GoFigure2-v0.9.0/ 0000755 0001750 0001750 00000000000 11667757442 013374 5 ustar mathieu mathieu GoFigure2-v0.9.0/KWStyle/ 0000755 0001750 0001750 00000000000 11667757442 014736 5 ustar mathieu mathieu GoFigure2-v0.9.0/KWStyle/GOFIGURE2_Files.txt.in 0000644 0001750 0001750 00000000713 11667757442 020520 0 ustar mathieu mathieu @GOFIGURE2_SOURCE_DIR@/Code/GUI/lib/*.h
@GOFIGURE2_SOURCE_DIR@/Code/GUI/lib/*.cxx
@GOFIGURE2_SOURCE_DIR@/Code/IO/*.h
@GOFIGURE2_SOURCE_DIR@/Code/IO/*.cxx
@GOFIGURE2_SOURCE_DIR@/Code/IO/*.txx
@GOFIGURE2_SOURCE_DIR@/Code/Filters/*.h
@GOFIGURE2_SOURCE_DIR@/Code/Filters/*.txx
@GOFIGURE2_SOURCE_DIR@/Code/Filters/*.cxx
@GOFIGURE2_SOURCE_DIR@/Interfaces/*.h
@GOFIGURE2_SOURCE_DIR@/Interfaces/*.cxx
@GOFIGURE2_SOURCE_DIR@/Main/*.h
@GOFIGURE2_SOURCE_DIR@/Main/*.cxx
GoFigure2-v0.9.0/KWStyle/KWStyle.cmake 0000644 0001750 0001750 00000007445 11667757442 017314 0 ustar mathieu mathieu OPTION(GOFIGURE2_USE_KWSTYLE "Enable the use of KWStyle for checking coding style." OFF)
IF(GOFIGURE2_USE_KWSTYLE)
# Set the required KWStyle version
SET(KWSTYLE_REQ_MAJOR 1)
SET(KWSTYLE_REQ_MINOR 0)
SET(KWSTYLE_REQ_PATCH 1)
OPTION(KWSTYLE_USE_VIM_FORMAT "Set KWStyle to generate errors with a VIM-compatible format." OFF)
OPTION(KWSTYLE_USE_MSVC_FORMAT "Set KWStyle to generate errors with a VisualStudio-compatible format." OFF)
FIND_PROGRAM(KWSTYLE_EXECUTABLE
NAMES KWStyle
PATHS
/usr/local/bin
)
IF(KWSTYLE_EXECUTABLE)
EXECUTE_PROCESS(
COMMAND ${KWSTYLE_EXECUTABLE} -version
OUTPUT_VARIABLE KWSTYLE_VERSION_TEXT
)
string(STRIP ${KWSTYLE_VERSION_TEXT} KWSTYLE_VERSION_TEXT)
IF(KWSTYLE_VERSION_TEXT STREQUAL "Version: Not defined")
MESSAGE("This project requires a newer version of KWStyle. Please upgrade the KWStyle executable.")
ELSE(${KWSTYLE_VERSION_TEXT} STREQUAL "Version: Not defined")
string(LENGTH ${KWSTYLE_VERSION_TEXT} KWSTYLE_VERSION_LENGTH)
math(EXPR KWSTYLE_VERSION_FINAL_LENGTH "${KWSTYLE_VERSION_LENGTH}-9")
string(SUBSTRING ${KWSTYLE_VERSION_TEXT} 9 ${KWSTYLE_VERSION_FINAL_LENGTH} KWSTYLE_VERSION)
# now parse the parts of the user given version string into variables
STRING(REGEX REPLACE "^([0-9]+)\\.[0-9]+\\.[0-9]+" "\\1" KWSTYLE_MAJOR_VERSION "${KWSTYLE_VERSION}")
STRING(REGEX REPLACE "^[0-9]+\\.([0-9])+\\.[0-9]+" "\\1" KWSTYLE_MINOR_VERSION "${KWSTYLE_VERSION}")
STRING(REGEX REPLACE "^[0-9]+\\.[0-9]+\\.([0-9]+)" "\\1" KWSTYLE_PATCH_VERSION "${KWSTYLE_VERSION}")
MATH(EXPR KWSTYLE_REQ_VERSION "${KWSTYLE_REQ_MAJOR}*10000 + ${KWSTYLE_REQ_MINOR}*100 + ${KWSTYLE_REQ_PATCH}")
MATH(EXPR KWSTYLE_LONG_VERSION "${KWSTYLE_MAJOR_VERSION}*10000 + ${KWSTYLE_MINOR_VERSION}*100 + ${KWSTYLE_PATCH_VERSION}")
# Set the minimum require version for batchmake
IF(KWSTYLE_LONG_VERSION LESS KWSTYLE_REQ_VERSION)
MESSAGE(FATAL_ERROR "This project requires a newer version of KWStyle. Please upgrade the KWStyle executable.")
ELSE(KWSTYLE_LONG_VERSION LESS KWSTYLE_REQ_VERSION)
SET(KWSTYLE_FOUND 1)
ENDIF(KWSTYLE_LONG_VERSION LESS KWSTYLE_REQ_VERSION)
ENDIF(KWSTYLE_VERSION_TEXT STREQUAL "Version: Not defined")
IF(KWSTYLE_FOUND)
#
# Define file names
#
SET(KWSTYLE_CONFIGURATION_FILE
${GOFIGURE2_BINARY_DIR}/KWStyle/GOFIGURE2.kws.xml)
SET(KWSTYLE_GOFIGURE2_FILES_LIST
${GOFIGURE2_BINARY_DIR}/KWStyle/GOFIGURE2_Files.txt)
SET(KWSTYLE_GOFIGURE2_OVERWRITE_FILE
${GOFIGURE2_SOURCE_DIR}/KWStyle/GOFIGURE2_Overwrite.txt )
#
# Configure the files
#
CONFIGURE_FILE(
${GOFIGURE2_SOURCE_DIR}/KWStyle/GOFIGURE2_Files.txt.in
${KWSTYLE_GOFIGURE2_FILES_LIST} )
CONFIGURE_FILE(
${GOFIGURE2_SOURCE_DIR}/KWStyle/GOFIGURE2.kws.xml.in
${KWSTYLE_CONFIGURATION_FILE} )
#
# Define formatting for error messages
#
SET(KWSTYLE_EDITOR_FORMAT " ")
SET(KWSTYLE_EDITOR_FORMAT "")
IF(${CMAKE_CXX_COMPILER} MATCHES "cl.exe$")
SET(KWSTYLE_USE_MSVC_FORMAT 1)
ENDIF(${CMAKE_CXX_COMPILER} MATCHES "cl.exe$")
IF(${CMAKE_C_COMPILER} MATCHES "g[cx][cx]$")
SET(KWSTYLE_USE_VIM_FORMAT 1)
ENDIF(${CMAKE_C_COMPILER} MATCHES "g[cx][cx]$")
IF(KWSTYLE_USE_VIM_FORMAT)
SET(KWSTYLE_EDITOR_FORMAT -vim)
ENDIF(KWSTYLE_USE_VIM_FORMAT)
IF(KWSTYLE_USE_MSVC_FORMAT)
SET(KWSTYLE_EDITOR_FORMAT -msvc)
ENDIF(KWSTYLE_USE_MSVC_FORMAT)
SET(KWSTYLE_ARGUMENTS_CODE
-xml ${KWSTYLE_CONFIGURATION_FILE} -v -D ${KWSTYLE_GOFIGURE2_FILES_LIST}
-o ${KWSTYLE_GOFIGURE2_OVERWRITE_FILE}
${KWSTYLE_EDITOR_FORMAT}
)
ADD_CUSTOM_COMMAND(
OUTPUT ${GOFIGURE2_BINARY_DIR}/KWStyleCodeReport.txt
COMMAND ${KWSTYLE_EXECUTABLE}
ARGS ${KWSTYLE_ARGUMENTS_CODE}
COMMENT "Coding Style Checker"
)
ADD_CUSTOM_TARGET(StyleCheckCode DEPENDS ${GOFIGURE2_BINARY_DIR}/KWStyleCodeReport.txt)
ADD_TEST(KWStyleCodeTest ${KWSTYLE_EXECUTABLE} ${KWSTYLE_ARGUMENTS_CODE})
ENDIF(KWSTYLE_FOUND)
ENDIF(KWSTYLE_EXECUTABLE)
ENDIF(GOFIGURE2_USE_KWSTYLE)
GoFigure2-v0.9.0/KWStyle/GOFIGURE2_Overwrite.txt 0000644 0001750 0001750 00000000000 11667757442 021024 0 ustar mathieu mathieu GoFigure2-v0.9.0/KWStyle/CopyrightSource.txt 0000644 0001750 0001750 00000003416 11667757442 020634 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-10
Copyright (c) 2009-10, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
GoFigure2-v0.9.0/KWStyle/CMakeLists.txt 0000644 0001750 0001750 00000000720 11667757442 017475 0 ustar mathieu mathieu #-----------------------------------------------------------------------------
# uses KWStyle for checking the coding style
INCLUDE(KWStyle.cmake)
IF(UNIX)
CONFIGURE_FILE(${GOFIGURE2_SOURCE_DIR}/KWStyle/doAllStyle.csh.in
${GOFIGURE2_BINARY_DIR}/doAllStyle.csh
@ONLY IMMEDIATE)
EXEC_PROGRAM(chmod ARGS 755 \"${GOFIGURE2_BINARY_DIR}/doAllStyle.csh\"
OUTPUT_VARIABLE ITK_EXEC_PLEASE_BE_QUIET)
ENDIF(UNIX)
GoFigure2-v0.9.0/KWStyle/GOFIGURE2.kws.xml.in 0000644 0001750 0001750 00000002417 11667757442 020165 0 ustar mathieu mathieu
GoFigure2
@GOFIGURE2_SOURCE_DIR@/Resources/fig/splash.jpg
/home/ajg23/CVSROOT/KWStyle/Web/images/TitleBar.jpg
120
0
1
2
[A-Z]
m_[A-Z]
0
[a-z]
0
1
1
3
/**
*
*/
false
@GOFIGURE2_SOURCE_DIR@/KWStyle/Header.h
false
true
SPACE
2
true
true
__[NameOfClass]_[Extension]
2
T
1
1
GoFigure2-v0.9.0/KWStyle/uncrustify.sh 0000755 0001750 0001750 00000006132 11667757442 017512 0 ustar mathieu mathieu #!/bin/sh
#
#
# =========================================================================
# Modifications were made by the GoFigure Dev. Team.
# while at Megason Lab, Systems biology, Harvard Medical school, 2009-11
#
# Copyright (c) 2009-11, President and Fellows of Harvard College.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# Neither the name of the President and Fellows of Harvard College
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
# BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
# OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# =========================================================================
#
#
# Linux Shell Script to run ITK tests in linux
#
function local_uncrustify {
configuration_file=$1;
directory=$2;
# find cxx files
for i in `find $directory -name *.cxx`;
do
echo "Correcting file style: $i";
uncrustify -c $configuration_file -f $i -o $i;
echo "Done";
done;
# find cxx.in files
for i in `find $directory -name *.cxx.in`;
do
echo "Correcting file style: $i";
uncrustify -c $configuration_file -f $i -o $i;
echo "Done";
done;
# find h files
for i in `find $directory -name *.h`;
do
echo "Correcting file style: $i";
uncrustify -c $configuration_file -f $i -o $i;
echo "Done";
done;
# find h.in files
for i in `find $directory -name *.h.in`;
do
echo "Correcting file style: $i";
uncrustify -c $configuration_file -f $i -o $i;
echo "Done";
done;
# find txx files
for i in `find $directory -name *.txx`;
do
echo "Correcting file style: $i";
uncrustify -c $configuration_file -f $i -o $i;
echo "Done";
done;
}
working_directory=`pwd`;
configuration_file="$working_directory"/uncrustify.cfg;
local_uncrustify $configuration_file "$working_directory"/../Code
local_uncrustify $configuration_file "$working_directory"/../Examples
local_uncrustify $configuration_file "$working_directory"/../Main
GoFigure2-v0.9.0/KWStyle/uncrustify.cfg 0000644 0001750 0001750 00000165542 11667757442 017647 0 ustar mathieu mathieu # Uncrustify 0.56
#
# General options
#
# The type of line endings
newlines = auto # auto/lf/crlf/cr
# The original size of tabs in the input
input_tab_size = 2 # number
# The size of tabs in the output (only used if align_with_tabs=true)
output_tab_size = 2 # number
# The ASCII value of the string escape char, usually 92 (\) or 94 (^). (Pawn)
string_escape_char = 92 # number
# Alternate string escape char for Pawn. Only works right before the quote char.
string_escape_char2 = 0 # number
#
# Indenting
#
# The number of columns to indent per level.
# Usually 2, 3, 4, or 8.
indent_columns = 2 # number
# The continuation indent. If non-zero, this overrides the indent of '(' and '=' continuation indents.
# For FreeBSD, this is set to 4.
indent_continue = 0 # number
# How to use tabs when indenting code
# 0=spaces only
# 1=indent with tabs to brace level, align with spaces
# 2=indent and align with tabs, using spaces when not on a tabstop
indent_with_tabs = 0 # number
# Comments that are not a brace level are indented with tabs on a tabstop.
# Requires indent_with_tabs=2. If false, will use spaces.
indent_cmt_with_tabs = false # false/true
# Whether to indent strings broken by '\' so that they line up
indent_align_string = false # false/true
# The number of spaces to indent multi-line XML strings.
# Requires indent_align_string=True
indent_xml_string = 0 # number
# Spaces to indent '{' from level
indent_brace = 0 # number
# Whether braces are indented to the body level
indent_braces = true # false/true
# Disabled indenting function braces if indent_braces is true
indent_braces_no_func = true # false/true
# Disabled indenting class braces if indent_braces is true
indent_braces_no_class = true # false/true
# Disabled indenting struct braces if indent_braces is true
indent_braces_no_struct = false # false/true
# Indent based on the size of the brace parent, i.e. 'if' => 3 spaces, 'for' => 4 spaces, etc.
indent_brace_parent = false # false/true
# Whether the 'namespace' body is indented
indent_namespace = false # false/true
# The number of spaces to indent a namespace block
indent_namespace_level = 0 # number
# If the body of the namespace is longer than this number, it won't be indented.
# Requires indent_namespace=true. Default=0 (no limit)
indent_namespace_limit = 3 # number
# Whether the 'extern "C"' body is indented
indent_extern = false # false/true
# Whether the 'class' body is indented
indent_class = true # false/true
# Whether to indent the stuff after a leading class colon
indent_class_colon = false # false/true
# False=treat 'else\nif' as 'else if' for indenting purposes
# True=indent the 'if' one level
indent_else_if = false # false/true
# Amount to indent variable declarations after a open brace. neg=relative, pos=absolute
indent_var_def_blk = 0 # number
# Indent continued variable declarations instead of aligning.
indent_var_def_cont = true # false/true
# True: indent continued function call parameters one indent level
# False: align parameters under the open paren
indent_func_call_param = false # false/true
# Same as indent_func_call_param, but for function defs
indent_func_def_param = false # false/true
# Same as indent_func_call_param, but for function protos
indent_func_proto_param = false # false/true
# Same as indent_func_call_param, but for class declarations
indent_func_class_param = false # false/true
# Same as indent_func_call_param, but for class variable constructors
indent_func_ctor_var_param = false # false/true
# Same as indent_func_call_param, but for templates
indent_template_param = false # false/true
# Double the indent for indent_func_xxx_param options
indent_func_param_double = false # false/true
# Indentation column for standalone 'const' function decl/proto qualifier
indent_func_const = 0 # number
# Indentation column for standalone 'throw' function decl/proto qualifier
indent_func_throw = 0 # number
# The number of spaces to indent a continued '->' or '.'
# Usually set to 0, 1, or indent_columns.
indent_member = 0 # number
# Spaces to indent single line ('//') comments on lines before code
indent_sing_line_comments = 0 # number
# If set, will indent trailing single line ('//') comments relative
# to the code instead of trying to keep the same absolute column
indent_relative_single_line_comments = false # false/true
# Spaces to indent 'case' from 'switch'
# Usually 0 or indent_columns.
indent_switch_case = 2 # number
# Spaces to shift the 'case' line, without affecting any other lines
# Usually 0.
indent_case_shift = 0 # number
# Spaces to indent '{' from 'case'.
# By default, the brace will appear under the 'c' in case.
# Usually set to 0 or indent_columns.
indent_case_brace = 0 # number
# Whether to indent comments found in first column
indent_col1_comment = false # false/true
# How to indent goto labels
# >0 : absolute column where 1 is the leftmost column
# <=0 : subtract from brace indent
indent_label = 1 # number
# Same as indent_label, but for access specifiers that are followed by a colon
indent_access_spec = 1 # number
# Indent the code after an access specifier by one level.
# If set, this option forces 'indent_access_spec=0'
indent_access_spec_body = false # false/true
# If an open paren is followed by a newline, indent the next line so that it lines up after the open paren (not recommended)
indent_paren_nl = false # false/true
# Controls the indent of a close paren after a newline.
# 0: Indent to body level
# 1: Align under the open paren
# 2: Indent to the brace level
indent_paren_close = 0 # number
# Controls the indent of a comma when inside a paren.If TRUE, aligns under the open paren
indent_comma_paren = false # false/true
# Controls the indent of a BOOL operator when inside a paren.If TRUE, aligns under the open paren
indent_bool_paren = false # false/true
# If 'indent_bool_paren' is true, controls the indent of the first expression. If TRUE, aligns the first expression to the following ones
indent_first_bool_expr = false # false/true
# If an open square is followed by a newline, indent the next line so that it lines up after the open square (not recommended)
indent_square_nl = false # false/true
# Don't change the relative indent of ESQL/C 'EXEC SQL' bodies
indent_preserve_sql = false # false/true
# Align continued statements at the '='. Default=True
# If FALSE or the '=' is followed by a newline, the next line is indent one tab.
indent_align_assign = false # false/true
#
# Spacing options
#
# Add or remove space around arithmetic operator '+', '-', '/', '*', etc
sp_arith = ignore # ignore/add/remove/force
# Add or remove space around assignment operator '=', '+=', etc
sp_assign = ignore # ignore/add/remove/force
# Add or remove space around assignment operator '=' in a prototype
sp_assign_default = ignore # ignore/add/remove/force
# Add or remove space before assignment operator '=', '+=', etc. Overrides sp_assign.
sp_before_assign = ignore # ignore/add/remove/force
# Add or remove space after assignment operator '=', '+=', etc. Overrides sp_assign.
sp_after_assign = ignore # ignore/add/remove/force
# Add or remove space around assignment '=' in enum
sp_enum_assign = ignore # ignore/add/remove/force
# Add or remove space before assignment '=' in enum. Overrides sp_enum_assign.
sp_enum_before_assign = ignore # ignore/add/remove/force
# Add or remove space after assignment '=' in enum. Overrides sp_enum_assign.
sp_enum_after_assign = ignore # ignore/add/remove/force
# Add or remove space around preprocessor '##' concatenation operator. Default=Add
sp_pp_concat = ignore # ignore/add/remove/force
# Add or remove space after preprocessor '#' stringify operator. Default=Add
sp_pp_stringify = ignore # ignore/add/remove/force
# Add or remove space around boolean operators '&&' and '||'
sp_bool = ignore # ignore/add/remove/force
# Add or remove space around compare operator '<', '>', '==', etc
sp_compare = ignore # ignore/add/remove/force
# Add or remove space inside '(' and ')'
sp_inside_paren = ignore # ignore/add/remove/force
# Add or remove space between nested parens
sp_paren_paren = add # ignore/add/remove/force
# Whether to balance spaces inside nested parens
sp_balance_nested_parens = false # false/true
# Style Guide Section 3.7.4.
# Add or remove space between ')' and '{'
sp_paren_brace = add # ignore/add/remove/force
# Add or remove space before pointer star '*'
sp_before_ptr_star = ignore # ignore/add/remove/force
# Add or remove space before pointer star '*' that isn't followed by a variable name
# If set to 'ignore', sp_before_ptr_star is used instead.
sp_before_unnamed_ptr_star = ignore # ignore/add/remove/force
# Add or remove space between pointer stars '*'
sp_between_ptr_star = ignore # ignore/add/remove/force
# Add or remove space after pointer star '*', if followed by a word.
sp_after_ptr_star = ignore # ignore/add/remove/force
# Add or remove space after a pointer star '*', if followed by a func proto/def.
sp_after_ptr_star_func = ignore # ignore/add/remove/force
# Add or remove space before a pointer star '*', if followed by a func proto/def.
sp_before_ptr_star_func = ignore # ignore/add/remove/force
# Add or remove space before a reference sign '&'
sp_before_byref = ignore # ignore/add/remove/force
# Add or remove space before a reference sign '&' that isn't followed by a variable name
# If set to 'ignore', sp_before_byref is used instead.
sp_before_unnamed_byref = ignore # ignore/add/remove/force
# Add or remove space after reference sign '&', if followed by a word.
sp_after_byref = ignore # ignore/add/remove/force
# Add or remove space after a reference sign '&', if followed by a func proto/def.
sp_after_byref_func = ignore # ignore/add/remove/force
# Add or remove space before a reference sign '&', if followed by a func proto/def.
sp_before_byref_func = ignore # ignore/add/remove/force
# Add or remove space between type and word. Default=Force
sp_after_type = add # ignore/add/remove/force
# Add or remove space in 'template <' vs 'template<'.
# If set to ignore, sp_before_angle is used.
sp_template_angle = ignore # ignore/add/remove/force
# Add or remove space before '<>'
sp_before_angle = ignore # ignore/add/remove/force
# Add or remove space inside '<' and '>'
sp_inside_angle = ignore # ignore/add/remove/force
# Add or remove space after '<>'
sp_after_angle = ignore # ignore/add/remove/force
# Add or remove space between '<>' and '(' as found in 'new List();'
sp_angle_paren = ignore # ignore/add/remove/force
# Add or remove space between '<>' and a word as in 'List m;'
sp_angle_word = add # ignore/add/remove/force
# Add or remove space before '(' of 'if', 'for', 'switch', and 'while'
sp_before_sparen = ignore # ignore/add/remove/force
# Add or remove space inside if-condition '(' and ')'
sp_inside_sparen = ignore # ignore/add/remove/force
# Add or remove space before if-condition ')'. Overrides sp_inside_sparen.
sp_inside_sparen_close = ignore # ignore/add/remove/force
# Add or remove space after ')' of 'if', 'for', 'switch', and 'while'
sp_after_sparen = ignore # ignore/add/remove/force
# Add or remove space between ')' and '{' of 'if', 'for', 'switch', and 'while'
sp_sparen_brace = ignore # ignore/add/remove/force
# Add or remove space between 'invariant' and '(' in the D language.
sp_invariant_paren = ignore # ignore/add/remove/force
# Add or remove space after the ')' in 'invariant (C) c' in the D language.
sp_after_invariant_paren = ignore # ignore/add/remove/force
# Add or remove space before empty statement ';' on 'if', 'for' and 'while'
sp_special_semi = ignore # ignore/add/remove/force
# Add or remove space before ';'. Default=Remove
sp_before_semi = ignore # ignore/ignore/remove/force
# Add or remove space before ';' in non-empty 'for' statements
sp_before_semi_for = ignore # ignore/add/remove/force
# Add or remove space before a semicolon of an empty part of a for statement.
sp_before_semi_for_empty = ignore # ignore/add/remove/force
# Add or remove space after ';', except when followed by a comment. Default=Add
sp_after_semi = ignore # ignore/add/remove/force
# Add or remove space after ';' in non-empty 'for' statements. Default=Force
sp_after_semi_for = ignore # ignore/add/remove/force
# Add or remove space after the final semicolon of an empty part of a for statement: for ( ; ; ).
sp_after_semi_for_empty = ignore # ignore/add/remove/force
# Add or remove space before '[' (except '[]')
sp_before_square = ignore # ignore/add/remove/force
# Add or remove space before '[]'
sp_before_squares = ignore # ignore/add/remove/force
# Add or remove space inside '[' and ']'
sp_inside_square = ignore # ignore/add/remove/force
# Add or remove space after ','
sp_after_comma = ignore # ignore/add/remove/force
# Add or remove space before ','
sp_before_comma = ignore # ignore/add/remove/force
# Add or remove space before the variadic '...' when preceded by a non-punctuator
sp_before_ellipsis = ignore # ignore/add/remove/force
# Add or remove space after class ':'
sp_after_class_colon = ignore # ignore/add/remove/force
# Add or remove space before class ':'
sp_before_class_colon = ignore # ignore/add/remove/force
# Add or remove space before case ':'. Default=Remove
sp_before_case_colon = remove # ignore/add/remove/force
# Add or remove space between 'operator' and operator sign
sp_after_operator = ignore # ignore/add/remove/force
# Add or remove space between the operator symbol and the open paren, as in 'operator ++('
sp_after_operator_sym = ignore # ignore/add/remove/force
# Add or remove space after C/D cast, i.e. 'cast(int)a' vs 'cast(int) a' or '(int)a' vs '(int) a'
sp_after_cast = ignore # ignore/add/remove/force
# Add or remove spaces inside cast parens
sp_inside_paren_cast = ignore # ignore/add/remove/force
# Add or remove space between the type and open paren in a C++ cast, i.e. 'int(exp)' vs 'int (exp)'
sp_cpp_cast_paren = ignore # ignore/add/remove/force
# Add or remove space between 'sizeof' and '('
sp_sizeof_paren = ignore # ignore/add/remove/force
# Add or remove space after the tag keyword (Pawn)
sp_after_tag = ignore # ignore/add/remove/force
# Add or remove space inside enum '{' and '}'
sp_inside_braces_enum = ignore # ignore/add/remove/force
# Add or remove space inside struct/union '{' and '}'
sp_inside_braces_struct = ignore # ignore/add/remove/force
# Add or remove space inside '{' and '}'
sp_inside_braces = ignore # ignore/add/remove/force
# Add or remove space inside '{}'
sp_inside_braces_empty = ignore # ignore/add/remove/force
# Add or remove space between return type and function name
# A minimum of 1 is forced except for pointer return types.
sp_type_func = add # ignore/add/remove/force
# Style Guide Section 3.7.3.
# Add or remove space between function name and '(' on function declaration
sp_func_proto_paren = remove # ignore/add/remove/force
# Style Guide Section 3.7.3.
# Add or remove space between function name and '(' on function definition
sp_func_def_paren = remove # ignore/add/remove/force
# Style Guide Section 3.7.3.
# Add or remove space inside empty function '()'
sp_inside_fparens = remove # ignore/add/remove/force
# Add or remove space inside function '(' and ')'
sp_inside_fparen = ignore # ignore/add/remove/force
# Add or remove space between ']' and '(' when part of a function call.
sp_square_fparen = ignore # ignore/add/remove/force
# Add or remove space between ')' and '{' of function
sp_fparen_brace = ignore # ignore/add/remove/force
# Add or remove space between function name and '(' on function calls
sp_func_call_paren = ignore # ignore/add/remove/force
# Add or remove space between the user function name and '(' on function calls
# You need to set a keyword to be a user function, like this: 'set func_call_user _' in the config file.
sp_func_call_user_paren = ignore # ignore/add/remove/force
# Add or remove space between a constructor/destructor and the open paren
sp_func_class_paren = ignore # ignore/add/remove/force
# Add or remove space between 'return' and '('
sp_return_paren = ignore # ignore/add/remove/force
# Add or remove space between '__attribute__' and '('
sp_attribute_paren = ignore # ignore/add/remove/force
# Add or remove space between 'defined' and '(' in '#if defined (FOO)'
sp_defined_paren = ignore # ignore/add/remove/force
# Add or remove space between 'throw' and '(' in 'throw (something)'
sp_throw_paren = ignore # ignore/add/remove/force
# Add or remove space between macro and value
sp_macro = ignore # ignore/add/remove/force
# Add or remove space between macro function ')' and value
sp_macro_func = ignore # ignore/add/remove/force
# Style Guide Section 3.7.4.
# Add or remove space between 'else' and '{' if on the same line
sp_else_brace = add # ignore/add/remove/force
# Style Guide Section 3.7.4.
# Add or remove space between '}' and 'else' if on the same line
sp_brace_else = add # ignore/add/remove/force
# Add or remove space between '}' and the name of a typedef on the same line
sp_brace_typedef = ignore # ignore/add/remove/force
# Add or remove space between 'catch' and '{' if on the same line
sp_catch_brace = ignore # ignore/add/remove/force
# Add or remove space between '}' and 'catch' if on the same line
sp_brace_catch = ignore # ignore/add/remove/force
# Add or remove space between 'finally' and '{' if on the same line
sp_finally_brace = ignore # ignore/add/remove/force
# Add or remove space between '}' and 'finally' if on the same line
sp_brace_finally = ignore # ignore/add/remove/force
# Add or remove space between 'try' and '{' if on the same line
sp_try_brace = ignore # ignore/add/remove/force
# Add or remove space between get/set and '{' if on the same line
sp_getset_brace = ignore # ignore/add/remove/force
# Style Guide Section 3.7.3.
# Add or remove space before the '::' operator
sp_before_dc = remove # ignore/add/remove/force
# Style Guide Section 3.7.3.
# Add or remove space after the '::' operator
sp_after_dc = remove # ignore/add/remove/force
# Add or remove around the D named array initializer ':' operator
sp_d_array_colon = ignore # ignore/add/remove/force
# Add or remove space after the '!' (not) operator. Default=Remove
sp_not = remove # ignore/add/remove/force
# Add or remove space after the '~' (invert) operator. Default=Remove
sp_inv = remove # ignore/add/remove/force
# Add or remove space after the '&' (address-of) operator. Default=Remove
# This does not affect the spacing after a '&' that is part of a type.
sp_addr = remove # ignore/add/remove/force
# Add or remove space around the '.' or '->' operators. Default=Remove
sp_member = remove # ignore/add/remove/force
# Add or remove space after the '*' (dereference) operator. Default=Remove
# This does not affect the spacing after a '*' that is part of a type.
sp_deref = remove # ignore/add/remove/force
# Add or remove space after '+' or '-', as in 'x = -5' or 'y = +7'. Default=Remove
sp_sign = remove # ignore/add/remove/force
# Add or remove space before or after '++' and '--', as in '(--x)' or 'y++;'. Default=Remove
sp_incdec = remove # ignore/add/remove/force
# Add or remove space before a backslash-newline at the end of a line. Default=Add
sp_before_nl_cont = add # ignore/add/remove/force
# Add or remove space after the scope '+' or '-', as in '-(void) foo;' or '+(int) bar;'
sp_after_oc_scope = ignore # ignore/add/remove/force
# Add or remove space after the colon in message specs
# '-(int) f:(int) x;' vs '-(int) f: (int) x;'
sp_after_oc_colon = ignore # ignore/add/remove/force
# Add or remove space before the colon in message specs
# '-(int) f: (int) x;' vs '-(int) f : (int) x;'
sp_before_oc_colon = ignore # ignore/add/remove/force
# Add or remove space after the colon in message specs
# '[object setValue:1];' vs '[object setValue: 1];'
sp_after_send_oc_colon = ignore # ignore/add/remove/force
# Add or remove space before the colon in message specs
# '[object setValue:1];' vs '[object setValue :1];'
sp_before_send_oc_colon = ignore # ignore/add/remove/force
# Add or remove space after the (type) in message specs
# '-(int)f: (int) x;' vs '-(int)f: (int)x;'
sp_after_oc_type = ignore # ignore/add/remove/force
# Add or remove space after the first (type) in message specs
# '-(int) f:(int)x;' vs '-(int)f:(int)x;'
sp_after_oc_return_type = ignore # ignore/add/remove/force
# Add or remove space between '@selector' and '('
# '@selector(msgName)' vs '@selector (msgName)'
# Also applies to @protocol() constructs
sp_after_oc_at_sel = ignore # ignore/add/remove/force
# Add or remove space between '@selector(x)' and the following word
# '@selector(foo) a:' vs '@selector(foo)a:'
sp_after_oc_at_sel_parens = ignore # ignore/add/remove/force
# Add or remove space inside '@selector' parens
# '@selector(foo)' vs '@selector( foo )'
# Also applies to @protocol() constructs
sp_inside_oc_at_sel_parens = ignore # ignore/add/remove/force
# Add or remove space before a block pointer caret
# '^int (int arg){...}' vs. ' ^int (int arg){...}'
sp_before_oc_block_caret = ignore # ignore/add/remove/force
# Add or remove space after a block pointer caret
# '^int (int arg){...}' vs. '^ int (int arg){...}'
sp_after_oc_block_caret = ignore # ignore/add/remove/force
# Add or remove space around the ':' in 'b ? t : f'
sp_cond_colon = ignore # ignore/add/remove/force
# Add or remove space around the '?' in 'b ? t : f'
sp_cond_question = ignore # ignore/add/remove/force
# Fix the spacing between 'case' and the label. Only 'ignore' and 'force' make sense here.
sp_case_label = ignore # ignore/add/remove/force
# Control the space around the D '..' operator.
sp_range = ignore # ignore/add/remove/force
# Control the space after the opening of a C++ comment '// A' vs '//A'
sp_cmt_cpp_start = ignore # ignore/add/remove/force
# Controls the spaces between #else or #endif and a trailing comment
sp_endif_cmt = ignore # ignore/add/remove/force
#
# Code alignment (not left column spaces/tabs)
#
# Whether to keep non-indenting tabs
align_keep_tabs = false # false/true
# Whether to use tabs for aligning
align_with_tabs = false # false/true
# Whether to bump out to the next tab when aligning
align_on_tabstop = false # false/true
# Whether to left-align numbers
align_number_left = false # false/true
# Align variable definitions in prototypes and functions
align_func_params = false # false/true
# Align parameters in single-line functions that have the same name.
# The function names must already be aligned with each other.
align_same_func_call_params = false # false/true
# The span for aligning variable definitions (0=don't align)
align_var_def_span = 1 # number
# How to align the star in variable definitions.
# 0=Part of the type 'void * foo;'
# 1=Part of the variable 'void *foo;'
# 2=Dangling 'void *foo;'
align_var_def_star_style = 0 # number
# How to align the '&' in variable definitions.
# 0=Part of the type
# 1=Part of the variable
# 2=Dangling
align_var_def_amp_style = 0 # number
# The threshold for aligning variable definitions (0=no limit)
align_var_def_thresh = 0 # number
# The gap for aligning variable definitions
align_var_def_gap = 1 # number
# Whether to align the colon in struct bit fields
align_var_def_colon = false # false/true
# Whether to align any attribute after the variable name
align_var_def_attribute = false # false/true
# Whether to align inline struct/enum/union variable definitions
align_var_def_inline = false # false/true
# The span for aligning on '=' in assignments (0=don't align)
align_assign_span = 0 # number
# The threshold for aligning on '=' in assignments (0=no limit)
align_assign_thresh = 0 # number
# The span for aligning on '=' in enums (0=don't align)
align_enum_equ_span = 0 # number
# The threshold for aligning on '=' in enums (0=no limit)
align_enum_equ_thresh = 0 # number
# The span for aligning struct/union (0=don't align)
align_var_struct_span = 0 # number
# The threshold for aligning struct/union member definitions (0=no limit)
align_var_struct_thresh = 0 # number
# The gap for aligning struct/union member definitions
align_var_struct_gap = 0 # number
# The span for aligning struct initializer values (0=don't align)
align_struct_init_span = 0 # number
# The minimum space between the type and the synonym of a typedef
align_typedef_gap = 1 # number
# The span for aligning single-line typedefs (0=don't align)
align_typedef_span = 1 # number
# How to align typedef'd functions with other typedefs
# 0: Don't mix them at all
# 1: align the open paren with the types
# 2: align the function type name with the other type names
align_typedef_func = 2 # number
# Controls the positioning of the '*' in typedefs. Just try it.
# 0: Align on typedef type, ignore '*'
# 1: The '*' is part of type name: typedef int *pint;
# 2: The '*' is part of the type, but dangling: typedef int *pint;
align_typedef_star_style = 0 # number
# Controls the positioning of the '&' in typedefs. Just try it.
# 0: Align on typedef type, ignore '&'
# 1: The '&' is part of type name: typedef int &pint;
# 2: The '&' is part of the type, but dangling: typedef int &pint;
align_typedef_amp_style = 0 # number
# The span for aligning comments that end lines (0=don't align)
align_right_cmt_span = 2 # number
# If aligning comments, mix with comments after '}' and #endif with less than 3 spaces before the comment
align_right_cmt_mix = false # false/true
# If a trailing comment is more than this number of columns away from the text it follows,
# it will qualify for being aligned. This has to be > 0 to do anything.
align_right_cmt_gap = 0 # number
# Align trailing comment at or beyond column N; 'pulls in' comments as a bonus side effect (0=ignore)
align_right_cmt_at_col = 0 # number
# The span for aligning function prototypes (0=don't align)
align_func_proto_span = 0 # number
# Minimum gap between the return type and the function name.
align_func_proto_gap = 0 # number
# Align function protos on the 'operator' keyword instead of what follows
align_on_operator = false # false/true
# Whether to mix aligning prototype and variable declarations.
# If true, align_var_def_XXX options are used instead of align_func_proto_XXX options.
align_mix_var_proto = false # false/true
# Align single-line functions with function prototypes, uses align_func_proto_span
align_single_line_func = false # false/true
# Aligning the open brace of single-line functions.
# Requires align_single_line_func=true, uses align_func_proto_span
align_single_line_brace = false # false/true
# Gap for align_single_line_brace.
align_single_line_brace_gap = 1 # number
# The span for aligning ObjC msg spec (0=don't align)
align_oc_msg_spec_span = 0 # number
# Whether to align macros wrapped with a backslash and a newline.
# This will not work right if the macro contains a multi-line comment.
align_nl_cont = false # false/true
# The minimum space between label and value of a preprocessor define
align_pp_define_gap = 0 # number
# The span for aligning on '#define' bodies (0=don't align)
align_pp_define_span = 0 # number
# Align lines that start with '<<' with previous '<<'. Default=true
align_left_shift = true # false/true
# Span for aligning parameters in an Obj-C message call on the ':' (0=don't align)
align_oc_msg_colon_span = 0 # number
# Aligning parameters in an Obj-C '+' or '-' declaration on the ':'
align_oc_decl_colon = false # false/true
#
# Newline adding and removing options
#
# Whether to collapse empty blocks between '{' and '}'
nl_collapse_empty_body = false # false/true
# Don't split one-line braced assignments - 'foo_t f = { 1, 2 };'
nl_assign_leave_one_liners = false # false/true
# Don't split one-line braced statements inside a class xx { } body
nl_class_leave_one_liners = false # false/true
# Don't split one-line enums: 'enum foo { BAR = 15 };'
nl_enum_leave_one_liners = false # false/true
# Don't split one-line get or set functions
nl_getset_leave_one_liners = false # false/true
# Don't split one-line function definitions - 'int foo() { return 0; }'
nl_func_leave_one_liners = false # false/true
# Don't split one-line if/else statements - 'if(a) b++;'
nl_if_leave_one_liners = false # false/true
# Add or remove newlines at the start of the file
nl_start_of_file = remove # ignore/add/remove/force
# The number of newlines at the start of the file (only used if nl_start_of_file is 'add' or 'force'
nl_start_of_file_min = 0 # number
# Add or remove newline at the end of the file
nl_end_of_file = remove # ignore/add/remove/force
# The number of newlines at the end of the file (only used if nl_end_of_file is 'add' or 'force')
nl_end_of_file_min = 1 # number
# Add or remove newline between '=' and '{'
nl_assign_brace = ignore # ignore/add/remove/force
# Add or remove newline between '=' and '[' (D only)
nl_assign_square = ignore # ignore/add/remove/force
# Add or remove newline after '= [' (D only). Will also affect the newline before the ']'
nl_after_square_assign = ignore # ignore/add/remove/force
# The number of blank lines after a block of variable definitions
nl_func_var_def_blk = 1 # number
# Add or remove newline between a function call's ')' and '{', as in:
# list_for_each(item, &list) { }
nl_fcall_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'enum' and '{'
nl_enum_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'struct and '{'
nl_struct_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'union' and '{'
nl_union_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'if' and '{'
nl_if_brace = ignore # ignore/add/remove/force
# Add or remove newline between '}' and 'else'
nl_brace_else = ignore # ignore/add/remove/force
# Add or remove newline between 'else if' and '{'
# If set to ignore, nl_if_brace is used instead
nl_elseif_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'else' and '{'
nl_else_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'else' and 'if'
nl_else_if = ignore # ignore/add/remove/force
# Add or remove newline between '}' and 'finally'
nl_brace_finally = ignore # ignore/add/remove/force
# Add or remove newline between 'finally' and '{'
nl_finally_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'try' and '{'
nl_try_brace = ignore # ignore/add/remove/force
# Add or remove newline between get/set and '{'
nl_getset_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'for' and '{'
nl_for_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'catch' and '{'
nl_catch_brace = ignore # ignore/add/remove/force
# Add or remove newline between '}' and 'catch'
nl_brace_catch = ignore # ignore/add/remove/force
# Add or remove newline between 'while' and '{'
nl_while_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'using' and '{'
nl_using_brace = ignore # ignore/add/remove/force
# Add or remove newline between two open or close braces.
# Due to general newline/brace handling, REMOVE may not work.
nl_brace_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'do' and '{'
nl_do_brace = ignore # ignore/add/remove/force
# Add or remove newline between '}' and 'while' of 'do' statement
nl_brace_while = ignore # ignore/add/remove/force
# Add or remove newline between 'switch' and '{'
nl_switch_brace = ignore # ignore/add/remove/force
# Add a newline between ')' and '{' if the ')' is on a different line than the if/for/etc.
# Overrides nl_for_brace, nl_if_brace, nl_switch_brace, nl_while_switch, and nl_catch_brace.
nl_multi_line_cond = false # false/true
# Force a newline in a define after the macro name for multi-line defines.
nl_multi_line_define = false # false/true
# Whether to put a newline before 'case' statement
nl_before_case = false # false/true
# Add or remove newline between ')' and 'throw'
nl_before_throw = ignore # ignore/add/remove/force
# Whether to put a newline after 'case' statement
nl_after_case = false # false/true
# Newline between namespace and {
nl_namespace_brace = ignore # ignore/add/remove/force
# Add or remove newline between 'template<>' and whatever follows.
nl_template_class = ignore # ignore/add/remove/force
# Add or remove newline between 'class' and '{'
nl_class_brace = ignore # ignore/add/remove/force
# Add or remove newline after each ',' in the constructor member initialization
nl_class_init_args = ignore # ignore/add/remove/force
# Add or remove newline between return type and function name in a function definition
nl_func_type_name = ignore # ignore/add/remove/force
# Add or remove newline between return type and function name inside a class {}
# Uses nl_func_type_name or nl_func_proto_type_name if set to ignore.
nl_func_type_name_class = ignore # ignore/add/remove/force
# Add or remove newline between function scope and name in a definition
# Controls the newline after '::' in 'void A::f() { }'
nl_func_scope_name = ignore # ignore/add/remove/force
# Add or remove newline between return type and function name in a prototype
nl_func_proto_type_name = ignore # ignore/add/remove/force
# Add or remove newline between a function name and the opening '('
nl_func_paren = ignore # ignore/add/remove/force
# Add or remove newline after '(' in a function declaration
nl_func_decl_start = ignore # ignore/add/remove/force
# Overrides nl_func_decl_start when there is only one paramter.
nl_func_decl_start_single = ignore # ignore/add/remove/force
# Add or remove newline after each ',' in a function declaration
nl_func_decl_args = ignore # ignore/add/remove/force
# Add or remove newline before the ')' in a function declaration
nl_func_decl_end = ignore # ignore/add/remove/force
# Overrides nl_func_decl_end when there is only one paramter.
nl_func_decl_end_single = ignore # ignore/add/remove/force
# Add or remove newline between '()' in a function declaration.
nl_func_decl_empty = ignore # ignore/add/remove/force
# Add or remove newline between function signature and '{'
nl_fdef_brace = ignore # ignore/add/remove/force
# Whether to put a newline after 'return' statement
nl_after_return = false # false/true
# Add or remove a newline between the return keyword and return expression.
nl_return_expr = ignore # ignore/add/remove/force
# Whether to put a newline after semicolons, except in 'for' statements
nl_after_semicolon = false # false/true
# Whether to put a newline after brace open.
# This also adds a newline before the matching brace close.
nl_after_brace_open = false # false/true
# If nl_after_brace_open and nl_after_brace_open_cmt are true, a newline is
# placed between the open brace and a trailing single-line comment.
nl_after_brace_open_cmt = false # false/true
# Whether to put a newline after a virtual brace open with a non-empty body.
# These occur in un-braced if/while/do/for statement bodies.
nl_after_vbrace_open = false # false/true
# Whether to put a newline after a virtual brace open with an empty body.
# These occur in un-braced if/while/do/for statement bodies.
nl_after_vbrace_open_empty = false # false/true
# Whether to put a newline after a brace close.
# Does not apply if followed by a necessary ';'.
nl_after_brace_close = false # false/true
# Whether to put a newline after a virtual brace close.
# Would add a newline before return in: 'if (foo) a++; return;'
nl_after_vbrace_close = false # false/true
# Whether to alter newlines in '#define' macros
nl_define_macro = false # false/true
# Whether to not put blanks after '#ifxx', '#elxx', or before '#endif'
nl_squeeze_ifdef = false # false/true
# Add or remove blank line before 'if'
nl_before_if = ignore # ignore/add/remove/force
# Add or remove blank line after 'if' statement
nl_after_if = ignore # ignore/add/remove/force
# Add or remove blank line before 'for'
nl_before_for = ignore # ignore/add/remove/force
# Add or remove blank line after 'for' statement
nl_after_for = ignore # ignore/add/remove/force
# Add or remove blank line before 'while'
nl_before_while = ignore # ignore/add/remove/force
# Add or remove blank line after 'while' statement
nl_after_while = ignore # ignore/add/remove/force
# Add or remove blank line before 'switch'
nl_before_switch = ignore # ignore/add/remove/force
# Add or remove blank line after 'switch' statement
nl_after_switch = ignore # ignore/add/remove/force
# Add or remove blank line before 'do'
nl_before_do = ignore # ignore/add/remove/force
# Add or remove blank line after 'do/while' statement
nl_after_do = ignore # ignore/add/remove/force
# Whether to double-space commented-entries in struct/enum
nl_ds_struct_enum_cmt = false # false/true
# Whether to double-space before the close brace of a struct/union/enum
# (lower priority than 'eat_blanks_before_close_brace')
nl_ds_struct_enum_close_brace = false # false/true
# Add or remove a newline around a class colon.
# Related to pos_class_colon, nl_class_init_args, and pos_comma.
nl_class_colon = ignore # ignore/add/remove/force
# Change simple unbraced if statements into a one-liner
# 'if(b)\n i++;' => 'if(b) i++;'
nl_create_if_one_liner = false # false/true
# Change simple unbraced for statements into a one-liner
# 'for (i=0;i<5;i++)\n foo(i);' => 'for (i=0;i<5;i++) foo(i);'
nl_create_for_one_liner = false # false/true
# Change simple unbraced while statements into a one-liner
# 'while (i<5)\n foo(i++);' => 'while (i<5) foo(i++);'
nl_create_while_one_liner = false # false/true
#
# Positioning options
#
# The position of arithmetic operators in wrapped expressions
pos_arith = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of assignment in wrapped expressions.
# Do not affect '=' followed by '{'
pos_assign = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of boolean operators in wrapped expressions
pos_bool = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of comparison operators in wrapped expressions
pos_compare = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of conditional (b ? t : f) operators in wrapped expressions
pos_conditional = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of the comma in wrapped expressions
pos_comma = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of the comma in the constructor initialization list
pos_class_comma = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
# The position of colons between constructor and member initialization
pos_class_colon = ignore # ignore/lead/lead_break/lead_force/trail/trail_break/trail_force
#
# Line Splitting options
#
# Try to limit code width to N number of columns
code_width = 120 # number
# Whether to fully split long 'for' statements at semi-colons
ls_for_split_full = false # false/true
# Whether to fully split long function protos/calls at commas
ls_func_split_full = false # false/true
#
# Blank line options
#
# The maximum consecutive newlines
nl_max = 2 # number
# The number of newlines after a function prototype, if followed by another function prototype
nl_after_func_proto = 2 # number
# The number of newlines after a function prototype, if not followed by another function prototype
nl_after_func_proto_group = 1 # number
# The number of newlines after '}' of a multi-line function body
nl_after_func_body = 2 # number
# The number of newlines after '}' of a single line function body
nl_after_func_body_one_liner = 0 # number
# The minimum number of newlines before a multi-line comment.
# Doesn't apply if after a brace open or another multi-line comment.
nl_before_block_comment = 0 # number
# The minimum number of newlines before a single-line C comment.
# Doesn't apply if after a brace open or other single-line C comments.
nl_before_c_comment = 0 # number
# The minimum number of newlines before a CPP comment.
# Doesn't apply if after a brace open or other CPP comments.
nl_before_cpp_comment = 0 # number
# Whether to force a newline after a multi-line comment.
nl_after_multiline_comment = false # false/true
# The number of newlines before a 'private:', 'public:', 'protected:', 'signals:', or 'slots:' label.
# Will not change the newline count if after a brace open.
# 0 = No change.
nl_before_access_spec = 1 # number
# The number of newlines after a 'private:', 'public:', 'protected:', 'signals:', or 'slots:' label.
# 0 = No change.
nl_after_access_spec = 0 # number
# The number of newlines between a function def and the function comment.
# 0 = No change.
nl_comment_func_def = 0 # number
# The number of newlines after a try-catch-finally block that isn't followed by a brace close.
# 0 = No change.
nl_after_try_catch_finally = 0 # number
# The number of newlines before and after a property, indexer or event decl.
# 0 = No change.
nl_around_cs_property = 0 # number
# The number of newlines between the get/set/add/remove handlers in C#.
# 0 = No change.
nl_between_get_set = 0 # number
# Whether to remove blank lines after '{'
eat_blanks_after_open_brace = false # false/true
# Whether to remove blank lines before '}'
eat_blanks_before_close_brace = false # false/true
#
# Code modifying options (non-whitespace)
#
# Add or remove braces on single-line 'do' statement
mod_full_brace_do = ignore # ignore/add/remove/force
# Add or remove braces on single-line 'for' statement
mod_full_brace_for = ignore # ignore/add/remove/force
# Add or remove braces on single-line function definitions. (Pawn)
mod_full_brace_function = ignore # ignore/add/remove/force
# Add or remove braces on single-line 'if' statement. Will not remove the braces if they contain an 'else'.
mod_full_brace_if = ignore # ignore/add/remove/force
# Make all if/elseif/else statements in a chain be braced or not. Overrides mod_full_brace_if.
# If any must be braced, they are all braced. If all can be unbraced, then the braces are removed.
mod_full_brace_if_chain = false # false/true
# Don't remove braces around statements that span N newlines
mod_full_brace_nl = 0 # number
# Add or remove braces on single-line 'while' statement
mod_full_brace_while = ignore # ignore/add/remove/force
# Add or remove braces on single-line 'using ()' statement
mod_full_brace_using = ignore # ignore/add/remove/force
# Add or remove unnecessary paren on 'return' statement
mod_paren_on_return = ignore # ignore/add/remove/force
# Whether to change optional semicolons to real semicolons
mod_pawn_semicolon = false # false/true
# Add parens on 'while' and 'if' statement around bools
mod_full_paren_if_bool = false # false/true
# Whether to remove superfluous semicolons
mod_remove_extra_semicolon = false # false/true
# If a function body exceeds the specified number of newlines and doesn't have a comment after
# the close brace, a comment will be added.
mod_add_long_function_closebrace_comment = 0 # number
# If a switch body exceeds the specified number of newlines and doesn't have a comment after
# the close brace, a comment will be added.
mod_add_long_switch_closebrace_comment = 0 # number
# If an #ifdef body exceeds the specified number of newlines and doesn't have a comment after
# the #else, a comment will be added.
mod_add_long_ifdef_endif_comment = 0 # number
# If an #ifdef or #else body exceeds the specified number of newlines and doesn't have a comment after
# the #endif, a comment will be added.
mod_add_long_ifdef_else_comment = 0 # number
# If TRUE, will sort consecutive single-line 'import' statements [Java, D]
mod_sort_import = false # false/true
# If TRUE, will sort consecutive single-line 'using' statements [C#]
mod_sort_using = false # false/true
# If TRUE, will sort consecutive single-line '#include' statements [C/C++] and '#import' statements [Obj-C]
# This is generally a bad idea, as it may break your code.
mod_sort_include = false # false/true
# If TRUE, it will move a 'break' that appears after a fully braced 'case' before the close brace.
mod_move_case_break = false # false/true
# Will add or remove the braces around a fully braced case statement.
# Will only remove the braces if there are no variable declarations in the block.
mod_case_brace = ignore # ignore/add/remove/force
# If TRUE, it will remove a void 'return;' that appears as the last statement in a function.
mod_remove_empty_return = false # false/true
#
# Comment modifications
#
# Try to wrap comments at cmt_width columns
cmt_width = 80 # number
# Set the comment reflow mode (default: 0)
# 0: no reflowing (apart from the line wrapping due to cmt_width)
# 1: no touching at all
# 2: full reflow
cmt_reflow_mode = 0 # number
# If false, disable all multi-line comment changes, including cmt_width. keyword substitution, and leading chars.
# Default is true.
cmt_indent_multi = false # false/true
# Whether to group c-comments that look like they are in a block
cmt_c_group = false # false/true
# Whether to put an empty '/*' on the first line of the combined c-comment
cmt_c_nl_start = false # false/true
# Whether to put a newline before the closing '*/' of the combined c-comment
cmt_c_nl_end = false # false/true
# Whether to group cpp-comments that look like they are in a block
cmt_cpp_group = false # false/true
# Whether to put an empty '/*' on the first line of the combined cpp-comment
cmt_cpp_nl_start = false # false/true
# Whether to put a newline before the closing '*/' of the combined cpp-comment
cmt_cpp_nl_end = false # false/true
# Whether to change cpp-comments into c-comments
cmt_cpp_to_c = false # false/true
# Whether to put a star on subsequent comment lines
cmt_star_cont = false # false/true
# The number of spaces to insert at the start of subsequent comment lines
cmt_sp_before_star_cont = 0 # number
# The number of spaces to insert after the star on subsequent comment lines
cmt_sp_after_star_cont = 0 # number
# For multi-line comments with a '*' lead, remove leading spaces if the first and last lines of
# the comment are the same length. Default=True
cmt_multi_check_last = false # false/true
# The filename that contains text to insert at the head of a file if the file doesn't start with a C/C++ comment.
# Will substitute $(filename) with the current file's name.
cmt_insert_file_header = "" # string
# The filename that contains text to insert at the end of a file if the file doesn't end with a C/C++ comment.
# Will substitute $(filename) with the current file's name.
cmt_insert_file_footer = "" # string
# The filename that contains text to insert before a function implementation if the function isn't preceded with a C/C++ comment.
# Will substitute $(function) with the function name and $(javaparam) with the javadoc @param and @return stuff.
# Will also substitute $(fclass) with the class name: void CFoo::Bar() { ... }
cmt_insert_func_header = "" # string
# The filename that contains text to insert before a class if the class isn't preceded with a C/C++ comment.
# Will substitute $(class) with the class name.
cmt_insert_class_header = "" # string
# If a preprocessor is encountered when stepping backwards from a function name, then
# this option decides whether the comment should be inserted.
# Affects cmt_insert_func_header and cmt_insert_class_header.
cmt_insert_before_preproc = false # false/true
#
# Preprocessor options
#
# Control indent of preprocessors inside #if blocks at brace level 0
pp_indent = add # ignore/add/remove/force
# Whether to indent #if/#else/#endif at the brace level (true) or from column 1 (false)
pp_indent_at_level = false # false/true
# If pp_indent_at_level=false, specifies the number of columns to indent per level. Default=1.
pp_indent_count = 0 # number
# Add or remove space after # based on pp_level of #if blocks
pp_space = ignore # ignore/add/remove/force
# Sets the number of spaces added with pp_space
pp_space_count = 0 # number
# The indent for #region and #endregion in C# and '#pragma region' in C/C++
pp_indent_region = 0 # number
# Whether to indent the code between #region and #endregion
pp_region_indent_code = false # false/true
# If pp_indent_at_level=true, sets the indent for #if, #else, and #endif when not at file-level
pp_indent_if = 2 # number
# Control whether to indent the code between #if, #else and #endif when not at file-level
pp_if_indent_code = false # false/true
# Whether to indent '#define' at the brace level (true) or from column 1 (false)
pp_define_at_level = false # false/true
# You can force a token to be a type with the 'type' option.
# Example:
# type myfoo1 myfoo2
#
# You can create custom macro-based indentation using macro-open,
# macro-else and macro-close.
# Example:
# macro-open BEGIN_TEMPLATE_MESSAGE_MAP
# macro-open BEGIN_MESSAGE_MAP
# macro-close END_MESSAGE_MAP
#
# You can assign any keyword to any type with the set option.
# set func_call_user _ N_
#
# The full syntax description of all custom definition config entries
# is shown below:
#
# define custom tokens as:
# - embed whitespace in token using '' escape character, or
# put token in quotes
# - these: ' " and ` are recognized as quote delimiters
#
# type token1 token2 token3 ...
# ^ optionally specify multiple tokens on a single line
# define def_token output_token
# ^ output_token is optional, then NULL is assumed
# macro-open token
# macro-close token
# macro-else token
# set id token1 token2 ...
# ^ optionally specify multiple tokens on a single line
# ^ id is one of the names in token_enum.h sans the CT_ prefix,
# e.g. PP_PRAGMA
#
# all tokens are separated by any mix of ',' commas, '=' equal signs
# and whitespace (space, tab)
#
GoFigure2-v0.9.0/KWStyle/doAllStyle.csh.in 0000644 0001750 0001750 00000002160 11667757442 020115 0 ustar mathieu mathieu #! /bin/tcsh -f
#
# Usage: @GOFIGURE2@/doAllStyle.csh
# Run KWStyle on all files in a directory.
# Creates a subdirectory kwstyle. This subdirectory has a
# file called 'all' that contains a list of files that show
# the style defects for files in the directory. For each file
# that has style defects, there is a corresponding file in
# kwstyle with a suffix .txt that contains a description of
# the defects.
rm -rf kwstyle
mkdir kwstyle
unalias -a
set files=`ls -1 *.h *.txx *.cxx`
rm -f defects.txt
foreach file ( $files )
##@KWSTYLE_EXECUTABLE@ -v -gcc -xml @GOFIGURE2_BINARY_DIR@/GOFIGURE2.kws.xml -o @ITK_SOURCE_DIR@/Utilities/KWStyle/ITKOverwrite.txt $file >kwstyle/$file.txt
@KWSTYLE_EXECUTABLE@ -v -gcc -xml @GOFIGURE2_BINARY_DIR@/GOFIGURE2.kws.xml $file >kwstyle/$file.txt
cat kwstyle/$file.txt >> defects.txt
echo -n .
end
echo .
cd kwstyle
rm -f defectiveFiles
set files=`ls -1 *.txt`
foreach file ( $files )
set n=`grep " error: " $file | wc -l`
if ( $n > 0 ) then
echo `basename $file .txt` has $n style defects
echo $file >>defectiveFiles
endif
end
cd ..
pwd
GoFigure2-v0.9.0/KWStyle/Header.h 0000644 0001750 0001750 00000003416 11667757442 016303 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-11
Copyright (c) 2009-11, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
GoFigure2-v0.9.0/GOFIGURE2CPack.cmake 0000644 0001750 0001750 00000006752 11667757442 016603 0 ustar mathieu mathieu # setup CPack
INCLUDE( ${GOFIGURE2_SOURCE_DIR}/CMake/InstallSupportLibraries.cmake )
CONFIGURE_FILE( "${GOFIGURE2_SOURCE_DIR}/GOFIGURE2CPackOptions.cmake.in"
"${GOFIGURE2_BINARY_DIR}/GOFIGURE2CPackOptions.cmake" @ONLY
)
SET( CPACK_PROJECT_CONFIG_FILE
"${GOFIGURE2_BINARY_DIR}/GOFIGURE2CPackOptions.cmake"
)
SET( CPACK_PACKAGE_DESCRIPTION_SUMMARY
"GoFigure2 is a cross-platform application for microscope image visualization and analysis"
)
SET( CPACK_PACKAGE_VENDOR "Megason Lab, Systems Biology, HMS" )
SET( CPACK_PACKAGE_CONTACT "gofigure2-developers@lists.sourceforge.net" )
SET( CPACK_PACKAGE_DESCRIPTION_FILE "${GOFIGURE2_SOURCE_DIR}/ReadMe.rst")
SET( CPACK_RESOURCE_FILE_LICENSE "${GOFIGURE2_SOURCE_DIR}/Licenses/Copyright.txt")
SET( CPACK_RESOURCE_FILE_WELCOME "${GOFIGURE2_SOURCE_DIR}/CPack.GenericWelcome.txt" )
SET( CPACK_PACKAGE_VERSION_MAJOR ${GOFIGURE2_MAJOR_VERSION} )
SET( CPACK_PACKAGE_VERSION_MINOR ${GOFIGURE2_MINOR_VERSION} )
SET( CPACK_PACKAGE_VERSION_PATCH ${GOFIGURE2_WC_REVISION} )
SET( CPACK_PACKAGE_INSTALL_DIRECTORY "GoFigure2" )
SET( CPACK_SOURCE_PACKAGE_FILE_NAME "GoFigure2-${GOFIGURE2_VERSION}" )
# taken from CMake
IF( NOT DEFINED CPACK_SYSTEM_NAME )
# make sure package is not Cygwin-unknown, for Cygwin just
# cygwin is good for the system name
IF("${CMAKE_SYSTEM_NAME}" STREQUAL "CYGWIN")
SET( CPACK_SYSTEM_NAME Cygwin )
ELSE("${CMAKE_SYSTEM_NAME}" STREQUAL "CYGWIN")
IF( CMAKE_SYSTEM_PROCESSOR MATCHES "unknown" )
EXEC_PROGRAM( uname ARGS "-m" OUTPUT_VARIABLE CMAKE_SYSTEM_PROCESSOR )
ENDIF( CMAKE_SYSTEM_PROCESSOR MATCHES "unknown" )
SET( CPACK_SYSTEM_NAME ${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR} )
ENDIF("${CMAKE_SYSTEM_NAME}" STREQUAL "CYGWIN")
ENDIF( NOT DEFINED CPACK_SYSTEM_NAME )
#set up the package name on mac
IF( ${CPACK_SYSTEM_NAME} MATCHES Darwin )
#use uname -m instead of uname -p
#EXECUTE_PROCESS( COMMAND uname -m
# OUTPUT_VARIABLE PLATFORM)
#remove end of line character
#STRING(REGEX REPLACE "/n" "" PLATFORM2 ${PLATFORM})
#set the system name
IF( CMAKE_OSX_ARCHITECTURES )
SET( CPACK_SYSTEM_NAME Darwin-${CMAKE_OSX_ARCHITECTURES} )
ENDIF( CMAKE_OSX_ARCHITECTURES )
ENDIF( ${CPACK_SYSTEM_NAME} MATCHES Darwin )
#set up the package name on windows
IF( ${CPACK_SYSTEM_NAME} MATCHES Windows )
IF( CMAKE_CL_64 )
SET( CPACK_SYSTEM_NAME win64-${CMAKE_SYSTEM_PROCESSOR} )
ELSE( CMAKE_CL_64 )
SET( CPACK_SYSTEM_NAME win32-${CMAKE_SYSTEM_PROCESSOR} )
ENDIF( CMAKE_CL_64 )
ENDIF( ${CPACK_SYSTEM_NAME} MATCHES Windows )
IF( NOT DEFINED CPACK_PACKAGE_FILE_NAME )
# if the CPACK_PACKAGE_FILE_NAME is not defined by the cache
# default to source package - system, on cygwin system is not
# needed
IF( CYGWIN )
SET( CPACK_PACKAGE_FILE_NAME
"${CPACK_SOURCE_PACKAGE_FILE_NAME}" )
ELSE( CYGWIN )
SET( CPACK_PACKAGE_FILE_NAME
"${CPACK_SOURCE_PACKAGE_FILE_NAME}-${CPACK_SYSTEM_NAME}" )
ENDIF( CYGWIN )
ENDIF( NOT DEFINED CPACK_PACKAGE_FILE_NAME )
IF( WIN32 AND NOT UNIX )
INCLUDE( ${CPACK_PROJECT_CONFIG_FILE} )
ELSE( WIN32 AND NOT UNIX )
SET( CPACK_STRIP_FILES "bin/gofigure" )
SET( CPACK_SOURCE_STRIP_FILES "" )
ENDIF( WIN32 AND NOT UNIX )
SET( CPACK_PACKAGE_EXECUTABLES "gofigure" "GoFigure2" )
# # # # cygwin specific packaging stuff
# # IF(CYGWIN)
# # ENDIF( CYGWIN )
IF( WIN32 )
INSTALL( PROGRAMS ${CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS}
DESTINATION bin COMPONENT Runtime )
ENDIF( WIN32 )
SET( CPACK_COMPONENTS_ALL
Runtime
Libraries
# headers
)
INCLUDE( CPack )
GoFigure2-v0.9.0/CPack.GenericWelcome.txt 0000644 0001750 0001750 00000000140 11667757442 020000 0 ustar mathieu mathieu Welcome to installation. This program will guide you through the installation of this software.
GoFigure2-v0.9.0/GoFigure2IncludeDirectories.cmake 0000644 0001750 0001750 00000003141 11667757442 021667 0 ustar mathieu mathieu set( GOFIGURE2_INCLUDE_DIRS_SOURCE_TREE
${GOFIGURE2_SOURCE_DIR}
${GOFIGURE2_SOURCE_DIR}/Code/
${GOFIGURE2_SOURCE_DIR}/Code/IO/
${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/
${GOFIGURE2_SOURCE_DIR}/Code/Filters/
${GOFIGURE2_SOURCE_DIR}/Main/
)
set( GOFIGURE2_INCLUDE_DIRS_MEGAVTK_SOURCE_TREE
${MEGAVTK2_SOURCE_DIR}/vtkItk
${MEGAVTK2_SOURCE_DIR}/vtkRenderingAddOn
${MEGAVTK2_SOURCE_DIR}
)
set( GOFIGURE2_INCLUDE_DIRS_EXTERNAL_SOURCE_TREE
${GOFIGURE2_EXTERNAL_SOURCE_DIR}
${GOFIGURE2_EXTERNAL_SOURCE_DIR}/vtkLSM
${GOFIGURE2_EXTERNAL_SOURCE_DIR}/itkQt
${GOFIGURE2_EXTERNAL_SOURCE_DIR}/PoissonReconstruction
${GOFIGURE2_EXTERNAL_SOURCE_DIR}/ctk
)
set( GOFIGURE2_INCLUDE_DIRS_BINARY_TRE
${GOFIGURE2_BINARY_DIR}
${GOFIGURE2_BINARY_DIR}/Code/
${GOFIGURE2_BINARY_DIR}/Code/IO/
${GOFIGURE2_BINARY_DIR}/Code/GUI/lib/
${GOFIGURE2_BINARY_DIR}/Code/Filters/
${GOFIGURE2_BINARY_DIR}/Main/
)
set( GOFIGURE2_INCLUDE_DIRS_MEGAVTK_BINARY_TREE
${MEGAVTK2_BINARY_DIR}/vtkItk
${MEGAVTK2_BINARY_DIR}/vtkRenderingAddOn
${MEGAVTK2_BINARY_DIR}
)
set( GOFIGURE2_INCLUDE_DIRS_EXTERNAL_BINARY_TREE
${GOFIGURE2_EXTERNAL_BINARY_DIR}
${GOFIGURE2_EXTERNAL_BINARY_DIR}/vtkLSM
${GOFIGURE2_EXTERNAL_BINARY_DIR}/itkQt
${GOFIGURE2_EXTERNAL_BINARY_DIR}/PoissonReconstruction
${GOFIGURE2_EXTERNAL_BINARY_DIR}/ctk
)
set( GOFIGURE2_INCLUDE_DIRS
${GOFIGURE2_INCLUDE_DIRS_SOURCE_TREE}
${GOFIGURE2_INCLUDE_DIRS_MEGAVTK_SOURCE_TREE}
${GOFIGURE2_INCLUDE_DIRS_EXTERNAL_SOURCE_TREE}
${GOFIGURE2_INCLUDE_DIRS_BINARY_TREE}
${GOFIGURE2_INCLUDE_DIRS_MEGAVTK_BINARY_TREE}
${GOFIGURE2_INCLUDE_DIRS_EXTERNAL_BINARY_TREE}
)
GoFigure2-v0.9.0/Code/ 0000755 0001750 0001750 00000000000 11667757442 014246 5 ustar mathieu mathieu GoFigure2-v0.9.0/Code/IO/ 0000755 0001750 0001750 00000000000 11667757442 014555 5 ustar mathieu mathieu GoFigure2-v0.9.0/Code/IO/GoFigureFileInfoMultiIndexContainerHelper.cxx 0000644 0001750 0001750 00000016505 11667757442 025441 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-11
Copyright (c) 2009-11, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#include "GoFigureFileInfoMultiIndexContainerHelper.h"
// method to speed up the display
std::map< unsigned int, std::list< std::string > >
GetAllFileNamesForGivenTCoord(
const GoFigureFileInfoHelperMultiIndexContainer & iContainer,
const unsigned int & iT,
const unsigned int & iMinCh,
const unsigned int & iMaxCh
)
{
std::map< unsigned int, std::list< std::string > > oList;
using boost::multi_index::index;
using boost::multi_index::get;
using boost::tuples::tie;
index< GoFigureFileInfoHelperMultiIndexContainer, m_TCoord >::type::iterator it0, it1;
tie(it0, it1) = get< m_TCoord >(iContainer).equal_range(iT);
GoFigureFileInfoHelperChannelViewContainer subset;
while ( it0 != it1 )
{
subset.insert(&*it0);
++it0;
}
GoFigureFileInfoHelperChannelViewContainer::nth_index< 0 >::type::iterator ic0, ic1;
ic0 = subset.get< 0 >().lower_bound(iMinCh);
ic1 = subset.get< 0 >().upper_bound(iMaxCh);
GoFigureFileInfoHelperZCoordViewContainer final_container;
while ( ic0 != ic1 )
{
final_container.insert(*ic0);
++ic0;
}
GoFigureFileInfoHelperZCoordViewContainer::iterator z_it0 = final_container.begin();
GoFigureFileInfoHelperZCoordViewContainer::iterator z_it1 = final_container.end();
while ( z_it0 != z_it1 )
{
oList[( *z_it0 )->m_Channel].push_back( ( *z_it0 )->m_Filename );
++z_it0;
}
return oList;
}
std::map< unsigned int, std::list< std::string > >
GetAllFileNamesForGivenZCoord(
const GoFigureFileInfoHelperMultiIndexContainer & iContainer,
const unsigned int & iZ,
const unsigned int & iMinCh,
const unsigned int & iMaxCh
)
{
std::map< unsigned int, std::list< std::string > > oList;
using boost::multi_index::index;
using boost::multi_index::get;
using boost::tuples::tie;
index< GoFigureFileInfoHelperMultiIndexContainer, m_ZCoord >::type::iterator it0, it1;
tie(it0, it1) = get< m_ZCoord >(iContainer).equal_range(iZ);
GoFigureFileInfoHelperChannelViewContainer subset;
while ( it0 != it1 )
{
subset.insert(&*it0);
++it0;
}
GoFigureFileInfoHelperChannelViewContainer::nth_index< 0 >::type::iterator ic0, ic1;
ic0 = subset.get< 0 >().lower_bound(iMinCh);
ic1 = subset.get< 0 >().upper_bound(iMaxCh);
GoFigureFileInfoHelperTCoordViewContainer final_container;
while ( ic0 != ic1 )
{
final_container.insert(*ic0);
++ic0;
}
GoFigureFileInfoHelperTCoordViewContainer::iterator z_it0 = final_container.begin();
GoFigureFileInfoHelperTCoordViewContainer::iterator z_it1 = final_container.end();
while ( z_it0 != z_it1 )
{
oList[( *z_it0 )->m_Channel].push_back( ( *z_it0 )->m_Filename );
++z_it0;
}
return oList;
}
std::list< std::string > GetAllFileNamesForGivenTCoordAndChannel(
const GoFigureFileInfoHelperMultiIndexContainer & iContainer,
const unsigned int & iT,
const unsigned int & iCh)
{
std::list< std::string > oList;
using boost::multi_index::index;
using boost::multi_index::get;
using boost::tuples::tie;
index< GoFigureFileInfoHelperMultiIndexContainer, m_TCoord >::type::iterator it0, it1;
tie(it0, it1) = get< m_TCoord >(iContainer).equal_range(iT);
GoFigureFileInfoHelperChannelViewContainer subset;
while ( it0 != it1 )
{
subset.insert(&*it0);
++it0;
}
GoFigureFileInfoHelperChannelViewContainer::nth_index< 0 >::type::iterator ic0, ic1;
ic0 = subset.get< 0 >().lower_bound(iCh);
ic1 = subset.get< 0 >().upper_bound(iCh);
GoFigureFileInfoHelperZCoordViewContainer final_container;
while ( ic0 != ic1 )
{
final_container.insert(*ic0);
++ic0;
}
GoFigureFileInfoHelperZCoordViewContainer::iterator z_it0 = final_container.begin();
GoFigureFileInfoHelperZCoordViewContainer::iterator z_it1 = final_container.end();
while ( z_it0 != z_it1 )
{
oList.push_back( ( *z_it0 )->m_Filename );
++z_it0;
}
return oList;
}
std::list< std::string > GetAllFileNamesForGivenZCoordPointAndChannel(
const GoFigureFileInfoHelperMultiIndexContainer & iContainer,
const unsigned int & iZ,
const unsigned int & iCh)
{
std::list< std::string > oList;
using boost::multi_index::index;
using boost::multi_index::get;
using boost::tuples::tie;
index< GoFigureFileInfoHelperMultiIndexContainer, m_ZCoord >::type::iterator it0, it1;
tie(it0, it1) = get< m_ZCoord >(iContainer).equal_range(iZ);
GoFigureFileInfoHelperChannelViewContainer subset;
while ( it0 != it1 )
{
subset.insert(&*it0);
++it0;
}
GoFigureFileInfoHelperChannelViewContainer::nth_index< 0 >::type::iterator ic0, ic1;
ic0 = subset.get< 0 >().lower_bound(iCh);
ic1 = subset.get< 0 >().upper_bound(iCh);
GoFigureFileInfoHelperTCoordViewContainer final_container;
while ( ic0 != ic1 )
{
final_container.insert(*ic0);
++ic0;
}
GoFigureFileInfoHelperTCoordViewContainer::iterator z_it0 = final_container.begin();
GoFigureFileInfoHelperTCoordViewContainer::iterator z_it1 = final_container.end();
while ( z_it0 != z_it1 )
{
oList.push_back( ( *z_it0 )->m_Filename );
++z_it0;
}
return oList;
}
std::map< unsigned int, std::list< std::string > >
GetAllFileNamesForGivenChannelAndTCoords(
const GoFigureFileInfoHelperMultiIndexContainer & iContainer,
const unsigned int & iCh,
const std::set< unsigned int > & iTCoordList
)
{
std::map< unsigned int, std::list< std::string > > oList;
std::set< unsigned int >::const_iterator t_it = iTCoordList.begin();
while ( t_it != iTCoordList.end() )
{
oList[*t_it] = GetAllFileNamesForGivenTCoordAndChannel(iContainer, *t_it, iCh);
++t_it;
}
return oList;
} GoFigure2-v0.9.0/Code/IO/QueryDataBaseHelper.cxx 0000644 0001750 0001750 00000035154 11667757442 021143 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-11
Copyright (c) 2009-11, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#include "QueryDataBaseHelper.h"
#include "vtkMySQLDatabase.h"
#include "vtkSQLQuery.h"
#include "vtkStdString.h"
#include "vtkVariant.h"
#include "QueryBuilderHelper.h"
#include
#include
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
std::pair< bool, vtkMySQLDatabase * > ConnectToServer(std::string ServerName, std::string login,
std::string Password)
{
std::pair< bool, vtkMySQLDatabase * > ConnectionServer;
vtkMySQLDatabase * ServerConnector = vtkMySQLDatabase::New();
ServerConnector->SetHostName( ServerName.c_str() );
ServerConnector->SetUser( login.c_str() );
ServerConnector->SetPassword( Password.c_str() );
if ( !ServerConnector->Open() )
{
std::cout << "Could not connect to the server." << std::endl;
std::cout << "Debug: In " << __FILE__ << ", line " << __LINE__;
std::cout << std::endl;
ConnectionServer.first = false;
return ConnectionServer;
}
ConnectionServer.first = true;
ConnectionServer.second = ServerConnector;
return ConnectionServer;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
std::pair< bool, vtkMySQLDatabase * > ConnectToDatabase(std::string ServerName, std::string login,
std::string Password, std::string DBName)
{
std::pair< bool, vtkMySQLDatabase * > ConnectionDatabase(false, (vtkMySQLDatabase *)0);
vtkMySQLDatabase * DatabaseConnector = vtkMySQLDatabase::New();
DatabaseConnector->SetHostName( ServerName.c_str() );
DatabaseConnector->SetUser( login.c_str() );
DatabaseConnector->SetPassword( Password.c_str() );
DatabaseConnector->SetDatabaseName( DBName.c_str() );
if ( !DatabaseConnector->Open() )
{
itkGenericExceptionMacro(
<< "Could not open database."
<< "DB will not be created.");
std::cout << "Could not connect to the database." << std::endl;
std::cout << "Debug: In " << __FILE__ << ", line " << __LINE__;
std::cout << std::endl;
return ConnectionDatabase;
}
ConnectionDatabase.first = true;
ConnectionDatabase.second = DatabaseConnector;
return ConnectionDatabase;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vtkMySQLDatabase * OpenDatabaseConnection(
std::string ServerName, std::string login,
std::string Password, std::string DBName)
{
std::pair< bool, vtkMySQLDatabase * > ConnectionDatabase = ConnectToDatabase(
ServerName, login, Password, DBName);
if ( !ConnectionDatabase.first )
{
std::cout << "No connection open for QGoOpenOrCreateImgSession" << std::endl;
std::cout << "Debug: In " << __FILE__ << ", line " << __LINE__;
std::cout << std::endl;
}
return ConnectionDatabase.second;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
bool CloseDatabaseConnection(
vtkMySQLDatabase *DatabaseConnector)
{
if ( DatabaseConnector != NULL )
{
DatabaseConnector->Close();
DatabaseConnector->Delete();
return true;
}
return false;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void ExecuteQuery(vtkMySQLDatabase *iDatabaseConnector, std::string iQuery)
{
vtkSQLQuery *query = iDatabaseConnector->GetQueryInstance();
query->SetQuery( iQuery.c_str() );
if ( !query->Execute() )
{
itkGenericExceptionMacro(
<< "Execute query failed"
<< query->GetLastErrorText() );
iDatabaseConnector->Close();
iDatabaseConnector->Delete();
}
query->Delete();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
std::vector< std::string > ListDatabases(vtkMySQLDatabase *ServerConnector)
{
std::vector< std::string > result;
vtkSQLQuery * query = ServerConnector->GetQueryInstance();
query->SetQuery("Show Databases;");
if ( !query->Execute() )
{
itkGenericExceptionMacro(
<< "Show Databases query failed."
<< query->GetLastErrorText() );
query->Delete();
return result;
}
// all set, proceed
// iterate over lines, we know there is only one column
// and as many rows as there is databases
while ( query->NextRow() )
{
result.push_back( query->DataValue(0).ToString() );
}
query->Delete();
return result;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
std::vector< std::string > ListTables(vtkMySQLDatabase *DatabaseConnector)
{
std::vector< std::string > result;
vtkSQLQuery * query = DatabaseConnector->GetQueryInstance();
query->SetQuery("Show tables;");
if ( !query->Execute() )
{
itkGenericExceptionMacro(
<< "Show tables query failed"
<< query->GetLastErrorText() );
DatabaseConnector->Close();
DatabaseConnector->Delete();
query->Delete();
return result;
}
// all set, proceed
// iterate over lines, we know there is only one column
// and as many rows as there is databases
while ( query->NextRow() )
{
result.push_back( query->DataValue(0).ToString() );
}
query->Delete();
return result;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void DropDatabase(vtkMySQLDatabase *ServerConnector, std::string DBName)
{
vtkSQLQuery * query = ServerConnector->GetQueryInstance();
std::ostringstream insertQuery;
insertQuery << "DROP DATABASE " << DBName;
query->SetQuery( insertQuery.str().c_str() );
if ( !query->Execute() )
{
itkGenericExceptionMacro(
<< "Drop query failed"
<< query->GetLastErrorText() );
query->Delete();
return;
}
query->Delete();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void DropTable(vtkMySQLDatabase *DatabaseConnector, std::string TableName)
{
vtkSQLQuery * query = DatabaseConnector->GetQueryInstance();
std::ostringstream insertQuery;
insertQuery << "DROP TABLE " << TableName;
query->SetQuery( insertQuery.str().c_str() );
if ( !query->Execute() )
{
itkGenericExceptionMacro(
<< "Drop query failed"
<< query->GetLastErrorText() );
query->Delete();
return;
}
query->Delete();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void DeleteRow(vtkMySQLDatabase *DatabaseConnector,
std::string TableName, std::string field, std::string value)
{
std::stringstream querystream;
querystream << "DELETE FROM ";
querystream << TableName;
querystream << " WHERE ";
querystream << field;
querystream << " = '";
querystream << value;
querystream << "';";
ExecuteQuery( DatabaseConnector, querystream.str() );
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void DeleteRows(vtkMySQLDatabase *DatabaseConnector, std::string TableName,
std::string field, std::vector< std::string > VectorValues)
{
std::stringstream querystream;
querystream << "DELETE FROM ";
querystream << TableName;
querystream << " WHERE (";
unsigned int i;
for ( i = 0; i < VectorValues.size() - 1; i++ )
{
querystream << field;
querystream << " = '";
querystream << VectorValues[i];
querystream << "' OR ";
}
querystream << field;
querystream << " = '";
querystream << VectorValues[i];
querystream << "');";
ExecuteQuery( DatabaseConnector, querystream.str() );
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
bool DoesDatabaseExist(vtkMySQLDatabase *ServerConnector, std::string DBName)
{
std::vector< std::string > list;
list = ListDatabases(ServerConnector);
std::string myString(DBName);
std::vector< std::string >::iterator start = list.begin();
std::vector< std::string >::iterator end = list.end();
while ( start != end )
{
if ( ( *start ) == myString )
{
return true;
}
++start;
}
return false;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
bool DoesTableExist(vtkMySQLDatabase *DatabaseConnector,
std::string TableName)
{
std::vector< std::string > list;
list = ListTables(DatabaseConnector);
std::string myString(TableName);
std::vector< std::string >::iterator start = list.begin();
std::vector< std::string >::iterator end = list.end();
while ( start != end )
{
if ( ( *start ) == myString )
{
return true;
}
++start;
}
return false;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void UpdateValueInDB(vtkMySQLDatabase *DatabaseConnector, std::string iTableName,
std::string iColumnName, std::string iNewValue, std::string iField,
std::vector< unsigned int > iVectIDs)
{
std::stringstream querystream;
querystream << "UPDATE ";
querystream << iTableName;
querystream << " SET ";
querystream << iColumnName;
querystream << " = '";
querystream << iNewValue;
querystream << "' WHERE ";
querystream << GetConditions< unsigned int >(iField, iVectIDs, "OR");
ExecuteQuery( DatabaseConnector, querystream.str() );
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void UpdateValueInDB(vtkMySQLDatabase *DatabaseConnector,
std::string TableName, std::string field, std::string newValue,
std::string ColumnName, std::string value)
{
std::stringstream querystream;
querystream << "UPDATE ";
querystream << TableName;
querystream << " SET ";
querystream << field;
querystream << " = '";
querystream << newValue;
querystream << "' WHERE ";
querystream << ColumnName;
querystream << " = '";
querystream << value;
querystream << "';";
ExecuteQuery( DatabaseConnector, querystream.str() );
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void UpdateValueInDB(vtkMySQLDatabase *DatabaseConnector,
std::string iTableName, std::string ifield,
std::string inewValue, std::vector< unsigned int > iVectIDs)
{
std::stringstream querystream;
querystream << "UPDATE ";
querystream << iTableName;
querystream << " SET ";
querystream << ifield;
querystream << " = '";
querystream << inewValue;
querystream << " WHERE (";
unsigned int i;
for ( i = 0; i < iVectIDs.size() - 1; i++ )
{
querystream << ifield;
querystream << " = '";
querystream << iVectIDs[i];
querystream << "' OR ";
}
querystream << ifield;
querystream << " = '";
querystream << iVectIDs[i];
querystream << "');";
ExecuteQuery( DatabaseConnector, querystream.str() );
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
std::vector< std::string > GetFieldNames(std::string TableName,
vtkMySQLDatabase *DatabaseConnector)
{
std::vector< std::string > result;
vtkSQLQuery * query = DatabaseConnector->GetQueryInstance();
std::stringstream querystream;
querystream << "DESCRIBE ";
querystream << TableName;
querystream << ";";
query->SetQuery( querystream.str().c_str() );
if ( !query->Execute() )
{
itkGenericExceptionMacro(
<< "describe table query failed"
<< query->GetLastErrorText() );
DatabaseConnector->Close();
DatabaseConnector->Delete();
query->Delete();
return result;
}
while ( query->NextRow() )
{
result.push_back( query->DataValue(0).ToString() );
}
query->Delete();
return result;
}
GoFigure2-v0.9.0/Code/IO/GoDBTraceInfoForVisu.h 0000644 0001750 0001750 00000004572 11667757442 020622 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-11
Copyright (c) 2009-11, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#ifndef __GoDBTraceInfoForVisu_h
#define __GoDBTraceInfoForVisu_h
#include "vtkPolyData.h"
/**\brief structure to pass the information between the visualization
and the Database*/
struct GoDBTraceInfoForVisu {
unsigned int TraceID;
vtkPolyData *Points;
unsigned int Red;
unsigned int Green;
unsigned int Blue;
unsigned int Alpha;
unsigned int TimePoint;
bool IsHighLighted;
GoDBTraceInfoForVisu() : Points( NULL )
{
TraceID = 0;
Red = 0;
Green = 0;
Blue = 0;
Alpha = 255;
TimePoint = 0;
IsHighLighted = false;
}
};
#endif
GoFigure2-v0.9.0/Code/IO/GoDBRow/ 0000755 0001750 0001750 00000000000 11667757442 016020 5 ustar mathieu mathieu GoFigure2-v0.9.0/Code/IO/GoDBRow/GoDBCellTypeRow.cxx 0000644 0001750 0001750 00000007314 11667757442 021456 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-11
Copyright (c) 2009-11, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#include "GoDBCellTypeRow.h"
#include "GoDBRecordSetHelper.h"
GoDBCellTypeRow::GoDBCellTypeRow() : GoDBNameDescRow()
{
this->InitializeMap();
}
//-------------------------------------------------------------------------
//-------------------------------------------------------------------------
void GoDBCellTypeRow::InitializeMap()
{
this->m_TableName = "celltype";
this->m_TableIDName = "CellTypeID";
this->m_MapRow[this->m_TableIDName] = std::string( "0" );//ConvertToString< int >(0);
}
//-------------------------------------------------------------------------
//-------------------------------------------------------------------------
int GoDBCellTypeRow::DoesThisEntityAlreadyExists(
vtkMySQLDatabase *DatabaseConnector)
{
return DoesThisNameAlreadyExists(DatabaseConnector);
}
//-------------------------------------------------------------------------
//-------------------------------------------------------------------------
/*int GoDBCellTypeRow::DoesThisEntityAlreadyExists(
vtkMySQLDatabase* DatabaseConnector, std::string& ioName)
{
int ID = DoesThisNameAlreadyExists(DatabaseConnector);
if (ID == -1)
{
return ID;
}
ioName = ReturnOnlyOneValue(DatabaseConnector, this->m_TableName, "Name",
this->m_TableIDName, ConvertToString(ID));
return ID;
}*/
//-------------------------------------------------------------------------
//-------------------------------------------------------------------------
int GoDBCellTypeRow::SaveInDB(vtkMySQLDatabase *iDatabaseConnector)
{
/*int CellTypeID = this->DoesThisEntityAlreadyExists(DatabaseConnector);
if (CellTypeID == -1)
{
CellTypeID = AddOnlyOneNewObjectInTable(DatabaseConnector,
this->m_TableName, *this, this->m_TableIDName);
}
return CellTypeID;*/
return GoDBNameDescRow::SaveInDBTemplate< GoDBCellTypeRow >(iDatabaseConnector, *this);
}
GoFigure2-v0.9.0/Code/IO/GoDBRow/GoDBProjectRow.h 0000644 0001750 0001750 00000004434 11667757442 020770 0 ustar mathieu mathieu /*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009-11
Copyright (c) 2009-11, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#ifndef __GoDBProjectRow_h
#define __GoDBProjectRow_h
#include
#include