if (suiv->nblm==0) {if ((int) suiv->z[0]==1) {l+=2; nf++; for (i=0;imarq[i][0]==1)+(suiv->marq[i][1]==1); ngenof[i][0]+=( (suiv->marq[i][0]==1) && (suiv->marq[i][1]==1)); ngenof[i][2]+=( (suiv->marq[i][0]==2) && (suiv->marq[i][1]==2) ); ngenof[i][1]+=( ((suiv->marq[i][0]==1) && (suiv->marq[i][1]==2)) || ((suiv->marq[i][0]==2) && (suiv->marq[i][1]==1))); } } else if ((int) suiv->z[0]==0) {l+=1; nh++; for (i=0;imarq[i][0]==1); ngenoh[i][0]+=(suiv->marq[i][0]==1) ; ngenoh[i][2]+=(suiv->marq[i][0]==2) ; } } } suiv=suiv->next; } for (i=0;ipresent==1) {tnbhnew->frqle=1.0; for (l=0;lfrqle*=alfreq[l]*(tnbhnew->listall[l]==1)+(1-alfreq[l])*(tnbhnew->listall[l]==2); } i=fcoda2[tnbhnew->numnew]; freqest[i]=tnbhnew->frqle; } tnbhnew=tnbhnew->down; } ngeno=NULL;nl=NULL;ngenoh=NULL;ngenof=NULL; // New DAVID free ((int **) ngeno);free ((int *) nl);free ((int **) ngenof);free ((int **) ngenoh); } /*************************Lecture des contraintes sur les effets *********************/ void lecteffe() { char rep;int i,j,v1,v2;double vv; short chgt; FILE *parfile; FILE *readParam; haplozero=1; readParam = fopen("paramData.thi","r"); printf("Do you want to estimate haplotypic effect (y/n) ?\n"); do { fscanf(readParam,"%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) { haplozero=0; } if ((haplozero==0) && (chxt>0)) { hypoth=0; printf("Do you want to test specific hypothesis on haplotypic effects (y/n) ?\n"); do { fscanf(readParam,"%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) { printf("How many constraints of equality do you wish to consider ?\n"); fscanf(readParam,"%d",&hypoth); tabhypo=(int **)malloc((size_t) (hypoth*sizeof(int *))); for (i=0;imaxhypor); tabinter=(int ***)malloc((size_t) (nbhypor*sizeof(int **))); nbor=(int *)malloc((size_t) (nbhypor*sizeof(int))); for (j=0;jmaxadd); tadd=(int **)malloc((size_t) (nbadd*sizeof(int *))); for (j=0;j0) { printf("Do you want to test haplotype * environment interactions (y/n) ?"); do { fscanf(readParam,"%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) { printf("How many interactions to be tested ?\n"); do { fscanf(readParam,"%d",&intercov); }while (intercov>maxcov); tabint=(int **)malloc((size_t) (intercov*sizeof(int *))); for (j=0;jmaxhypint); tabhypint=(int **)malloc((size_t) (hypint*sizeof(int *))); for (j=0;j0) { for (i=0;i1)) { effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]>1)) { effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]-effest[tabinter[j][0][0]-1]; } else if ( (tabinter[j][i][0]==1) && (tabinter[j][0][0]==1)) { effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]; } else { effest[tabinter[j][i][1]-1]=effest[tabinter[j][0][1]-1]+effest[tabinter[j][i][0]-1]-effest[tabinter[j][0][0]-1]; } } } } /* Contrainst on haplotype * covariate interactions */ if (hypint>0) { for (i=0;i0) && (haplozero==1)) { itp[0]=1; for (i=1;i0) { for (i=0;i0) { for (i=0;i0)) { hypoth=0; printf("Do you want to test specific hypothesis on haplotypic effects (y/n) ?\n"); do { fscanf(readParam,"%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) { printf("How many constraints of equality do you wish to consider ?\n"); fscanf(readParam,"%d",&hypoth); tabhypo=(int **)malloc((size_t) (hypoth*sizeof(int *))); for (i=0;imaxhypor); tabinter=(int ***)malloc((size_t) (nbhypor*sizeof(int **))); nbor=(int *)malloc((size_t) (nbhypor*sizeof(int))); for (j=0;jmaxadd); tadd=(int **)malloc((size_t) (nbadd*sizeof(int *))); for (j=0;j0) { printf("Do you want to test haplotype * environment interactions (y/n) ?"); do { fscanf(readParam,"%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) { printf("How many interactions to be tested ?\n"); do { fscanf(readParam,"%d",&intercov); }while (intercov>maxcov); tabint=(int **)malloc((size_t) (intercov*sizeof(int *))); for (j=0;j0) {for (i=0;i0) {for (i=0;i0)) {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]+effest[tabinter[j][i][0]]; } else if ( (div(tabinter[j][i][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]-effest[tabinter[j][0][0]]; } else if ( (div(tabinter[j][i][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]; } else {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]+effest[tabinter[j][i][0]]-effest[tabinter[j][0][0]]; } } } } if (parfile != NULL) fclose(parfile); /*12-10-06 Modif David pour ajouter dans Para.txt le nombre de classe nkat*/ parfile=NULL; if ((parfile=fopen("para.txt","a+"))==NULL) {printf("Error in Para file reading....\n");exit(0);} printf("nkat: %d\n",nkat); fprintf(parfile,"%d\n",nkat); if (parfile != NULL) fclose(parfile);parfile=NULL; if (readParam != NULL) fclose(readParam);readParam=NULL; //Fin des modif } /*************************Generation alatoire des haplotypes ambigus*********************/ void generhap() {double probacum,aleat,quot,dum; int i,j,nh=0,nf=0,nh0=0,nh1=0,nf0=0,nf1=0,nls=0; short fini; for (i=0;inext!=NULL)) {if (suiv!=NULL) { nls++; if (suiv->tnbhapo==1) {suiv->hapest[0]=suiv->idnb[0][0]; suiv->hapest[1]=suiv->idnb[0][1]; } else if (suiv->tnbhapo>1) {probacum=0; aleat=rand()/(1.0*RAND_MAX); fini=0; quot=probatot(); for (i=0;itnbhapo;i++) {if (fini==0) {dum=probacond(i)/quot; probacum=probacum+dum; if (probacum>aleat) {fini=1; suiv->hapest[0]=suiv->idnb[i][0]; suiv->hapest[1]=suiv->idnb[i][1]; } } } } if (suiv->tnbhapo>0) {tempfreq[suiv->hapest[0]]+=1;tempfreq[suiv->hapest[1]]+=1; if ( (chxt==1) || (chxt==3) || (chxt==4) || (chxt==6)) {tempdist[suiv->hapest[0]][0]+=1*(suiv->phen[0]==0); tempdist[suiv->hapest[1]][0]+=1*(suiv->phen[0]==0); tempdist[suiv->hapest[0]][1]+=1*(suiv->phen[0]==1); tempdist[suiv->hapest[1]][1]+=1*(suiv->phen[0]==1); } if (chxt==5) {for (i=0;ihapest[0]][i]+=1*(suiv->phen[0]==(i+1)); tempdist[suiv->hapest[1]][i]+=1*(suiv->phen[0]==(i+1)); } } } suiv=suiv->next; } } for (i=0;inext!=NULL)) {if (((int) suiv->z[0])==0) { if (suiv->tnbhapo==1) {nh+=1; suiv->hapest[0]=suiv->idnb[0][0]; suiv->hapest[1]=suiv->idnb[0][1]; tempfreq[suiv->hapest[0]]+=1; if ( (chxt==1) || (chxt==3) || (chxt==4) || (chxt==6)) {tempdist[suiv->hapest[0]][0]+=1*(suiv->phen[0]==0); nh0+=(suiv->phen[0]==0); tempdist[suiv->hapest[0]][1]+=1*(suiv->phen[0]==1); nh1+=(suiv->phen[0]==1); } } //else {printf("Option not handled \n");exit(0);} } else if (((int) suiv->z[0])==1) {if (suiv->tnbhapo==1) {suiv->hapest[0]=suiv->idnb[0][0]; suiv->hapest[1]=suiv->idnb[0][1]; } else if (suiv->tnbhapo>1) {probacum=0; aleat=rand()/(1.0*RAND_MAX); fini=0; quot=Xprobatot(); for (i=0;itnbhapo;i++) {if (fini==0) {dum=Xprobacond(i)/quot; probacum=probacum+dum; if (probacum>aleat) {fini=1; suiv->hapest[0]=suiv->idnb[i][0]; suiv->hapest[1]=suiv->idnb[i][1]; } } } } if (suiv->tnbhapo>0) {tempfreq[suiv->hapest[0]]+=1;tempfreq[suiv->hapest[1]]+=1; nf+=1; if ( (chxt==1) || (chxt==3) || (chxt==4) || (chxt==6)) {tempdist[suiv->hapest[0]][0]+=1*(suiv->phen[0]==0); tempdist[suiv->hapest[1]][0]+=1*(suiv->phen[0]==0); tempdist[suiv->hapest[0]][1]+=1*(suiv->phen[0]==1); tempdist[suiv->hapest[1]][1]+=1*(suiv->phen[0]==1); nf0+=(suiv->phen[0]==0); nf1+=(suiv->phen[0]==1); } if (chxt==5) {printf("PARTIE A REMPLIR \n");exit(0);} } } suiv=suiv->next; } for (i=0;inext!=NULL)) {if ( (pv1->tnbhapo>0) && (pv1->phen[0]==1.0) && (pv1->phen[1]<=temps)) {pv2=base; res1=0; while ((pv2!= NULL) && (pv2->next!=NULL)) {if ((pv2->phen[1]>=pv1->phen[1]) && (pv2->tnbhapo>0)) {val1=0; for (i=0;iz[i]; if (haplozero==0) {h1=pv2->hapest[0];h2=pv2->hapest[1]; hh1=coding(h1); hh2=coding(h2); if (hh1>0) {val1+=effest[hh1];} if (hh2>0) {val1+=effest[hh2];} if (nbadd>0) {for (j=0;jz[tabint[j][1]-1]*effest[nbhest+ajust+nbadd+j]*((hh1==tabint[j][0]-1)+(hh2==tabint[j][0]-1)); } } res1+=exp(val1); } pv2=pv2->next; } /*pv2*/ res+=(1/res1); }/*if*/ pv1=pv1->next; }/*pv1*/ // New DAVID free ((dindividu *) pv1);free ((dindividu *) pv2);pv1=NULL;pv2=NULL; return (res); } /**************************Calcul des probabilits conditionnelles*****************************/ double probacond(int val) {double res=1.0,val1,val2,vv2,likeli,ss=0,ls=0,ps=0,num,denom; int h1,h2,hh1,hh2,idx,i,j; idx=1*(haplozero==1)+nbhest*(haplozero==0); h1=suiv->idnb[val][0]; h2=suiv->idnb[val][1]; if (chxt==0) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2));} else if (chxt<5) { val1=suiv->phen[0];val2=2*effest[0]; for (i=0;iz[i]; if ((chxt==1) && (offset==1)) val2+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(h1);hh2=coding(h2); if (hh1>0) {val2+=effest[hh1];} if (hh2>0) {val2+=effest[hh2];} if (nbadd>0) {for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } if ((chxt==1) || (chxt==4)) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2))*exp(val2*val1)/(1+exp(val2)); } else if (chxt==2) {vv2=-0.5*(val1-val2)*(val1-val2)/(ste*ste); likeli=exp(vv2)/(ste*sqrt(2.0*pi)); res*=freqest[h1]*freqest[h2]*(2-(h1==h2))*likeli; } else if (chxt==3) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2)); if (suiv->phen[0]==0) {res*=exp(-exp(val2)); } else if (suiv->phen[0]==1) {res*=exp(val2)*exp(-exp(val2)); } } /*else if (chxt==6) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2)); ss=exp(-exp(val2)*pow(effest[nall-1]*suiv->phen[1],effest[nall-2])); ls=effest[nall-1]*effest[nall-2]*pow(suiv->phen[1]*effest[nall-1],effest[nall-2]-1)*exp(val2); ps=ss*ls; res*=ss; if (suiv->phen[0]==1) {res*=ls;} correction for P(S=1) res/=(suiv->wgt+(1-suiv->wgt)*ps); }*/ } else if (chxt==5) {idx= ((int) suiv->phen[0])-1; val2=0; denom=1; for (i=0;iz[j]; if (haplozero==0) {hh1=coding(h1);hh2=coding(h2); if (hh1>0) {val2+=effest[hh1*nkat+i];} if (hh2>0) {val2+=effest[hh2*nkat+i];} for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } denom+=exp(val2); } if (idx==0) num=1; else if (idx>0) {val2=2*effest[idx-1]; for (j=0;jz[j]; if (haplozero==0) {hh1=coding(h1);hh2=coding(h2); if (hh1>0) {val2+=effest[nkat*hh1+idx-1];} if (hh2>0) {val2+=effest[nkat*hh2+idx-1];} for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+idx-1)==tabint[j][0])+ ((hh2*nkat+idx-1)==tabint[j][0])); } } num=exp(val2); } res*=freqest[h1]*freqest[h2]*(2-(h1==h2))*num/denom; } return(res); } /**************************Calcul des probabilits conditionnelles*****************************/ double Xprobacond(int val) {double res=1.0,val1,val2,vv2,likeli,ss=0,ls=0,ps=0; int h1,h2,hh1,hh2,idx,i; idx=1*(haplozero==1)+nbhest*(haplozero==0); h1=suiv->idnb[val][0]; h2=suiv->idnb[val][1]; if (chxt==0) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2));} else {val1=suiv->phen[0];val2=effest[0]; for (i=0;iz[i]; if ((chxt==1) && (offset==1)) val2+=suiv->z[ajust]; if (haplozero==0) {hh1=coding(h1);hh2=coding(h2); if (hh1>0) {val2+=0.5*effest[hh1];} if (hh2>0) {val2+=0.5*effest[hh2];} if (nbadd>0) {for (i=0;iz[tabint[i][1]-1]*effest[nbhest+ajust+nbadd+i]*((hh1==tabint[i][0]-1)+(hh2==tabint[i][0]-1)); } } if ((chxt==1) || (chxt==4)) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2))*exp(val2*val1)/(1+exp(val2)); } else if (chxt==2) {vv2=-0.5*(val1-val2)*(val1-val2)/(ste*ste); likeli=exp(vv2)/(ste*sqrt(2.0*pi)); res*=freqest[h1]*freqest[h2]*(2-(h1==h2))*likeli; } else if (chxt==3) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2)); if (suiv->phen[0]==0) {res*=exp(-exp(val2)); } else if (suiv->phen[0]==1) {res*=exp(val2)*exp(-exp(val2)); } } else if (chxt==6) {res*=freqest[h1]*freqest[h2]*(2-(h1==h2)); ss=exp(-exp(val2)*pow(effest[nall-1]*suiv->phen[1],effest[nall-2])); ls=effest[nall-1]*effest[nall-2]*pow(suiv->phen[1]*effest[nall-1],effest[nall-2]-1)*exp(val2); ps=ss*ls; res*=ss; if (suiv->phen[0]==1) {res*=ls;} /* correction for P(S=1)*/ res/=(suiv->wgt+(1-suiv->wgt)*ps); } } return(res); } /**************************Calcul des probabilits totales************************************/ double probatot() {double som; int j; som=0; for (j=0;j<(suiv->tnbhapo);j++) {som+=probacond(j);} return(som); } double Xprobatot() {double som; int j; som=0; for (j=0;jtnbhapo;j++) {som+=Xprobacond(j);} return(som); } /**************************Programme Principal*********************************************/ //int main() int thesiasRun(char *fileName, int pMaxvarfic, int pNbloci, int *pIdloci, int pLdmatrix, int pMsdata, int pR2, int pChxt, int pNum0, int pIdtime, int pOffset, int pIdoffset, int pAjust, int *pNumajust, int pXlnk, int pNumsx) {int i,mynit,j,k,ii,ll,imn,imnk,idn,idk,ll2; char l,rep; short trouve,ik,il; int maxhap,*numord,*numobs,*place,v1,v2,nbwald,nc, noUse; double *freqcas,*freqtem,somt,res,*frqobs,*frqord,vraise,vraiscond,valse,valef; double **ldp,**lr2,**chidp,mink,minl,dmax; double *hwc,*bresl; double **vinter,**vintra; double **freqkat; int *idwald; div_t biz; double timedif; double time1 = (double)clock(); matrixp matse; time_t now; FILE *outres,*outfile; //VG 14112006 : initialisation des variables globales interor=0;hypoth=0;nbhypor=0;nbadd=0;hypint=0;intercov=0;xlnk=0; maxhapair=0;nbloci=0; nbhhypo=0;nnt=0;ajust=0;nbcatego=0;nkat=0;nall=0;n=0; //lecture(); printf("DEBUT\n"); noUse = lecture(fileName, pMaxvarfic, pNbloci, pIdloci, pLdmatrix, pMsdata, pR2, pChxt, pNum0, pIdtime, pOffset, pIdoffset, pAjust, pNumajust, pXlnk, pNumsx); maxhap=ipow(2,nbloci); fcoda1=(short *) malloc((size_t) (maxhap*sizeof(short))); fcoda2=(int *) malloc((size_t) (maxhap*sizeof(int))); for (i=0;i0) && (chxt!=5)) {lecteffe();} if (chxt==5) {lecteffe5();} modif2=(double *) malloc((size_t) ((nall)*sizeof(double ))); for (i=0;inburn) {for (i=0;i0) {for (i=0;i0) {for (i=0;inburn) {if (chxt==2) meanste+=ste; else if (chxt==3) {for (i=0;i0) {for (i=0;i0) {for (i=0;inburn) {for (i=0;i\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,""); fprintf(outfile,"\n",nbtot); for (i=0;i\n",i); fprintf(outfile,"\n",tabmq[i]); fprintf(outres,"Number of individuals with %d missing data: %d\n",i,tabmq[i]); } if (xlnk==1) {fprintf(outres,"\nTotal number of males/females: %d / %d\n",nbhf[0][0],nbhf[1][0]); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",nbhf[0][0],nbhf[1][0]); } fprintf(outres,"\n"); fprintf(outfile,"\n"); if ((chxt==1) || (chxt==4)) {fprintf(outfile,"\n"); fprintf(outfile,"\n",nbcas); fprintf(outfile,"\n"); fprintf(outfile,"\n",nbcasm); fprintf(outres,"Total number of cas: %d\n",nbcas); fprintf(outres,"Total number of cas without missing data: %d\n",nbcasm); if (xlnk==1) {fprintf(outres,"\nTotal number of males /females in cases: %d / %d\n",nbhf[0][2],nbhf[1][2]); fprintf(outres,"\nTotal number of males /females in controls: %d / %d\n",nbhf[0][1],nbhf[1][1]); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",nbhf[0][2],nbhf[1][2]); fprintf(outfile,"\n"); fprintf(outfile,"\n",nbhf[0][1],nbhf[1][1]); } } else if (chxt==2) {fprintf(outfile,"\n",mean); fprintf(outfile,"\n\n",ste0); fprintf(outres,"Phenotypic Mean = %f\n",mean); fprintf(outres,"Standard Error = %f\n\n",ste0); } else if ( (chxt==3) || (chxt==6)) {fprintf(outfile,"\n"); fprintf(outfile,"\n",nbcas); fprintf(outfile,"\n"); fprintf(outfile,"\n",nbcasm); fprintf(outres,"Total number of uncensored individuals: %d\n",nbcas); fprintf(outres,"Total number of uncensored individuals without missing data: %d\n",nbcasm); } else if (chxt==5) {fprintf(outfile,""); for (i=0;iPhenotypic Level %d",i+1); fprintf(outfile,"",nbsujktgo[i]); fprintf(outfile,""); } fprintf(outres,"\n"); for (i=0;i
Total number of individuals:%d
Number of individuals with %d missing data:%d
Total number of males/females %d / %d
Total number of cas %d
Total number of cas without missing data %d
Total number of males/females in cases%d / %d
Total number of males/females in controls%d / %d
Phenotypic Mean = %fStandard Error = %f
Total number of uncensored individuals %d
Total number of uncensored individuals without missing data %d
%d
\n"); fprintf(outres,"\n\n"); fprintf(outfile,"
\n"); for (i=0;i\n",i+1); fprintf(outfile,"\n",letter[i][0],letter[i][1]); fprintf(outres,"Allele frequency at locus %d ",i+1); fprintf(outres,"(%c/%c) ",letter[i][0],letter[i][1]); fprintf(outfile,"\n",alfreq[i],1-alfreq[i],chdtrc(1.0,hwc[i])); fprintf(outres,"%.5f / %.5f\tp(HWE) = %f\n",alfreq[i],1-alfreq[i],chdtrc(1.0,hwc[i])); } fprintf(outres,"\n"); fprintf(outfile,"
Allele frequency at locus %d (%c/%c)%.5f / %.5f p(HWE) = %f
\n"); fprintf(outres,"Frequencies of Plausible Haplotype under Linkage Equilibrium\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n\n\n"); fprintf(outfile,"\n"); vect1=tnbhbase;i=0; while (vect1!=NULL) {if (vect1->present==1) {fprintf(outres,"Haplotype [%d]\t",i); fprintf(outfile,"\n",i); fprintf(outfile,"\n",vect1->frqle); fprintf(outres,"\t%f\n",vect1->frqle); } i++; vect1=vect1->down; } fprintf(outres,"\n\n"); fprintf(outfile,"\n"); if (chxt==2) {ste=meanste;} if (chxt==4) {bresl=(double *)malloc((size_t) (3*sizeof(double))); likematchpair(moyfreq,moyeff,bresl); nnt=nbhest+n-1; /* fishpair(moyfreq,moyeff,matse); ANCIENNE FORMULATION*/ vinter=(double **) malloc ((size_t) (nall*sizeof(double *))); for (i=0;i0) {if (xlnk==1) {Xfishem(moyfreq,moyeff,matse);} else fishem(moyfreq,moyeff,matse); } else if (chxt==0) {if (xlnk==1) {Xfishnull(moyfreq,matse);} else fishnull(moyfreq,matse); } place=(int *) malloc((size_t) (nbhhypo*sizeof(int))); for (i=0;i0) {place[i]=j;j++;} vect1=NULL; fprintf(outfile,"\n\n\n",mymaxit,nburn); fprintf(outfile,"\n"); fprintf(outres,"After %d iterations burn at step %d\n\n",mymaxit,nburn); if (chxt==0) {fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"Frequencies of Plausible Haplotypes under Linkage Disequilibrium\n\n"); fprintf(outres,"\t\t\t\tEstimation\tStError\tT-Test\n\n"); vect1=tnbhbase;i=0;somt=0; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if (vect1->present==1) {if (moyfreq[ll]>0) {fprintf(outfile,"\n",i); fprintf(outfile,"",res); fprintf(outres," %f\t",res); if ((place[ll]!=0) && (res>0)) {valse=sqrt(matse[place[ll]-1][place[ll]-1]); fprintf(outfile,"\n",valse,res/valse); fprintf(outres,"%f\t%f\n",valse,res/valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } } i++; vect1=vect1->down; } vect1=NULL; } if (chxt==0) {frqobs=(double *) malloc((size_t) (nbhhypo*sizeof(double))); frqord=(double *) malloc((size_t) (nbhhypo*sizeof(double))); numobs=(int *) malloc((size_t) (nbhhypo*sizeof(int))); numord=(int *) malloc((size_t) (nbhhypo*sizeof(int))); for (i=0;ipresent==1) {i=fcoda2[vect1->numnew]; if (moyfreq[i]>0) {frqobs[j]=moyfreq[i]/*/(mymaxit-nburn-1)*/;numobs[j]=vect1->numnew;j++;} } vect1=vect1->down; } for (i=0;ifrqord[k]) {trouve=1;} k++; } if (trouve==0) {numord[i]=numobs[i];frqord[i]=frqobs[i];} else if (trouve==1) {for (ll=i;ll>k-1;ll--) {numord[ll]=numord[ll-1];frqord[ll]=frqord[ll-1];} numord[k-1]=numobs[i];frqord[k-1]=frqobs[i]; } } } parafile=NULL; if ((parafile=fopen("para.txt","w"))==NULL) {printf("Error in Output file writing....\n");exit(0);} fprintf(parafile,"%d\n",j); for (i=0;i\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\n"); fprintf(outres,"\t\t\t\tEstimation\tStError\t\tT-Test\n\n"); vect1=tnbhbase;i=0;somt=0; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if (vect1->present==1) {if (moyfreq[ll]>0) {fprintf(outfile,"\n",coding(ll)+1,i); fprintf(outres,"Haplotype %d [%d] \t",coding(ll)+1,i); fprintf(outfile,"\n",valse,res/valse); fprintf(outres,"\t%f\t%f\n",valse,res/valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } somt+=res; } } i++; vect1=vect1->down; } vect1=NULL; } else if ((chxt==3) || (chxt==4) || (chxt==6) || (chxt==5)) {fprintf(outres,"\n"); fprintf(outres,"Estimated Haplotype Frequencies under Linkage Disequilibrium\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\n"); fprintf(outres,"\t\t\t\tEstimation\t\t\t\n\n"); vect1=tnbhbase;i=0;somt=0; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if (vect1->present==1) {if (moyfreq[ll]>0) {fprintf(outfile,"\n",coding(ll)+1,i); fprintf(outres,"Haplotype %d [%d] \t",coding(ll)+1,i); fprintf(outfile,"\n"); fprintf(outres,"\n"); somt+=res; } } i++; vect1=vect1->down; } vect1=NULL; } if ((chxt==1)) {fprintf(outres,"\n\n"); fprintf(outres,"Estimated Haplotype Frequencies in\tControls (=0)\tCases (=1)\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); vect1=tnbhbase;i=0; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if (vect1->present==1) {if (moyfreq[ll]>0) {fprintf(outres,"Haplotype %d [%d] \t",coding(ll)+1,i); fprintf(outfile,"\n",coding(ll)+1,i); fprintf(outfile,"\n",freqtem[ll],freqcas[ll]); fprintf(outres,"\t\t%f\t%f\n",freqtem[ll],freqcas[ll]); } } i++; vect1=vect1->down; } vect1=NULL; } else if ((chxt==3) || (chxt==4) || (chxt==6) ) {fprintf(outres,"\n\n"); fprintf(outres,"Estimated Haplotype Frequencies in\tCensored (=0)\tUncensored (=1) individuals\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); vect1=tnbhbase;i=0; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if (vect1->present==1) {if (moyfreq[ll]>0) {fprintf(outres,"Haplotype %d [%d] \t",coding(ll)+1,i); fprintf(outfile,"\n",coding(ll)+1,i); fprintf(outfile,"\n",freqtem[ll],freqcas[ll]); fprintf(outres,"\t\t%f\t%f\n",freqtem[ll],freqcas[ll]); } } i++; vect1=vect1->down; } vect1=NULL; } else if (chxt==5) {fprintf(outres,"\n\n"); fprintf(outres,"Estimated Haplotype Frequencies in\n\n\t\t\t\t"); for (i=0;i\n"); fprintf(outfile,"\n"); fprintf(outfile,""); fprintf(outfile,"\n"); for (i=0;iClass Level %d",i+1); fprintf(outfile,"\n"); fprintf(outfile,"\n"); vect1=tnbhbase;i=0; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if (vect1->present==1) {if (moyfreq[ll]>0) {fprintf(outres,"Haplotype %d [%d] \t",coding(ll)+1,i); fprintf(outfile,"\n",coding(ll)+1,i); fprintf(outfile,""); for (j=0;j%lf",freqkat[j][ll]); fprintf(outres,"\t%f",freqkat[j][ll]); } fprintf(outfile,"");fprintf(outres,"\n"); } } i++; vect1=vect1->down; } vect1=NULL; } fprintf(outres,"\n\n"); fprintf(outfile,"\n"); if ((chxt==1) || (chxt==2)) {fprintf(outres,"\n"); fprintf(outres,"\t\t\tHaplotype Effects\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); if ((chxt==1) && (haplozero==0)) {fprintf(outfile,"\n\n"); fprintf(outres,"\t\t(Haplotypic OR by comparison to the reference with its 95%% CI)\n\n"); } if ((chxt==2) && (haplozero==0)) {fprintf(outfile,"\n"); fprintf(outres,"\t\t(Haplotypic effect by comparison to the reference with its 95%% CI)\n\n"); } fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\t\tEstimation\tStError\t\tT-Test\n\n"); if (haplozero==1) {valse=sqrt(matse[nbhest-1][nbhest-1]); fprintf(outfile,"\n",effest[0]); fprintf(outfile,"\n",valse); fprintf(outres,"Intercept\t%f\t%f\n",effest[0],valse); } else if (haplozero==0) {vect1=tnbhbase;trouve=0; j=0;k=0; while (vect1!=NULL) {trouve=0; i=0; while ((trouve==0) && (inumnew]==numhap[i]) { trouve=1; if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"Intercept 1\t"); } else {fprintf(outres,"Haplotype %d\t",i+1); fprintf(outfile,"",i+1); } fprintf(outfile,"");fprintf(outres,"\t"); if (i==0) {valse=sqrt(matse[nbhest-1][nbhest-1]); fprintf(outfile,"\n\n",effest[0],valse,effest[0]/valse); fprintf(outfile,"\n"); fprintf(outres,"\t%f\t%f\n\n",effest[0],valse,effest[0]/valse); } else { fprintf(outfile,"",effest[i]); fprintf(outres,"\t%.5f\t",effest[i]); if (itp[i]==1) {valse=sqrt(matse[nbhest-1+nitp[i]][nbhest-1+nitp[i]]); valef=effest[i]; affichage(outfile,valef,valse); affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } } i++; } vect1=vect1->down;trouve=0; } } } else if ( (chxt==3) || (chxt==4) || (chxt==6) ) {fprintf(outres,"\n"); fprintf(outres,"\t\t\tHaplotype Effects\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); if ((chxt==1) && (haplozero==0)) {fprintf(outfile,"\n\n"); fprintf(outres,"\t\t(Haplotypic OR by comparison to the reference with its 95%% CI)\n\n"); } if ((chxt==2) && (haplozero==0)) {fprintf(outfile,"\n"); fprintf(outres,"\t\t(Haplotypic effect by comparison to the reference with its 95%% CI)\n\n"); } fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\t\tEstimation\tStError\t\tT-Test\n\n"); if (haplozero==1) { } else if (haplozero==0) {vect1=tnbhbase;trouve=0; j=0;k=0; while (vect1!=NULL) {trouve=0; i=0; while ((trouve==0) && (inumnew]==numhap[i]) { trouve=1; if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"Intercept 1\t"); } else {fprintf(outres,"Haplotype %d\t",i+1); fprintf(outfile,"",i+1); } fprintf(outfile,"");fprintf(outres,"\t"); if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"\n"); } else { fprintf(outfile,"",effest[i]); fprintf(outres,"\t%.5f\t",effest[i]); if (itp[i]==1) {valse=sqrt(matse[nbhest-1+nitp[i]-1][nbhest-1+nitp[i]-1]); valef=effest[i]; affichage(outfile,valef,valse); affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } } i++; } vect1=vect1->down;trouve=0; } } } else if (chxt==5) {fprintf(outres,"\n"); fprintf(outres,"\t\t\tHaplotype Effects\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\t\tEstimation\tStError\t\tT-Test\n\n"); for (nc=0;nc\n"); fprintf(outres,"\n\n"); if (haplozero==1) {valse=sqrt(matse[nbhest-1+nc][nbhest-1+nc]); fprintf(outfile,"\n",nc+2,effest[nc]); fprintf(outfile,"\n",valse); fprintf(outres,"Intercept for Class Level %d\t%f\t%f\n",nc+2,effest[nc],valse); } else if (haplozero==0) {fprintf(outfile,"\n\n",nc+2); fprintf(outres,"\t\tHaplotypic OR for Class Level %d by comparison to Class Level 1\n\n",nc+2); vect1=tnbhbase;trouve=0; j=0;k=0; while (vect1!=NULL) {trouve=0; i=0; while ((trouve==0) && (inumnew]==numhap[i]) {trouve=1; if (i==0) {fprintf(outfile,"\n",nc); fprintf(outres,"Intercept (ID:%d)\t",nc); } else {fprintf(outres,"Haplotype %d (ID:%d)\t",i+1,i*nkat+nc); fprintf(outfile,"",i+1,i*nkat+nc); } fprintf(outfile,"");fprintf(outres,"\t"); if (i==0) {valse=sqrt(matse[nbhest-1+nc][nbhest-1+nc]); fprintf(outfile,"\n\n",effest[nc],valse,effest[nc]/valse); fprintf(outfile,"\n"); fprintf(outres,"\t%f\t%f\n\n",effest[nc],valse,effest[nc]/valse); } else {fprintf(outfile,"",effest[i*nkat+nc]); fprintf(outres,"\t%.5f\t",effest[i*nkat+nc]); if (itp[i*nkat+nc]==1) {valse=sqrt(matse[nbhest-1+nitp[i*nkat+nc]][nbhest-1+nitp[i*nkat+nc]]); valef=effest[i*nkat+nc]; affichage(outfile,valef,valse); affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } } i++; } vect1=vect1->down;trouve=0; } } } fprintf(outres,"\n\n"); fprintf(outres,"Log-likelihood = %f ",vraise); fprintf(outres,"(Nb studied subjects = %d)\n",nbused); fprintf(outfile,"\n");fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",vraise); fprintf(outfile,"",nbused); fprintf(outfile,"\n"); fprintf(outres,"Conditionnal Log-likelihood = %f ",vraiscond); fprintf(outres,"(df = %2d)\n\n\n",n); fprintf(outfile,"\n",vraiscond); fprintf(outfile,"",n); fprintf(outfile,"\n"); if (ajust>0) {fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tCovariable Adjustment\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); for (nc=0;nc\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",nc+2); fprintf(outfile,"\n"); fprintf(outres,"\n"); fprintf(outres,"\n"); fprintf(outres,"Information for CLASS LEVEL %d\n",nc+2); fprintf(outres,"\n"); for (i=0;i\n",i+1); fprintf(outfile,"\n",numajust[i]); fprintf(outfile,"\n",effest[nbhest*nkat+i*nkat+nc]); fprintf(outres,"Covariate %d \n",i+1); fprintf(outres,"Column Number %d \t\t",numajust[i]); fprintf(outres,"%f\t",effest[nbhest*nkat+i*nkat+nc]); if (itp[nbhest*nkat+i*nkat+nc]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest*nkat+i*nkat+nc]][nbhest-1+nitp[nbhest*nkat+i*nkat+nc]]); valef=effest[nbhest*nkat+i*nkat+nc]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } } } if (nbadd>0) {fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tNon additivity of haplotypic effects\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); for (nc=0;nc\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",nc+2); fprintf(outfile,"\n"); fprintf(outres,"\n"); fprintf(outres,"\n"); fprintf(outres,"Information for CLASS LEVEL %d\n",nc+2); fprintf(outres,"\n"); for (i=0;i\n",tadd[i][0],tadd[i][1]); fprintf(outfile,"\n",effest[(nbhest+ajust)*nkat+i*nkat+nc]); fprintf(outres,"Haplotype %d x Haplotype %d\t",tadd[i][0],tadd[i][1]); fprintf(outres,"%f\t",effest[(nbhest+ajust)*nkat+i*nkat+nc]); if (itp[(nbhest+ajust)*nkat+i*nkat+nc]==1) {valse=sqrt(matse[nbhest-1+nitp[(nbhest+ajust)*nkat+i*nkat+nc]][nbhest-1+nitp[(nbhest+ajust)*nkat+i*nkat+nc]]); valef=effest[(nbhest+ajust)*nkat+i*nkat+nc]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } } } if (intercov>0) {fprintf(outfile,"\n"); fprintf(outfile,""); fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tHaplotype x Covariable Interaction\n\n"); for (i=0;i\n",biz.rem+2,biz.quot+1,tabint[i][1]); fprintf(outres,"CLASS LEVEL %d Haplotype %d with Covariate %d\t",biz.rem+2,biz.quot+1,tabint[i][1]); fprintf(outfile,"\n",effest[(nbhest+ajust+nbadd)*nkat+i]); fprintf(outres,"%f\t",effest[(nbhest+ajust+nbadd)*nkat+i]); if (itp[(nbhest+ajust+nbadd)*nkat+i]==1) {valse=sqrt(matse[nbhest-1+nitp[(nbhest+ajust+nbadd)*nkat+i]][nbhest-1+nitp[(nbhest+ajust+nbadd)*nkat+i]]); valef=effest[(nbhest+ajust+nbadd)*nkat+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n");fprintf(outres,"\n");} } } } if (chxt==2) {fprintf(outfile,"\n"); fprintf(outfile,"\n",ste0); fprintf(outfile,"\n",ste); fprintf(outres,"\n\n"); fprintf(outres,"Global Standard Error %f\n",ste0); fprintf(outres,"Residual Standard Error %f\n",ste); } if ( (chxt==1) || (chxt==2)) {if (ajust>0) {fprintf(outres,"\n"); fprintf(outres,"\t\t\tCovariable Adjustment\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); for (i=0;i\n"); fprintf(outres,"Gender %d \n",i+1); } else {fprintf(outfile,"\n",i+1); fprintf(outres,"Covariate %d \n",i+1); } fprintf(outfile,"\n",numajust[i]); fprintf(outfile,"\n",effest[nbhest+i]); fprintf(outres,"Column Number %d \t\t",numajust[i]); fprintf(outres,"%f\t",effest[nbhest+i]); if (itp[nbhest+i]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest+i]][nbhest-1+nitp[nbhest+i]]); valef=effest[nbhest+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } if (intercov>0) {fprintf(outfile,"\n"); fprintf(outfile,""); fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tHaplotype x Covariable Interaction\n\n"); for (i=0;i\n",tabint[i][0]); fprintf(outres,"Haplotype %d x Gender\t",tabint[i][0]); } else {fprintf(outfile,"\n",tabint[i][0],tabint[i][1]); fprintf(outres,"Haplotype %d x Covariate %d\t",tabint[i][0],tabint[i][1]); } fprintf(outfile,"\n",effest[nbhest+ajust+i+nbadd]); fprintf(outres,"%f\t",effest[nbhest+ajust+i+nbadd]); if (itp[nbhest+ajust+nbadd+i]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest+ajust+nbadd+i]][nbhest-1+nitp[nbhest+ajust+nbadd+i]]); valef=effest[nbhest+ajust+nbadd+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n");fprintf(outres,"\n");} } } } if (nbadd>0) {fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tNon additivity of haplotypic effects\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); for (i=0;i\n",tadd[i][0],tadd[i][1]); fprintf(outfile,"\n",effest[nbhest+ajust+i]); fprintf(outres,"Haplotype %d x Haplotype %d\t",tadd[i][0],tadd[i][1]); fprintf(outres,"%f\t",effest[nbhest+ajust+i]); if (itp[nbhest+ajust+i]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest+ajust+i]][nbhest-1+nitp[nbhest+ajust+i]]); valef=effest[nbhest+ajust+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n");fprintf(outres,"\n");} } } } else if ((chxt==3) || (chxt==4) || (chxt==6)) {if (ajust>0) {fprintf(outres,"\n"); fprintf(outres,"\t\t\tCovariable Adjustment\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); for (i=0;i\n",i+1); fprintf(outfile,"\n",numajust[i]); fprintf(outfile,"\n",effest[nbhest+i]); fprintf(outres,"Covariate %d \n",i+1); fprintf(outres,"Column Number %d \t\t",numajust[i]); fprintf(outres,"%f\t",effest[nbhest+i]); if (itp[nbhest+i]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest+i]-1][nbhest-1+nitp[nbhest+i]-1]); valef=effest[nbhest+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n"); fprintf(outres,"\n"); } } if (intercov>0) {fprintf(outfile,"\n"); fprintf(outfile,""); fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tHaplotype x Covariable Interaction\n\n"); for (i=0;i\n",tabint[i][0],tabint[i][1]); fprintf(outfile,"\n",effest[nbhest+ajust+i+nbadd]); fprintf(outres,"Haplotype %d x Covariate %d\t",tabint[i][0],tabint[i][1]); fprintf(outres,"%f\t",effest[nbhest+ajust+i+nbadd]); if (itp[nbhest+ajust+nbadd+i]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest+ajust+nbadd+i]-1][nbhest-1+nitp[nbhest+ajust+nbadd+i]-1]); valef=effest[nbhest+ajust+nbadd+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n");fprintf(outres,"\n");} } } } if (nbadd>0) {fprintf(outres,"\n\n"); fprintf(outres,"\t\t\tNon additivity of haplotypic effects\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); for (i=0;i\n",tadd[i][0],tadd[i][1]); fprintf(outfile,"\n",effest[nbhest+ajust+i]); fprintf(outres,"Haplotype %d x Haplotype %d\t",tadd[i][0],tadd[i][1]); fprintf(outres,"%f\t",effest[nbhest+ajust+i]); if (itp[nbhest+ajust+i]==1) {valse=sqrt(matse[nbhest-1+nitp[nbhest+ajust+i]-1][nbhest-1+nitp[nbhest+ajust+i]-1]); valef=effest[nbhest+ajust+i]; affichage(outfile,valef,valse);affichage2(outres,valef,valse); } else {fprintf(outfile,"\n");fprintf(outres,"\n");} } } } if (chxt>0) {if (chxt<3) {if (xlnk==1) {vraise=Xlikelihood(moyfreq,moyeff); vraiscond=vraise-Xcondlike(moyfreq); } else if (xlnk==0) {vraise=likelihood(moyfreq,moyeff); vraiscond=vraise-condlike(moyfreq); } fprintf(outres,"\n\n"); fprintf(outres,"Log-likelihood = %f ",vraise); fprintf(outres,"(Nb studied subjects = %d)\n",nbused); fprintf(outres,"Conditionnal Log-likelihood = %f ",vraiscond); fprintf(outres,"(df = %2d)\n\n\n",nnt-nbhest+1); fprintf(outfile,"\n");fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",vraise); fprintf(outfile,"",nbused); fprintf(outfile,"\n"); fprintf(outfile,"\n",vraiscond); fprintf(outfile,"",nnt-nbhest+1); fprintf(outfile,"
Frequencies of Plausible Haplotype under Linkage Equilibrium
Haplotype [%d]"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l); fprintf(outres,"%c",l); } fprintf(outfile,"%f
After %d iterations burn at step %d
Haplotype Frequencies under Linkage Disequilibrium
EstimationStErrorT-Test
Haplotype [%d] "); fprintf(outres,"Haplotype [%d] \t",i); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l); fprintf(outres,"%c",l); } fprintf(outfile,""); res=moyfreq[ll]; fprintf(outfile,"%f%f%f
Haplotypes Frequencies under Linkage Disequilibrium
EstimationStErrorT-Test
Haplotype %d [%d]"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,""); res=moyfreq[ll]; fprintf(outfile,"\t%f",res);fprintf(outres,"\t%f",res); if ((place[ll]!=0) && (res>0)) {valse=sqrt(matse[place[ll]-1][place[ll]-1]); fprintf(outfile,"%f%f
Haplotypes Frequencies under Linkage Disequilibrium
Estimation  
Haplotype %d [%d]"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,""); res=moyfreq[ll]; fprintf(outfile,"\t%f",res);fprintf(outres,"\t%f",res); fprintf(outfile,"
Haplotype Frequencies inControls (=0)Cases (=1)
Haplotype %d [%d]"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,""); fprintf(outfile,"%f%f
Haplotype Frequencies inCensored (=0)Uncensored (=1)
Haplotype %d [%d]"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,""); fprintf(outfile,"%f%f
Haplotype Frequencies
  
Haplotype %d [%d]"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,"
Haplotype Effects
(Haplotypic OR by comparison to the reference with its 95%% CI)
(Haplotypic effect by comparison to the reference with its 95%% CI)
EstimationStErrorT-Test
Intercept %f%f
Intercept 1
Haplotype %d "); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,"%.5f%f%f
%.5f
Haplotype Effects
(Haplotypic OR by comparison to the reference with its 95%% CI)
(Haplotypic effect by comparison to the reference with its 95%% CI)
EstimationStErrorT-Test
Intercept 1
Haplotype %d "); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,"
%.5f
Haplotype Effects
EstimationStErrorT-Test
Intercept for Class Level %d %f%f
Haplotypic OR for Class Level %d by comparison to Class Level 1
Intercept (ID:%d)
Haplotype %d (ID:%d)"); for (j=0;jlistall[j]==1)+letter[j][1]*(vect1->listall[j]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } fprintf(outfile,"%.5f%f%f
%.5f
Log-likelihood %f(Nb studied subjects = %d)
Conditionnal Log-likelihood=%f(df = %2d)
Covariable Adjustment
Information for CLASS LEVEL %d
Covariate %dColumn Number %d%f
Non additivity of haplotypic effects
Information for CLASS LEVEL %d
Haplotype %d x Haplotype %d %f
Haplotype x Covariable Interaction
CLASS LEVEL %d Haplotype %d with Covariate %d %f
Global Standard Error %f
Residual Standard Error %f
Covariable Adjustment
Gender
Covariate %dColumn Number %d%f
Haplotype x Covariable Interaction
Haplotype %d x Gender
Haplotype %d x Covariate %d %f
Non additivity of haplotypic effects
Haplotype %d x Haplotype %d %f
Covariable Adjustment
Covariate %dColumn Number %d%f
Haplotype x Covariable Interaction
Haplotype %d x Covariate %d %f
Non additivity of haplotypic effects
Haplotype %d x Haplotype %d %f
Log-likelihood %f(Nb studied subjects = %d)
Conditionnal Log-likelihood=%f(df = %2d)
\n"); } else if ( (chxt==3) || (chxt==4)) {fprintf(outres,"\n\n"); fprintf(outres,"-2 x Log-likelihood (with covariates) = %f ",2*bresl[2]); fprintf(outres,"(Nb studied subjects = %d)\n",nbused); fprintf(outres,"-2 x Log-likelihood (without covariates) = %f ",2*bresl[0]); fprintf(outres," (df = %2d)\n\n\n",nnt-nbhest+1-1); fprintf(outfile," \n");fprintf(outfile," \n"); fprintf(outfile," \n"); fprintf(outfile,"-2x Log-likelihood (with covariates) = %f\n",2*bresl[2]); fprintf(outfile,"(Nb studied subjects = %d)",nbused); fprintf(outfile," \n"); fprintf(outfile,"-2 x Log-likelihood (without covariates) =%f\n",2*bresl[0]); fprintf(outfile,"(df = %2d)",nnt-nbhest+1-1); fprintf(outfile," \n"); } if ((haplozero==0) && (chxt!=5)) {fprintf(outfile,"\n"); for (i=1;i\n"); fprintf(outfile,"\n",i,letter[i-1][0],letter[i-1][1]); fprintf(outres,"\n"); fprintf(outres,"Polymorphism %d %c/%c\n",i,letter[i-1][0],letter[i-1][1]); k=pow(2,nbloci-i); j=0; vect1=tnbhbase; while ( (vect1!=NULL) ) {ll=fcoda2[vect1->numnew]; ll2=fcoda2[vect1->numnew+k]; if ((vect1->present==1) && (ll2>-1) && (vect1->listall[i-1]==1) && (coding(ll)>-1) && (coding(ll2)>-1) && (moyfreq[ll]>0.00) && (moyfreq[ll2]!=0.00)) {fprintf(outfile,"\n"); fprintf(outfile,"\n");fprintf(outres,"\n"); } vect1=vect1->down; } } fprintf(outfile,"
Polymorphism %d %c/%c
Haplotypic Background"); fprintf(outres,"Haplotypic Background "); for (ii=0;iilistall[ii]==1)+letter[ii][1]*(vect1->listall[ii]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } else if (ii+1==i) {fprintf(outfile,"-"); fprintf(outres,"-"); } } fprintf(outfile,""); fprintf(outfile," %d-%d \t",coding(fcoda2[vect1->numnew])+1,coding(fcoda2[vect1->numnew+k])+1); fprintf(outfile,""); fprintf(outres,"\t%d-%d\t",coding(fcoda2[vect1->numnew])+1,coding(fcoda2[vect1->numnew+k])+1); imn=coding(fcoda2[vect1->numnew]); imnk=coding(fcoda2[vect1->numnew+k]); if ((imn==0) && (itp[imnk]==1)) {valef=effest[imnk]; if ( (chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]);} else {valse=sqrt(matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]);} } else if ((imn==0) && (itp[imnk]==0)) {valef=effest[imnk]; if (valef!=0) {if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]);} else {valse=sqrt(matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]);} } else valse=-1; } else if ((imnk==0) && (itp[imn]==1)) {valef=-effest[imn]; if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]);} else {valse=sqrt(matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]);} } else if ((itp[imn]==1) && (itp[imnk]==1)) {if ((imn!=0) && (imnk!=0)) {if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valef=matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]; valef+=matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]; valef-=2*matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imnk]]; } else {valef=matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]; valef+=matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]; valef-=2*matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imnk]-1]; } valse=sqrt(valef); valef=effest[imnk]-effest[imn]; } else if (imn==0) {if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]);} else {valse=sqrt(matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]);} valef=effest[imnk]; } else if (imnk==0) {if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]);} else {valse=sqrt(matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]);} valef=-effest[imn]; } } else if (itp[imn]==0) {if (nitp[imn]==-2) {if (nitp[imnk]>0) {valef=effest[imnk]; if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]);} else {valse=sqrt(matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]);} } else if (nitp[imnk]!=-1) {valef=0;valse=0;} else {valef=0;valse=-1;} } else if ((nitp[imn]>-1) && (nitp[imnk]==-2)) {valef=-effest[imn]; if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]);} else {valse=sqrt(matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]);} } else if ( (nitp[imn]>-1) && (nitp[imnk]==-1)) {valef=0;valse=-1;} else if ( (nitp[imn]==-1) && (effest[imn]==0)) {valef=0;valse=-1; } else if ((nitp[imnk]==-1) && (nitp[imn]==-1)) {valef=0;valse=-1; } else if (nitp[imn]==0) {valef=effest[imnk]; if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]);} else {valse=sqrt(matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]);} } else if (nitp[imn]>0) {if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valef= matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]; valef+=matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]; valef-=2*matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imnk]]; } else {valef= matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]; valef+=matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]; valef-=2*matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imnk]-1]; } valse=sqrt(valef); valef=effest[imnk]-effest[imn]; } else {valef=effest[imnk]-effest[imn];valse=0; } } else if (itp[imnk]==0) { if (nitp[imnk]==-2) {if(nitp[imn]>0) {valef=-effest[imn]; if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]);} else {valse=sqrt(matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]);} } else if (nitp[imn]!=-1) {valef=0;valse=0;} else {valef=0;valse=-1;} } else if ( (nitp[imnk]>-1) && (nitp[imn]==-1)) {valef=0;valse=-1;} else if ((nitp[imnk]==-1) && (effest[imnk]==0)) {valef=0;valse=-1; } else if ((nitp[imnk]==-1) && (nitp[imn]==-1)) {valef=0;valse=-1; } else if (nitp[imnk]==0) {valef=-effest[imn]; if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valse=sqrt(matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]);} else {valse=sqrt(matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]);} } else if (nitp[imnk]>0) {if ((chxt!=3) && (chxt!=6) && (chxt!=4)) {valef= matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imn]]; valef+=matse[nbhest-1+nitp[imnk]][nbhest-1+nitp[imnk]]; valef-=2*matse[nbhest-1+nitp[imn]][nbhest-1+nitp[imnk]]; } else {valef= matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imn]-1]; valef+=matse[nbhest-1+nitp[imnk]-1][nbhest-1+nitp[imnk]-1]; valef-=2*matse[nbhest-1+nitp[imn]-1][nbhest-1+nitp[imnk]-1]; } valse=sqrt(valef); valef=effest[imnk]-effest[imn]; } else {valef=effest[imnk]-effest[imn];valse=0; } } affich3(outres,valef,valse); affich3(outfile,valef,valse); fprintf(outfile,"
\n"); } } if ((haplozero==0) && (chxt==5)) { fprintf(outfile,"\n"); for (nc=0;nc\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",nc+2); fprintf(outfile,"\n"); fprintf(outres,"\n"); fprintf(outres,"\n"); fprintf(outres,"Information for CLASS LEVEL %d\n",nc+2); fprintf(outres,"\n"); for (i=1;i\n"); fprintf(outfile,"\n",i,letter[i-1][0],letter[i-1][1]); fprintf(outres,"\n"); fprintf(outres,"Polymorphism %d %c/%c\n",i,letter[i-1][0],letter[i-1][1]); k=pow(2,nbloci-i); j=0; vect1=tnbhbase;trouve=0; while ( (vect1!=NULL) && (trouve==0)) {imn=coding(fcoda2[vect1->numnew]); imnk=coding(fcoda2[vect1->numnew+k]); if ((vect1->listall[i-1]==1) && (imn>-1) && (imnk>-1) && (freqkat[nc+1][fcoda2[vect1->numnew]]>0) && (freqkat[nc+1][fcoda2[vect1->numnew+k]]>0)) {fprintf(outfile,"\n"); fprintf(outfile,"\n");fprintf(outres,"\n"); } vect1=vect1->down; } }/*i*/ }/*nc*/ fprintf(outfile,"
Information for CLASS LEVEL %d
Polymorphism %d %c/%c
Haplotypic Background"); fprintf(outres,"Haplotypic Background "); for (ii=0;iilistall[ii]==1)+letter[ii][1]*(vect1->listall[ii]==2); fprintf(outfile,"%c",l);fprintf(outres,"%c",l); } else if (ii+1==i) {fprintf(outfile,"-"); fprintf(outres,"-"); } } fprintf(outfile,""); fprintf(outfile," ID %d-%d \t",imn*nkat+nc,imnk*nkat+nc); fprintf(outfile,""); fprintf(outres,"\tID %d-%d\t",imn*nkat+nc,imnk*nkat+nc); idn=imn*nkat+nc; idk=imnk*nkat+nc; if ((idn==nc) && (itp[idk]==1)) {valef=effest[idk]; valse=sqrt(matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]); } else if ((idn==nc) && (itp[idk]==0)) {valef=effest[idk]; if (valef!=0) {valse=sqrt(matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]); } else valse=-1; } else if ((idk==nc) && (itp[idn]==1)) {valef=-effest[idn]; valse=sqrt(matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]); } else if ((itp[idn]==1) && (itp[idk]==1)) {if ((idn!=0) && (idk!=0)) {valef=matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]; valef+=matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]; valef-=2*matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idk]]; valse=sqrt(valef); valef=effest[idk]-effest[idn]; } else if (idn==0) {valse=sqrt(matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]); valef=effest[idk]; } else if (idk==0) {valse=sqrt(matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]); valef=-effest[idn]; } } else if (itp[idn]==0) {if (nitp[idn]==-2) {if (nitp[idk]>0) {valef=effest[idk];valse=sqrt(matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]); } else if (nitp[idk]!=-1) {valef=0;valse=0;} else {valef=0;valse=-1;} } else if ((nitp[idn]>-1) && (nitp[idk]==-2)) {valef=-effest[idn];valse=sqrt(matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]); } else if ( (nitp[idn]>-1) && (nitp[idk]==-1)) {valef=0;valse=-1;} else if ( (nitp[idn]==-1) && (effest[idn]==0)) {valef=0;valse=-1;} else if ((nitp[idk]==-1) && (nitp[idn]==-1)) {valef=0;valse=-1;} else if (nitp[idn]==0) {valef=effest[idk];valse=sqrt(matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]);} else if (nitp[idn]>0) {valef= matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]; valef+=matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]; valef-=2*matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idk]]; valse=sqrt(valef); valef=effest[idk]-effest[idn]; } else {valef=effest[idk]-effest[idn];valse=0; } } else if (itp[idk]==0) {if (nitp[idk]==-2) {if(nitp[idn]>0) {valef=-effest[idn];valse=sqrt(matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]);} else if (nitp[idn]!=-1) {valef=0;valse=0;} else {valef=0;valse=-1;} } else if ( (nitp[idk]>-1) && (nitp[idn]==-1)) {valef=0;valse=-1;} else if ((nitp[idk]==-1) && (effest[idk]==0)) {valef=0;valse=-1; } else if ((nitp[idk]==-1) && (nitp[idn]==-1)) {valef=0;valse=-1; } else if (nitp[idk]==0) {valef=-effest[idn];valse=sqrt(matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]);} /*else if (nitp[idk]>0) {valef= matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idn]]; valef+=matse[nbhest-1+nitp[idk]][nbhest-1+nitp[idk]]; valef-=2*matse[nbhest-1+nitp[idn]][nbhest-1+nitp[idk]]; valse=sqrt(valef); valef=effest[idk]-effest[idn]; }*/ else {valef=effest[idk]-effest[idn];valse=0;} } else {valef=0;valse=-1;} affich3(outfile,valef,valse); affich3(outres,valef,valse); fprintf(outfile,"
\n"); } //printf("BOU\n"); if (chxt==2) {phenomean(outres,outfile,matse);} //printf("BOU3\n"); if (rsq==1) {fprintf(outres,"\n\n\n"); fprintf(outfile,"\n"); if (xlnk==0) rsquare(moyfreq,outfile,outres); fprintf(outfile,"
"); } if ((ldmatrix==1) && (xlnk==1)) {fprintf(outres,"\n\n\n"); fprintf(outfile,"\n"); ldp=(double **) malloc ((size_t) (nbloci*sizeof(double *))); lr2=(double **) malloc ((size_t) (nbloci*sizeof(double *))); chidp=(double **) malloc ((size_t) (nbloci*sizeof(double *))); for (i=0;inumnew]; if ((vect1->present==1) && (moyfreq[ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (moyfreq[ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=moyfreq[ll]; } } } } vect1=vect1->down; } for (k=0;k=0.5); minl=alfreq[ii]*(alfreq[ii]<0.5)+(1-alfreq[ii])*(alfreq[ii]>=0.5); ldp[k][ii]-=mink*minl; chidp[k][ii]=(ldp[k][ii]*ldp[k][ii]*(2*nbhf[1][0]+nbhf[0][0]))/(alfreq[k]*alfreq[ii]*(1-alfreq[k])*(1-alfreq[ii])); if (ldp[k][ii]<0) {dmax=mink*minl;} else {if (mink1.0) {ldp[k][ii]/=fabs(ldp[k][ii]);} } fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\tLD MATRIX\n\n"); for (k=0;k");fprintf(outres,"\n"); } fprintf(outfile,"\n");fprintf(outres,"\n\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\tP-Value MATRIX\n\n"); fprintf(outfile,"\n"); for (k=0;k"); fprintf(outres,"\n");for (ii=0;ii\n");fprintf(outfile,"\n\n"); } else if (chxt==1) {for (i=0;i<2;i++) {for (k=0;knumnew]; if ((vect1->present==1) && (freqtem[ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqtem[ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=freqtem[ll]; } } } } vect1=vect1->down; } } if (i==1) {while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqcas[ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqcas[ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=freqcas[ll]; } } } } vect1=vect1->down; } } for (k=0;k=0.5); minl=alfreq[ii]*(alfreq[ii]<0.5)+(1-alfreq[ii])*(alfreq[ii]>=0.5); ldp[k][ii]-=mink*minl; chidp[k][ii]=(ldp[k][ii]*ldp[k][ii])/(alfreq[k]*alfreq[ii]*(1-alfreq[k])*(1-alfreq[ii])); if (i==0) {chidp[k][ii]*=(2*nbhf[1][1]+nbhf[0][1]);} else if (i==1) {chidp[k][ii]*=(2*nbhf[1][2]+nbhf[0][2]);} if (ldp[k][ii]<0) {dmax=mink*minl;} else {if (mink1.0) {ldp[k][ii]/=fabs(ldp[k][ii]);} } fprintf(outres,"\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tLD MATRIX IN CONTROLS\n\n"); } if (i==1) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tLD MATRIX IN CASES\n\n"); } fprintf(outfile,"\n"); for (k=0;k");fprintf(outres,"\n"); } fprintf(outfile,"\n"); fprintf(outres,"\n\n"); if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tP-Value IN CONTROLS\n\n"); } if (i==1) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tP-Value IN CASES\n\n"); } fprintf(outfile,"\n"); for (k=0;k");fprintf(outres,"\n"); for (ii=0;ii\n");fprintf(outres,"\n"); } } fprintf(outfile,"
LD MATRIX
"); fprintf(outres,"\t\t"); for (ii=0;iik) {fprintf(outfile," %3.2f",ldp[k][ii]); fprintf(outres," %3.2f\t",ldp[k][ii]); } } fprintf(outfile,"
P-Value MATRIX
");fprintf(outres,"\t\t"); fprintf(outfile," X ");fprintf(outres," X\t"); for (ii=k+1;ii
LD MATRIX IN CONTROLS
LD MATRIX IN CASES
"); for (ii=0;iik) {fprintf(outfile," %3.2f",ldp[k][ii]); fprintf(outres," %3.2f\t",ldp[k][ii]); } } fprintf(outfile,"
P-Value IN CONTROLS
P-Value IN CASES
");fprintf(outres,"\t\t"); fprintf(outfile," X ");fprintf(outres," X\t"); for (ii=k+1;ii
"); } else if ((ldmatrix==1) && (xlnk==0)) {fprintf(outres,"\n\n\n"); fprintf(outfile,"\n"); ldp=(double **) malloc ((size_t) (nbloci*sizeof(double *))); lr2=(double **) malloc ((size_t) (nbloci*sizeof(double *))); chidp=(double **) malloc ((size_t) (nbloci*sizeof(double *))); for (i=0;inumnew]; if ((vect1->present==1) && (moyfreq[ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (moyfreq[ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=moyfreq[ll]; } } } } vect1=vect1->down; } for (k=0;k=0.5); minl=alfreq[ii]*(alfreq[ii]<0.5)+(1-alfreq[ii])*(alfreq[ii]>=0.5); ldp[k][ii]-=mink*minl; chidp[k][ii]=2*(ldp[k][ii]*ldp[k][ii]*nbused)/(alfreq[k]*alfreq[ii]*(1-alfreq[k])*(1-alfreq[ii])); if (ldp[k][ii]<0) {dmax=mink*minl;} else {if (mink1.0) {ldp[k][ii]/=fabs(ldp[k][ii]);} } fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\tLD MATRIX\n\n"); for (k=0;k");fprintf(outres,"\n"); } fprintf(outfile,"\n");fprintf(outres,"\n\n"); fprintf(outfile,"\n"); fprintf(outres,"\t\t\tP-Value MATRIX\n\n"); fprintf(outfile,"\n"); for (k=0;k"); fprintf(outres,"\n");for (ii=0;ii\n");fprintf(outfile,"\n\n"); } else if ((chxt==1) || (chxt==3)) {for (i=0;i<2;i++) {for (k=0;knumnew]; if ((vect1->present==1) && (freqtem[ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqtem[ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=freqtem[ll]; } } } } vect1=vect1->down; } } if (i==1) {while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqcas[ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqcas[ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=freqcas[ll]; } } } } vect1=vect1->down; } } for (k=0;k=0.5); minl=alfreq[ii]*(alfreq[ii]<0.5)+(1-alfreq[ii])*(alfreq[ii]>=0.5); ldp[k][ii]-=mink*minl; chidp[k][ii]=2*(ldp[k][ii]*ldp[k][ii])/(alfreq[k]*alfreq[ii]*(1-alfreq[k])*(1-alfreq[ii])); if (i==0) {chidp[k][ii]*=nbtem;} else if (i==1) {chidp[k][ii]*=nbcas;} if (ldp[k][ii]<0) {dmax=mink*minl;} else {if (mink1.0) {ldp[k][ii]/=fabs(ldp[k][ii]);} } fprintf(outres,"\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tLD MATRIX IN CONTROLS\n\n"); } if (i==1) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tLD MATRIX IN CASES\n\n"); } fprintf(outfile,"\n"); for (k=0;k");fprintf(outres,"\n"); } fprintf(outfile,"\n"); fprintf(outres,"\n\n"); if (i==0) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tP-Value IN CONTROLS\n\n"); } if (i==1) {fprintf(outfile,"\n"); fprintf(outres,"\t\t\tP-Value IN CASES\n\n"); } fprintf(outfile,"\n"); for (k=0;k");fprintf(outres,"\n"); for (ii=0;ii\n");fprintf(outres,"\n"); } } else if (chxt==5) {for (i=0;inumnew]; if ((vect1->present==1) && (freqkat[i][ll]>0)) {for (k=0;klistall[k]==1); } vect1=vect1->down; } vect1=tnbhbase; while (vect1!=NULL) {ll=fcoda2[vect1->numnew]; if ((vect1->present==1) && (freqkat[i][ll]>0)) {for (k=0;klistall[k]==ik) && (vect1->listall[ii]==il)) {ldp[k][ii]+=freqkat[i][ll]; } } } } vect1=vect1->down; } for (k=0;k=0.5); minl=alfreq[ii]*(alfreq[ii]<0.5)+(1-alfreq[ii])*(alfreq[ii]>=0.5); ldp[k][ii]-=mink*minl; chidp[k][ii]=2*(ldp[k][ii]*ldp[k][ii])/(alfreq[k]*alfreq[ii]*(1-alfreq[k])*(1-alfreq[ii])); chidp[k][ii]*=nbsujktgo[i]; if (ldp[k][ii]<0) {dmax=mink*minl;} else {if (mink1.0) {ldp[k][ii]/=fabs(ldp[k][ii]);} } fprintf(outres,"\n\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n"); fprintf(outfile,"\n",i+1); fprintf(outres,"\t\t\tLD MATRIX IN CLASS LEVEL %d\n\n",i+1); fprintf(outfile,"\n"); for (k=0;k");fprintf(outres,"\n"); } fprintf(outfile,"\n"); fprintf(outres,"\n\n"); fprintf(outfile,"\n",i+1); fprintf(outres,"\t\t\tP-Value IN CLASS LEVEL %d\n\n",i+1); fprintf(outfile,"\n"); for (k=0;k");fprintf(outres,"\n"); for (ii=0;ii\n");fprintf(outres,"\n"); } } fprintf(outfile,"
LD MATRIX
");fprintf(outres,"\t\t"); for (ii=0;iik) {fprintf(outfile," %3.2f",ldp[k][ii]); fprintf(outres," %3.2f\t",ldp[k][ii]); } } fprintf(outfile,"
P-Value MATRIX
");fprintf(outres,"\t\t"); fprintf(outfile," X ");fprintf(outres," X\t"); for (ii=k+1;ii
LD MATRIX IN CONTROLS
LD MATRIX IN CASES
"); for (ii=0;iik) {fprintf(outfile," %3.2f",ldp[k][ii]); fprintf(outres," %3.2f\t",ldp[k][ii]); } } fprintf(outfile,"
P-Value IN CONTROLS
P-Value IN CASES
");fprintf(outres,"\t\t"); fprintf(outfile," X ");fprintf(outres," X\t"); for (ii=k+1;ii
LD MATRIX IN CLASS LEVEL %d
"); for (ii=0;iik) {fprintf(outfile," %3.2f",ldp[k][ii]); fprintf(outres," %3.2f\t",ldp[k][ii]); } } fprintf(outfile,"
P-Value IN CLASS LEVEL %d
");fprintf(outres,"\t\t"); fprintf(outfile," X ");fprintf(outres," X\t"); for (ii=k+1;ii
"); } /* POUR JAVA CECI EST INDISPONIBLE if ((chxt>0) && (haplozero==0) && (hypoth==0) && (interor==0) && (chxt<5)) {wald=0; printf("Do you want some variance-covariance matrix to be display (y/n)? \n"); do {scanf("%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) {wald=1;} if (wald==1) {printf("How many parameters involved in this matrix ?\n"); do {scanf("%d",&nbwald); }while (nbwald<2); idwald =(int *)malloc((size_t) (nbwald*sizeof(int))); for (i=0;i"); fprintf(outfile,""); for (i=0;i\n",idwald[i],effest[idwald[i]-1]); fprintf(outfile,""); fprintf(outfile,"\n"); for (i=0;i"); } fprintf(outfile,"
Information for Generalized Test Statistic\nVector of regression parameters
Haplotype effect %d :  %lf
Variance-Covariance matrix of regression parameters
"); for (j=0;j
"); idwald=NULL; free(idwald); } } if ((chxt==5) && (haplozero==0) && (hypoth==0) && (interor==0)) {wald=0; printf("Do you want some variance-covariance matrix to be display (y/n)? \n"); do {scanf("%c",&rep); }while ( (rep!='y') && (rep!='Y') && (rep!='n') && (rep!='N')); if ((rep=='y') || (rep=='Y')) {wald=1;} if (wald==1) {printf("How many parameters involved in this matrix ?\n"); do {scanf("%d",&nbwald); }while (nbwald<2); idwald =(int *)malloc((size_t) (nbwald*sizeof(int))); for (i=0;i"); fprintf(outfile,""); for (i=0;i\n",idwald[i],effest[idwald[i]]); fprintf(outfile,""); fprintf(outfile,"\n"); for (i=0;i"); } fprintf(outfile,"
Information for Generalized Test Statistic\nVector of regression parameters
Haplotype effect %d :  %lf
Variance-Covariance matrix of regression parameters
"); for (j=0;j
"); idwald=NULL; free(idwald); } } */ fprintf(outfile,""); // New DAvid if (ldmatrix==1) {for (i=0;i2) {for (i=0;i0) {for (i=0;i0) {for (i=0;i0) {for (i=0;i0) {for (i=0;i0) {for (i=0;inext!=NULL)) {if (suiv->phen[0]>nbcatego) nbcatego=(int) suiv->phen[0]; suiv=suiv->next; } nkat=nbcatego-1; nbsujktgo=(int *) malloc ((size_t) (nbcatego*sizeof(int))); for (i=0;inext!=NULL)) {nbsujktgo[(int) suiv->phen[0]-1]+=(suiv->nblm==0); suiv=suiv->next; } else if (msdata==1) while ((suiv!=NULL) && (suiv->next!=NULL)) {nbsujktgo[(int) suiv->phen[0]-1]+=(suiv->nblmnext; } } void polytomous() {double val1,val2,val3,varest,det,res,denom,num,numm,probb; int hh1,hh2,v1,v2,nused=0,i,j,idx,k; char rep; double *dmat,probv0; dmat=(double *) malloc((size_t) (n*sizeof(double))); for (i=0;inext!=NULL)) {probv0=0; if (suiv->tnbhapo>0) {for (i=0;iphen[0])-1; if (haplozero==0) {hh1=coding(suiv->hapest[0]); hh2=coding(suiv->hapest[1]); } denom=1; for (i=0;iz[j]; if (haplozero==0) {if (hh1>0) {val2+=effest[hh1*nkat+i];} if (hh2>0) {val2+=effest[hh2*nkat+i];} for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } /*penser nbadd+interecov*/ denom+=exp(val2); } probv0=1/denom; if (idx==0) {for (i=0;i0) res+=effest[hh1*nkat+i]; if (hh2>0) res+=effest[hh2*nkat+i]; for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]; num=exp(res); val1=-num*probv0; dmat[i]+=2*val1; if (haplozero==0) {if ((hh1>0) && (itptp[hh1*nkat+i]==1)) dmat[nitptp[hh1*nkat+i]]+=val1; if ((hh2>0) && (itptp[hh2*nkat+i]==1)) dmat[nitptp[hh2*nkat+i]]+=val1; if (hypoth>0) {for (j=0;j-1)) {dmat[nitptp[hh1*nkat+i]]+=val1;} if ( ((hh2*nkat+i)==v2) && (nitptp[hh2*nkat+i]>-1)) {dmat[nitptp[hh2*nkat+i]]+=val1;} } } if (interor==1) {for (j=0;j0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} } else {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } } } } for (j=0;jz[tabint[j][1]-1]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]*val1;} } } else if (idx>0) {for (i=0;i0) res+=effest[hh1*nkat+i]; if (hh2>0) res+=effest[hh2*nkat+i]; for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]; num=exp(res); val1=-num*probv0; dmat[i]+=2*val1; if (haplozero==0) {if ((hh1>0) && (itptp[hh1*nkat+i]==1)) dmat[nitptp[hh1*nkat+i]]+=val1; if ((hh2>0) && (itptp[hh2*nkat+i]==1)) dmat[nitptp[hh2*nkat+i]]+=val1; if (hypoth>0) {for (j=0;j-1)) {dmat[nitptp[hh1*nkat+i]]+=val1;} if ( ((hh2*nkat+i)==v2) && (nitptp[hh2*nkat+i]>-1)) {dmat[nitptp[hh2*nkat+i]]+=val1;} } } if (interor==1) {for (j=0;j0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} } else {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } } } } for (j=0;jz[tabint[j][1]-1]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]*val1;} } dmat[idx-1]+=2; if (haplozero==0) {if ((hh1>0) && (itptp[hh1*nkat+idx-1]==1)) dmat[nitptp[hh1*nkat+idx-1]]+=1; if ((hh2>0) && (itptp[hh2*nkat+idx-1]==1)) dmat[nitptp[hh2*nkat+idx-1]]+=1; if (hypoth>0) {for (j=0;j-1)) {dmat[nitptp[hh1*nkat+idx-1]]+=1;} if ( ((hh2*nkat+idx-1)==v2) && (nitptp[hh2*nkat+idx-1]>-1)) {dmat[nitptp[hh2*nkat+idx-1]]+=1;} } } if (interor==1) {for (j=0;j0)) {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; } if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1;} if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1;} } else {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } } } } } for (j=0;jz[tabint[j][1]-1]*(((hh1*nkat+idx-1)==tabint[j][0])+ ((hh2*nkat+idx-1)==tabint[j][0])); } } for (j=0;jz[j];} } for (i=0;inext; } sysl(mdvd2,n); for (i=0;i-1) {effest[i]+=modif2[nitptp[i]];j++;} if (hypoth>0) {for (j=0;j0)) {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]+effest[tabinter[j][i][0]]; } else if ( (div(tabinter[j][i][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]-effest[tabinter[j][0][0]]; } else if ( (div(tabinter[j][i][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]; } else {effest[tabinter[j][i][1]]=effest[tabinter[j][0][1]]+effest[tabinter[j][i][0]]-effest[tabinter[j][0][0]]; } } } } /* if (hypint>0) {for (i=0;inext!=NULL)) {probv0=0; if (suiv->tnbhapo>0) {for (i=0;iphen[0])-1; if (haplozero==0) {hh1=coding(suiv->hapest[0]); hh2=coding(suiv->hapest[1]); } denom=1; for (i=0;iz[j]; if (haplozero==0) {if (hh1>0) {val2+=effest[hh1*nkat+i];} if (hh2>0) {val2+=effest[hh2*nkat+i];} for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } denom+=exp(val2); } probv0=1/denom; if (idx==0) {for (i=0;i0) res+=effest[hh1*nkat+i]; if (hh2>0) res+=effest[hh2*nkat+i]; for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]; num=exp(res); val1=-num*probv0; dmat[i]+=2*val1; if (haplozero==0) {if ((hh1>0) && (itptp[hh1*nkat+i]==1)) dmat[nitptp[hh1*nkat+i]]+=val1; if ((hh2>0) && (itptp[hh2*nkat+i]==1)) dmat[nitptp[hh2*nkat+i]]+=val1; if (hypoth>0) {for (j=0;j-1)) {dmat[nitptp[hh1*nkat+i]]+=val1;} if ( ((hh2*nkat+i)==v2) && (nitptp[hh2*nkat+i]>-1)) {dmat[nitptp[hh2*nkat+i]]+=val1;} } } if (interor==1) {for (j=0;j0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} } else {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } } } } for (j=0;jz[tabint[j][1]-1]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]*val1;} } } else if (idx>0) {for (i=0;i0) res+=effest[hh1*nkat+i]; if (hh2>0) res+=effest[hh2*nkat+i]; for (j=0;jz[tabint[j][1]-1]*effest[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]; num=exp(res); val1=-num*probv0; dmat[i]+=2*val1; if (haplozero==0) {if ((hh1>0) && (itptp[hh1*nkat+i]==1)) dmat[nitptp[hh1*nkat+i]]+=val1; if ((hh2>0) && (itptp[hh2*nkat+i]==1)) dmat[nitptp[hh2*nkat+i]]+=val1; if (hypoth>0) {for (j=0;j-1)) {dmat[nitptp[hh1*nkat+i]]+=val1;} if ( ((hh2*nkat+i)==v2) && (nitptp[hh2*nkat+i]>-1)) {dmat[nitptp[hh2*nkat+i]]+=val1;} } } if (interor==1) {for (j=0;j0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1;} } else {if ((hh1*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } if ((hh2*nkat+i)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=val1; dmat[nitptp[tabinter[j][k][0]]]+=val1; dmat[nitptp[tabinter[j][0][0]]]-=val1; } } } } } for (j=0;jz[tabint[j][1]-1]*(((hh1*nkat+i)==tabint[j][0])+ ((hh2*nkat+i)==tabint[j][0])); } } for (j=0;jz[j]*val1;} } dmat[idx-1]+=2; if (haplozero==0) {if ((hh1>0) && (itptp[hh1*nkat+idx-1]==1)) dmat[nitptp[hh1*nkat+idx-1]]+=1; if ((hh2>0) && (itptp[hh2*nkat+idx-1]==1)) dmat[nitptp[hh2*nkat+idx-1]]+=1; if (hypoth>0) {for (j=0;j-1)) {dmat[nitptp[hh1*nkat+idx-1]]+=1;} if ( ((hh2*nkat+idx-1)==v2) && (nitptp[hh2*nkat+idx-1]>-1)) {dmat[nitptp[hh2*nkat+idx-1]]+=1;} } } if (interor==1) {for (j=0;j0)) {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; } if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot>0)) {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } } else if ( (div(tabinter[j][k][0],nkat).quot==0) && (div(tabinter[j][0][0],nkat).quot==0)) {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1;} if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1;} } else {if ((hh1*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } if ((hh2*nkat+idx-1)==tabinter[j][k][1]) {dmat[nitptp[tabinter[j][0][1]]]+=1; dmat[nitptp[tabinter[j][k][0]]]+=1; dmat[nitptp[tabinter[j][0][0]]]-=1; } } } } } for (j=0;jz[tabint[j][1]-1]*(((hh1*nkat+idx-1)==tabint[j][0])+ ((hh2*nkat+idx-1)==tabint[j][0])); } } for (j=0;jz[j];} } for (i=0;inext; } sysl(mdvd2,n); for (i=0;i-1) && (nitptp[j]>-1)) vintra[i][j]+=mdvd2[nitptp[i]][nitptp[j]]; dmat=NULL; free (dmat); } /*********************CALCUL DE LA VRAISEMBLANCE TOTALE ******************************************/ double likepoly(double *frqsem, double *lgoddsem) {double val1,v1,vrais,h1,h2,like,p1,vraisfa=0,vv2,denom,num,val2; int hh1,hh2/*,idx*/,i,j,ii,idx; suiv = base; while ((suiv!=NULL) && (suiv->next!=NULL)) /*ATTENTION AU PB EVENTUEL DES DONNES MANQUANTES*/ {val1=suiv->phen[0]; if (suiv->tnbhapo>0) {vrais=0; idx=((int) suiv->phen[0])-1; for (i=0;itnbhapo;i++) {h1=frqsem[suiv->idnb[i][0]];h2=frqsem[suiv->idnb[i][1]]; if ( (h1>0) && (h2>0)) {p1=h1*h2*(2-(suiv->idnb[i][0]==suiv->idnb[i][1])); if (haplozero==0) {hh1=coding(suiv->idnb[i][0]); hh2=coding(suiv->idnb[i][1]); } denom=1; for (ii=0;iiz[j]; if (haplozero==0) {if (hh1>0) {val2+=lgoddsem[hh1*nkat+ii];} if (hh2>0) {val2+=lgoddsem[hh2*nkat+ii];} for (j=0;jz[tabint[j][1]-1]*lgoddsem[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+ii)==tabint[j][0])+ ((hh2*nkat+ii)==tabint[j][0])); } } denom+=exp(val2); } num=1; if (idx>0) {val2=2*lgoddsem[idx-1]; for (j=0;jz[j]; if (haplozero==0) {if (hh1>0) {val2+=lgoddsem[nkat*hh1+idx-1];} if (hh2>0) {val2+=lgoddsem[nkat*hh2+idx-1];} for (j=0;jz[tabint[j][1]-1]*lgoddsem[(nbhest+ajust+nbadd)*nkat+j]*(((hh1*nkat+idx-1)==tabint[j][0])+ ((hh2*nkat+idx-1)==tabint[j][0])); } } /*Penser nbadd+intercov*/ num=exp(val2); } like=num/denom; vrais+=p1*like; } } if (vrais>0) {vraisfa -= log(vrais);} } suiv= suiv->next; } return(-vraisfa); } thesias-3.1.1/src/polevl.c000066400000000000000000000031051360777755100154310ustar00rootroot00000000000000/* polevl.c * p1evl.c * * Evaluate polynomial * * * * SYNOPSIS: * * int N; * double x, y, coef[N+1], polevl[]; * * y = polevl( x, coef, N ); * * * * DESCRIPTION: * * Evaluates polynomial of degree N: * * 2 N * y = C + C x + C x +...+ C x * 0 1 2 N * * Coefficients are stored in reverse order: * * coef[0] = C , ..., coef[N] = C . * N 0 * * The function p1evl() assumes that coef[N] = 1.0 and is * omitted from the array. Its calling arguments are * otherwise the same as polevl(). * * * SPEED: * * In the interest of speed, there are no checks for out * of bounds arithmetic. This routine is used by most of * the functions in the library. Depending on available * equipment features, the user may wish to rewrite the * program in microcode or assembly language. * */ /* Cephes Math Library Release 2.1: December, 1988 Copyright 1984, 1987, 1988 by Stephen L. Moshier Direct inquiries to 30 Frost Street, Cambridge, MA 02140 */ double polevl( x, coef, N ) double x; double coef[]; int N; { double ans; int i; double *p; p = coef; ans = *p++; i = N; do ans = ans * x + *p++; while( --i ); return( ans ); } /* p1evl() */ /* N * Evaluate polynomial when coefficient of x is 1.0. * Otherwise same as polevl. */ double p1evl( x, coef, N ) double x; double coef[]; int N; { double ans; double *p; int i; p = coef; ans = x + *p++; i = N-1; do ans = ans * x + *p++; while( --i ); return( ans ); } thesias-3.1.1/src/thesiaslib.c000066400000000000000000000046241360777755100162660ustar00rootroot00000000000000/* * This file is part of THESIAS * Copyright (C) 2004-2020 David-Alexandre Trgout, Valrie Garelle * All rights reserved. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "thesiaslib.h" extern double igam ( double, double ); extern double igami ( double, double ); extern double polevl ( double, double *, int ); extern double ndtri (double); extern double gamma (double); extern double chdtrc(double, double); extern int mtherr(char *, int ); JNIEXPORT jint JNICALL Java_thesiaslib_thesiasRun (JNIEnv *env, jobject obj, jstring sFileName, jint maxvarfic, jint nbloci, jintArray idloci, jint ldmatrix, jint msdata, jint R2, jint chxt, jint num0, jint idtime, jint offset, jint idoffset, jint ajust, jintArray numajust, jint xlnk, jint numsx) { int i; jint *aNdloci = (*env)->GetIntArrayElements(env, idloci, 0); jint *aNumajust = (*env)->GetIntArrayElements(env, numajust, 0); const char *cFileName = (*env)->GetStringUTFChars(env, sFileName, 0); printf("Entre dans le pivot JNI: appel natif de thesiasRun VGT \n"); i = thesiasRun(cFileName, maxvarfic, nbloci, aNdloci, ldmatrix, msdata, R2, chxt, num0, idtime, offset, idoffset, ajust, aNumajust, xlnk, numsx); (*env)->ReleaseIntArrayElements(env, idloci, aNdloci, 0); (*env)->ReleaseIntArrayElements(env, numajust, aNumajust, 0); (*env)->ReleaseStringUTFChars(env, sFileName, cFileName); return i; } JNIEXPORT jint JNICALL JNI_OnLoad(JavaVM *vm, void *reserved){ return JNI_VERSION_1_4; } void JNICALL JNI_OnUnload(JavaVM *vm, void *reserved){ return; } thesias-3.1.1/src/thesiaslib.h000066400000000000000000000010231360777755100162610ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class thesiaslib */ #ifndef _Included_thesiaslib #define _Included_thesiaslib #ifdef __cplusplus extern "C" { #endif /* * Class: thesiaslib * Method: thesiasRun * Signature: (Ljava/lang/String;II[IIIIIIIIII[III)I */ JNIEXPORT jint JNICALL Java_thesiaslib_thesiasRun (JNIEnv *, jobject, jstring, jint, jint, jintArray, jint, jint, jint, jint, jint, jint, jint, jint, jint, jintArray, jint, jint); #ifdef __cplusplus } #endif #endif