ghmm-0.9-rc3/ghmm/discrime.h000664 001750 001750 00000005671 12154244034 015617 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/discrime.h * Authors: Janne Grunau * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1713 $ * from $Date: 2006-10-16 10:06:28 -0400 (Mon, 16 Oct 2006) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_DISCRIME_H #define GHMM_DISCRIME_H #ifdef __cplusplus extern "C" { #endif /*----------------------------------------------------------------------------*/ /** Trains two or more models to opimise the discrimination between the classes in the trainingset. @return 0/-1 success/error @param mo: array of pointers to some models @param sqs: array of annotated sequence sets @param noC: number of classes @param max_steps: maximum number of training steps for a class @param gradient: if gradient == 0 try a closed form solution otherwise a gradient descent */ int ghmm_dmodel_label_discriminative (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int max_steps, int gradient); /*----------------------------------------------------------------------------*/ /** Returns the value of teh in this discriminative training algorithm optimised function for a tupel of HMMs and sequencesets. @return value of funcion @param mo: array of pointers to some models @param sqs: array of annotated sequence sets @param noC: number of classes */ double ghmm_dmodel_label_discrim_perf (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC); #ifdef __cplusplus } #endif #endif ghmm-0.9-rc3/ghmm/unsupported.h000664 001750 001750 00000011213 12154244034 016375 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/unsupported.h * Authors: Janne Grunau * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1977 $ * from $Date: 2007-11-16 10:49:06 -0500 (Fri, 16 Nov 2007) $ * last change by $Author: grunau $. * *******************************************************************************/ #include "ghmmconfig.h" #ifdef GHMM_UNSUPPORTED #ifndef GHMM_UNSUPPORTED_H #define GHMM_UNSUPPORTED_H #ifdef __cplusplus extern "C" { #endif /*================== matrix.h ===============================================*/ /** Reads in an integer matrix. @return 0 for succes; -1 for error @param s: scanner @param matrix: matrix to read @param max_row: number of rows @param max_column: number of columns */ int ighmm_dmatrix_read (scanner_t * s, int **matrix, int max_row, int max_column); /** Writes a double matrix (without parenthesis) with specifically many decimal places. @param file: output file @param matrix: matrix to write @param rows: number of rows @param columns: number of columns @param width: format: number of places altogether @param prec: format: number of decimal places @param tab: format: leading tabs @param separator: format: separator for columns @param ending: format: end of a row */ void ighmm_cmatrix_print_prec (FILE * file, double **matrix, int rows, int columns, int width, int prec, char *tab, char *separator, char *ending); /** Writes an integer matrix (without parenthesis). @param file: output file @param matrix: matrix to write @param rows: number of rows @param columns: number of columns @param tab: format: leading tabs @param separator: format: separator for columns @param ending: format: end of a row */ void ighmm_dmatrix_print (FILE * file, int **matrix, int rows, int columns, char *tab, char *separator, char *ending); /*================== mes.h ==================================================*/ /** */ void ighmm_mes_fformat (char *txt, char *filename, int line, char *proc_info); /** */ int ighmm_mes_insert (FILE * fp, char src, int cnt); /** */ int ighmm_mes_copy (char *oldname, char *newname); /** */ int ighmm_mes_fgetc (FILE * fp); /** */ int ighmm_mes_fflush (FILE * fp); /** */ int ighmm_mes_fprintf (FILE * fp, char *format, ...); /** */ int ighmm_mes_fputc (FILE * fp, char chr); /** */ int ighmm_mes_fputs (FILE * fp, char *str); /** */ int ighmm_mes_fread (FILE * fp, void *mem, int bytes); /** */ int ighmm_mes_fread_quiet (FILE * fp, void *mem, int bytes); /** */ int ighmm_mes_fseek (FILE * fp, long offset, int fromwhere); #ifdef WIN32 /** */ int mes_fseek64 (FILE * fp, unsigned int uoff, unsigned int loff, int fromwhere); #endif /** */ int ighmm_mes_ftell (FILE * fp); /** */ int ighmm_mes_fwrite (FILE * fp, void *mem, int bytes); /** */ int ighmm_mes_move (char *oldname, char *newname); /** */ int ighmm_mes_remove (char *filename); /** */ int ighmm_mes_rename (char *oldname, char *newname); /** */ FILE *ighmm_mes_tmpfile (void); #ifdef __cplusplus } #endif #endif /* GHMM_UNSUPPORTED_H */ #endif /* GHMM_UNSUPPORTED */ ghmm-0.9-rc3/ghmm/gradescent.c000664 001750 001750 00000037772 12154244034 016141 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/gradescent.c * Authors: Janne Grunau, Alexander Riemer * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2262 $ * from $Date: 2009-04-22 09:44:25 -0400 (Wed, 22 Apr 2009) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include #include "ghmm.h" #include "mes.h" #include "mprintf.h" #include "matrix.h" #include "model.h" #include "foba.h" #include "gradescent.h" #include "ghmm_internals.h" static double compute_performance (ghmm_dmodel * mo, ghmm_dseq * sq); /*----------------------------------------------------------------------------*/ static void gradient_descent_gfree (double **matrix_b, double *matrix_a, double *matrix_pi, int N) { #define CUR_PROC "gradient_descent_gfree" int i; if (matrix_b) for (i = 0; i < N; i++) { m_free (matrix_b[i]); } m_free (matrix_b); m_free (matrix_a); m_free (matrix_pi); #undef CUR_PROC } /*----------------------------------------------------------------------------*/ /** allocates memory for m and n matrices: */ static int gradient_descent_galloc (double ***matrix_b, double **matrix_a, double **matrix_pi, ghmm_dmodel * mo) { #define CUR_PROC "gradient_descent_galloc" int i; /* first allocate memory for matrix_b */ ARRAY_MALLOC (*matrix_b, mo->N); for (i = 0; i < mo->N; i++) ARRAY_CALLOC ((*matrix_b)[i], ghmm_ipow (mo, mo->M, mo->order[i] + 1)); /* matrix_a(i,j) = matrix_a[i*mo->N+j] */ ARRAY_CALLOC (*matrix_a, mo->N * mo->N); /* allocate memory for matrix_pi */ ARRAY_CALLOC (*matrix_pi, mo->N); return 0; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ gradient_descent_gfree (*matrix_b, *matrix_a, *matrix_pi, mo->N); return -1; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ int ghmm_dmodel_label_gradient_expectations (ghmm_dmodel* mo, double **alpha, double **beta, double *scale, int *seq, int seq_len, double **matrix_b, double *matrix_a, double *vec_pi) { #define CUR_PROC "ghmm_dmodel_label_gradient_expectations" int h, i, j, t; int size, j_id, e_index; double gamma, xi; double foba_sum; /* initialise matrices with zeros */ for (i = 0; i < mo->N; i++) { for (j = 0; j < mo->N; j++) matrix_a[i * mo->N + j] = 0; size = ghmm_ipow (mo, mo->M, mo->order[i] + 1); for (h = 0; h < size; h++) matrix_b[i][h] = 0; } for (t = 0; t < seq_len; t++) { /* sum products of forward and backward variables over all states: */ foba_sum = 0.0; for (i = 0; i < mo->N; i++) foba_sum += alpha[t][i] * beta[t][i]; if (GHMM_EPS_PREC > fabs (foba_sum)) { printf ("gradescent_compute_expect: foba_sum (%g) smaller as EPS_PREC (%g). t = %d.\n", foba_sum, GHMM_EPS_PREC, t); return -1; } for (i = 0; i < mo->N; i++) { /* compute gamma implicit */ gamma = alpha[t][i] * beta[t][i] / foba_sum; /* n_pi is easiest: n_pi(i) = gamma(0,i) */ if (0 == t) vec_pi[i] = gamma; /* n_b(i,c) = sum[t, hist(t)=c | gamma(t,i)] / sum[t | gamma(t,i)] */ e_index = get_emission_index (mo, i, seq[t], t); if (-1 != e_index) matrix_b[i][e_index] += gamma; } /* updating history, xi needs the right e_index for the next state */ update_emission_history (mo, seq[t]); for (i = 0; i < mo->N; i++) { /* n_a(i,j) = sum[t=0..T-2 | xi(t,i,j)] / sum[t=0..T-2 | gamma(t,i)] */ /* compute xi only till the state before the last */ for (j = 0; (j < mo->s[i].out_states) && (t < seq_len - 1); j++) { j_id = mo->s[i].out_id[j]; /* compute xi implicit */ xi = 0; e_index = get_emission_index (mo, j_id, seq[t + 1], t + 1); if (e_index != -1) xi = alpha[t][i] * beta[t + 1][j_id] * mo->s[i].out_a[j] * mo->s[j_id].b[e_index] / (scale[t + 1] * foba_sum); matrix_a[i * mo->N + j_id] += xi; } } } return 0; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static double compute_performance (ghmm_dmodel * mo, ghmm_dseq * sq) { #define CUR_PROC "compute_performance" int k, seq_len, success = 1; /* log P[O | lambda, labeling] as computed by the forward algorithm */ double log_p; /* sum over log P (calculated by forward_label) for all sequences used to compute the performance of the training */ double log_p_sum = 0.0; /* loop over all sequences */ for (k = 0; k < sq->seq_number && success; k++) { success = 0; seq_len = sq->seq_len[k]; if (-1 != ghmm_dmodel_label_logp (mo, sq->seq[k], sq->state_labels[k], seq_len, &log_p)) { success = 1; log_p_sum += log_p; if (-1 != ghmm_dmodel_logp (mo, sq->seq[k], seq_len, &log_p)) log_p_sum -= log_p; else { printf ("ghmm_dmodel_logp error in sequence %d, length: %d\n", k, seq_len); success = 0; } } else printf ("ghmm_dl_logp error in sequence %d, length: %d\n", k, seq_len); } /* return log_p_sum in success or +1.0 a probality of 0.0 on error */ if (success) return log_p_sum; else return 1.0; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ /** Trains the model with a set of annotated sequences using gradient descent. Model must not have silent states. (one iteration) @return 0/-1 success/error @param mo: pointer to a ghmm_dmodel @param sq: struct of annotated sequences @param eta: training parameter for gradient descent */ static int gradient_descent_onestep (ghmm_dmodel * mo, ghmm_dseq * sq, double eta) { #define CUR_PROC "gradient_descent_onestep" int g, h, i, j, k; int seq_len, j_id, hist, size; /* expected usage of model parameters (A and B entries) */ double *m_pi, *n_pi, *m_a, *n_a; double **m_b, **n_b; /* forward & backward variables w/ their scaling vector */ double **alpha, **beta, *scale; /* variables to store values associated with the algorithm */ double pi_sum, a_row_sum, b_block_sum, gradient; /* log P[O | lambda, labeling] as computed by the forward algorithm */ double log_p; /* allocate memory for the parameters used for reestimation */ if (-1 == gradient_descent_galloc (&m_b, &m_a, &m_pi, mo)) return -1; if (-1 == gradient_descent_galloc (&n_b, &n_a, &n_pi, mo)) return -1; /* loop over all sequences */ for (k = 0; k < sq->seq_number; k++) { seq_len = sq->seq_len[k]; if (-1 == ighmm_reestimate_alloc_matvek (&alpha, &beta, &scale, seq_len, mo->N)) continue; /* calculate forward and backward variables without labels: */ if (-1 == ghmm_dmodel_forward (mo, sq->seq[k], seq_len, alpha, scale, &log_p)) { printf ("forward error!\n"); goto FREE; } if (-1 == ghmm_dmodel_backward (mo, sq->seq[k], seq_len, beta, scale)) { printf ("backward error!\n"); goto FREE; } /* compute n matrices (no labels): */ if (-1 == ghmm_dmodel_label_gradient_expectations (mo, alpha, beta, scale, sq->seq[k], seq_len, m_b, m_a, m_pi)) printf ("Error in sequence %d, length %d (no labels)\n", k, seq_len); /* calculate forward and backward variables with labels: */ if (-1 == ghmm_dmodel_label_forward (mo, sq->seq[k], sq->state_labels[k], seq_len, alpha, scale, &log_p)) { printf ("forward labels error!\n"); goto FREE; } if (-1 == ghmm_dmodel_label_backward (mo, sq->seq[k], sq->state_labels[k], seq_len, beta, scale, &log_p)) { printf ("backward labels error!\n"); goto FREE; } /* compute m matrices (labels): */ if (-1 == ghmm_dmodel_label_gradient_expectations (mo, alpha, beta, scale, sq->seq[k], seq_len, m_b, m_a, m_pi)) printf ("Error in sequence %d, length %d (with labels)\n", k, seq_len); /* reestimate model parameters: */ /* PI */ pi_sum = 0; /* update */ for (i = 0; i < mo->N; i++) { if (mo->s[i].pi > 0.0) { gradient = eta * (m_pi[i] - n_pi[i]); if (mo->s[i].pi + gradient > GHMM_EPS_PREC) mo->s[i].pi += gradient; else mo->s[i].pi = GHMM_EPS_PREC; } /* sum over new PI vector */ pi_sum += mo->s[i].pi; } if (pi_sum < GHMM_EPS_PREC) { /* never get here */ fprintf (stderr, "Training ruined the model. You lose.\n"); k = sq->seq_number; goto FREE; } /* normalise */ for (i = 0; i < mo->N; i++) mo->s[i].pi /= pi_sum; /* A */ for (i = 0; i < mo->N; i++) { a_row_sum = 0; /* update */ for (j = 0; j < mo->s[i].out_states; j++) { j_id = mo->s[i].out_id[j]; gradient = eta * (m_a[i * mo->N + j_id] - n_a[i * mo->N + j_id]) / (seq_len - 1); if (mo->s[i].out_a[j] + gradient > GHMM_EPS_PREC) mo->s[i].out_a[j] += gradient; else mo->s[i].out_a[j] = GHMM_EPS_PREC; /* sum over rows of new A matrix */ a_row_sum += mo->s[i].out_a[j]; } if (a_row_sum < GHMM_EPS_PREC) { /* never get here */ fprintf (stderr, "Training ruined the model. You lose.\n"); k = sq->seq_number; goto FREE; } /* normalise */ for (j = 0; j < mo->s[i].out_states; j++) { mo->s[i].out_a[j] /= a_row_sum; /* mirror out_a to corresponding in_a */ j_id = mo->s[i].out_id[j]; for (g = 0; g < mo->s[j_id].in_states; g++) if (i == mo->s[j_id].in_id[g]) { mo->s[j_id].in_a[g] = mo->s[i].out_a[j]; break; } } } /* B */ for (i = 0; i < mo->N; i++) { /* don't update fix states */ if (mo->s[i].fix) continue; /* update */ size = ghmm_ipow (mo, mo->M, mo->order[i]); for (h = 0; h < size; h++) { b_block_sum = 0; for (g = 0; g < mo->M; g++) { hist = h * mo->M + g; gradient = eta * (m_b[i][hist] - n_b[i][hist]) / seq_len; /* printf("gradient[%d][%d] = %g, m_b = %g, n_b = %g\n" , i, hist, gradient, m_b[i][hist], n_b[i][hist]); */ if (gradient + mo->s[i].b[hist] > GHMM_EPS_PREC) mo->s[i].b[hist] += gradient; else mo->s[i].b[hist] = GHMM_EPS_PREC; /* sum over M-length blocks of new B matrix */ b_block_sum += mo->s[i].b[hist]; } if (b_block_sum < GHMM_EPS_PREC) { /* never get here */ fprintf (stderr, "Training ruined the model. You lose.\n"); k = sq->seq_number; goto FREE; } /* normalise */ for (g = 0; g < mo->M; g++) { hist = h * mo->M + g; mo->s[i].b[hist] /= b_block_sum; } } } /* restore "tied_to" property */ if (mo->model_type & GHMM_kTiedEmissions) ghmm_dmodel_update_tie_groups (mo); FREE: ighmm_reestimate_free_matvek (alpha, beta, scale, seq_len); } gradient_descent_gfree (m_b, m_a, m_pi, mo->N); gradient_descent_gfree (n_b, n_a, n_pi, mo->N); return 0; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ /** Trains the ghmm_dmodel with a set of annotated sequences till convergence using gradient descent. Model must not have silent states. (checked in Python wrapper) @return trained model/NULL pointer success/error @param mo: pointer to a ghmm_dmodel @param sq: struct of annotated sequences @param eta: intial parameter eta (learning rate) @param no_steps number of training steps */ ghmm_dmodel* ghmm_dmodel_label_gradient_descent (ghmm_dmodel* mo, ghmm_dseq * sq, double eta, int no_steps) { #define CUR_PROC "ghmm_dmodel_label_gradient_descent" char * str; int runs = 0; double cur_perf, last_perf; ghmm_dmodel *last; last = ghmm_dmodel_copy(mo); last_perf = compute_performance (last, sq); while (eta > GHMM_EPS_PREC && runs < no_steps) { runs++; if (-1 == gradient_descent_onestep(mo, sq, eta)) { ghmm_dmodel_free(&last); return NULL; } cur_perf = compute_performance(mo, sq); if (last_perf < cur_perf) { /* if model is degenerated, lower eta and try again */ if (cur_perf > 0.0) { str = ighmm_mprintf(NULL, 0, "current performance = %g", cur_perf); GHMM_LOG(LINFO, str); m_free(str); ghmm_dmodel_free(&mo); mo = ghmm_dmodel_copy(last); eta *= .5; } else { /* Improvement insignificant, assume convergence */ if (fabs (last_perf - cur_perf) < cur_perf * (-1e-8)) { ghmm_dmodel_free(&last); str = ighmm_mprintf(NULL, 0, "convergence after %d steps.", runs); GHMM_LOG(LINFO, str); m_free(str); return 0; } if (runs < 175 || 0 == runs % 50) { str = ighmm_mprintf(NULL, 0, "Performance: %g\t improvement: %g\t step %d", cur_perf, cur_perf - last_perf, runs); GHMM_LOG(LINFO, str); m_free(str); } /* significant improvement, next iteration */ ghmm_dmodel_free(&last); last = ghmm_dmodel_copy(mo); last_perf = cur_perf; eta *= 1.07; } } /* no improvement */ else { if (runs < 175 || 0 == runs % 50) { str = ighmm_mprintf(NULL, 0, "Performance: %g\t !IMPROVEMENT: %g\t step %d", cur_perf, cur_perf - last_perf, runs); GHMM_LOG(LINFO, str); m_free(str); } /* try another training step */ runs++; eta *= .85; if (-1 == gradient_descent_onestep(mo, sq, eta)) { ghmm_dmodel_free(&last); return NULL; } cur_perf = compute_performance (mo, sq); str = ighmm_mprintf(NULL, 0, "Performance: %g\t ?Improvement: %g\t step %d", cur_perf, cur_perf - last_perf, runs); GHMM_LOG(LINFO, str); m_free(str); /* improvement, save and proceed with next iteration */ if (last_perf < cur_perf && cur_perf < 0.0) { ghmm_dmodel_free (&last); last = ghmm_dmodel_copy(mo); last_perf = cur_perf; } /* still no improvement, revert to saved model */ else { runs--; ghmm_dmodel_free(&mo); mo = ghmm_dmodel_copy(last); eta *= .9; } } } ghmm_dmodel_free(&last); return mo; #undef CUR_PROC } ghmm-0.9-rc3/ghmm/sfoba.h000775 001750 001750 00000010636 12154244034 015112 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/sfoba.h * Authors: Bernhard Knab, Benjamin Georgi * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2262 $ * from $Date: 2009-04-22 09:44:25 -0400 (Wed, 22 Apr 2009) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_SFOBA_H #define GHMM_SFOBA_H #include "smodel.h" #ifdef __cplusplus extern "C" { #endif /**@name SHMM Forward-Backward-Algorithm */ /*@{ (Doc++-Group: sfoba) */ /** Forward-Backward-Algorithm for multiple double sequences with scaling. For reference see: Rabiner, L.R.: "`A Tutorial on Hidden {Markov} Models and Selected Applications in Speech Recognition"', Proceedings of the IEEE, 77, no 2, 1989, pp 257--285 */ /** Forward-Algorithm. Calculates alpha[t][i], scaling factors scale[t] and log( P(O|lambda) ) for a given double sequence and a given model. @param smo model @param O sequence @param T length of sequence (O is actually T*smo->dim long) @param b optionally precomputed emission probabilities @param alpha alpha[t][i] @param scale scale factors @param log_p log likelihood log( P(O|lambda) ) @return 0 for success, -1 for error */ int ghmm_cmodel_forward (ghmm_cmodel * smo, double *O, int T, double ***b, double **alpha, double *scale, double *log_p); /** Backward-Algorithm. Calculates beta[t][i] given a double sequence and a model. Scale factors given as parameter (come from ghmm_cmodel_forward()). @param smo model @param O sequence @param T length of sequence (O is actually T*smo->dim long) @param b matrix with precalculated output probabilities. May be NULL @param beta beta[t][i] @param scale scale factors @return 0 for success, -1 for error */ int ghmm_cmodel_backward (ghmm_cmodel * smo, double *O, int T, double ***b, double **beta, const double *scale); /** Calculation of log( P(O|lambda) ). Done by calling ghmm_cmodel_forward(). Use this function if only the log likelihood and not alpha[t][i] is needed, alpha matrix is allocated with ighmm_cmatrix_stat_alloc @param smo model @param O sequence @param T length of sequence (O is actually T*smo->dim long) @param log_p log likelihood log( P(O|lambda) ) @return 0 for success, -1 for error */ int ghmm_cmodel_logp (ghmm_cmodel * smo, double *O, int T, double *log_p); /** Calculation of log( P(O,S | lambda) ). 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" >&6; } if ${ac_cv_path_FGREP+:} false; then : $as_echo_n "(cached) " >&6 else if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1 then ac_cv_path_FGREP="$GREP -F" else if test -z "$FGREP"; then ac_path_FGREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_prog in fgrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext" as_fn_executable_p "$ac_path_FGREP" || continue # Check for GNU ac_path_FGREP and select it if it is found. # Check for GNU $ac_path_FGREP case `"$ac_path_FGREP" --version 2>&1` in *GNU*) ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;; *) ac_count=0 $as_echo_n 0123456789 >"conftest.in" while : do cat "conftest.in" "conftest.in" >"conftest.tmp" mv "conftest.tmp" "conftest.in" cp "conftest.in" "conftest.nl" $as_echo 'FGREP' >> "conftest.nl" "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break as_fn_arith $ac_count + 1 && ac_count=$as_val if test $ac_count -gt ${ac_path_FGREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_max=$ac_count fi # 10*(2^10) chars as input seems more than enough test $ac_count -gt 10 && break done rm -f conftest.in conftest.tmp conftest.nl conftest.out;; esac $ac_path_FGREP_found && break 3 done done done IFS=$as_save_IFS if test -z "$ac_cv_path_FGREP"; then as_fn_error $? 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[\\/]* | ?:[\\/]*) re_direlt='/[^/][^/]*/\.\./' # Canonicalize the pathname of ld ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` done test -z "$LD" && LD="$ac_prog" ;; "") # If it fails, then pretend we aren't using GCC. ac_prog=ld ;; *) # If it is relative, then search for the first ld in PATH. with_gnu_ld=unknown ;; esac elif test "$with_gnu_ld" = yes; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5 $as_echo_n "checking for GNU ld... " >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5 $as_echo_n "checking for non-GNU ld... 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" >&6; } if ${lt_cv_path_NM+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_NM" >&5 $as_echo "$lt_cv_path_NM" >&6; } if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. if test -n "$DUMPBIN"; then : # Let the user override the test. else if test -n "$ac_tool_prefix"; then for ac_prog in dumpbin "link -dump" do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... 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" >&6; } if ${lt_cv_to_host_file_cmd+:} false; then : $as_echo_n "(cached) " >&6 else case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_w32 ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_cygwin_to_w32 ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_w32 ;; esac ;; *-*-cygwin* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_cygwin ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_noop ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_cygwin ;; esac ;; * ) # unhandled hosts (and "normal" native builds) lt_cv_to_host_file_cmd=func_convert_file_noop ;; esac fi to_host_file_cmd=$lt_cv_to_host_file_cmd { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_to_host_file_cmd" >&5 $as_echo "$lt_cv_to_host_file_cmd" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to convert $build file names to toolchain format" >&5 $as_echo_n "checking how to convert $build file names to toolchain format... " >&6; } if ${lt_cv_to_tool_file_cmd+:} false; then : $as_echo_n "(cached) " >&6 else #assume ordinary cross tools, or native build. lt_cv_to_tool_file_cmd=func_convert_file_noop case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_tool_file_cmd=func_convert_file_msys_to_w32 ;; esac ;; esac fi to_tool_file_cmd=$lt_cv_to_tool_file_cmd { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_to_tool_file_cmd" >&5 $as_echo "$lt_cv_to_tool_file_cmd" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5 $as_echo_n "checking for $LD option to reload object files... " >&6; } if ${lt_cv_ld_reload_flag+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_reload_flag='-r' fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5 $as_echo "$lt_cv_ld_reload_flag" >&6; } reload_flag=$lt_cv_ld_reload_flag case $reload_flag in "" | " "*) ;; *) reload_flag=" $reload_flag" ;; esac reload_cmds='$LD$reload_flag -o $output$reload_objs' case $host_os in cygwin* | mingw* | pw32* | cegcc*) if test "$GCC" != yes; then reload_cmds=false fi ;; darwin*) if test "$GCC" = yes; then reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' else reload_cmds='$LD$reload_flag -o $output$reload_objs' fi ;; esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. set dummy ${ac_tool_prefix}objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OBJDUMP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OBJDUMP"; then ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OBJDUMP=$ac_cv_prog_OBJDUMP if test -n "$OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5 $as_echo "$OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OBJDUMP"; then ac_ct_OBJDUMP=$OBJDUMP # Extract the first word of "objdump", so it can be a program name with args. set dummy objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OBJDUMP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if ${lt_cv_deplibs_check_method+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. # func_win32_libid assumes BSD nm, so disallow it if using MS dumpbin. if ( test "$lt_cv_nm_interface" = "BSD nm" && file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else # Keep this pattern in sync with the one in func_win32_libid. lt_cv_deplibs_check_method='file_magic file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc*) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; haiku*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF[ -][0-9][0-9])(-bit)?( [LM]SB)? shared object( file)?[, -]* PA-RISC [0-9]\.[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9]\.[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_glob= want_nocaseglob=no if test "$build" = "$host"; then case $host_os in mingw* | pw32*) if ( shopt | grep nocaseglob ) >/dev/null 2>&1; then want_nocaseglob=yes else file_magic_glob=`echo aAbBcCdDeEfFgGhHiIjJkKlLmMnNoOpPqQrRsStTuUvVwWxXyYzZ | $SED -e "s/\(..\)/s\/[\1]\/[\1]\/g;/g"` fi ;; esac fi file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dlltool", so it can be a program name with args. set dummy ${ac_tool_prefix}dlltool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DLLTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DLLTOOL"; then ac_cv_prog_DLLTOOL="$DLLTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DLLTOOL="${ac_tool_prefix}dlltool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DLLTOOL=$ac_cv_prog_DLLTOOL if test -n "$DLLTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DLLTOOL" >&5 $as_echo "$DLLTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DLLTOOL"; then ac_ct_DLLTOOL=$DLLTOOL # Extract the first word of "dlltool", so it can be a program name with args. set dummy dlltool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DLLTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DLLTOOL"; then ac_cv_prog_ac_ct_DLLTOOL="$ac_ct_DLLTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DLLTOOL="dlltool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DLLTOOL=$ac_cv_prog_ac_ct_DLLTOOL if test -n "$ac_ct_DLLTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DLLTOOL" >&5 $as_echo "$ac_ct_DLLTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DLLTOOL" = x; then DLLTOOL="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DLLTOOL=$ac_ct_DLLTOOL fi else DLLTOOL="$ac_cv_prog_DLLTOOL" fi test -z "$DLLTOOL" && DLLTOOL=dlltool { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to associate runtime and link libraries" >&5 $as_echo_n "checking how to associate runtime and link libraries... " >&6; } if ${lt_cv_sharedlib_from_linklib_cmd+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_sharedlib_from_linklib_cmd='unknown' case $host_os in cygwin* | mingw* | pw32* | cegcc*) # two different shell functions defined in ltmain.sh # decide which to use based on capabilities of $DLLTOOL case `$DLLTOOL --help 2>&1` in *--identify-strict*) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib ;; *) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib_fallback ;; esac ;; *) # fallback: assume linklib IS sharedlib lt_cv_sharedlib_from_linklib_cmd="$ECHO" ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sharedlib_from_linklib_cmd" >&5 $as_echo "$lt_cv_sharedlib_from_linklib_cmd" >&6; } sharedlib_from_linklib_cmd=$lt_cv_sharedlib_from_linklib_cmd test -z "$sharedlib_from_linklib_cmd" && sharedlib_from_linklib_cmd=$ECHO if test -n "$ac_tool_prefix"; then for ac_prog in ar do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_AR+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_AR="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$AR" && break done fi if test -z "$AR"; then ac_ct_AR=$AR for ac_prog in ar do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_AR+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_AR="$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$ac_ct_AR" && break done if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi fi : ${AR=ar} : ${AR_FLAGS=cru} { $as_echo "$as_me:${as_lineno-$LINENO}: checking for archiver @FILE support" >&5 $as_echo_n "checking for archiver @FILE support... " >&6; } if ${lt_cv_ar_at_file+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ar_at_file=no cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : echo conftest.$ac_objext > conftest.lst lt_ar_try='$AR $AR_FLAGS libconftest.a @conftest.lst >&5' { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$lt_ar_try\""; } >&5 (eval $lt_ar_try) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if test "$ac_status" -eq 0; then # Ensure the archiver fails upon bogus file names. rm -f conftest.$ac_objext libconftest.a { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$lt_ar_try\""; } >&5 (eval $lt_ar_try) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if test "$ac_status" -ne 0; then lt_cv_ar_at_file=@ fi fi rm -f conftest.* libconftest.a fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ar_at_file" >&5 $as_echo "$lt_cv_ar_at_file" >&6; } if test "x$lt_cv_ar_at_file" = xno; then archiver_list_spec= else archiver_list_spec=$lt_cv_ar_at_file fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_STRIP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_STRIP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_RANLIB+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_RANLIB+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib" fi case $host_os in darwin*) lock_old_archive_extraction=yes ;; *) lock_old_archive_extraction=no ;; esac # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if ${lt_cv_sys_global_symbol_pipe+:} false; then : $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\)[ ]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\)[ ]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi lt_cv_sys_global_symbol_pipe="$lt_cv_sys_global_symbol_pipe | sed '/ __gnu_lto/d'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then # Now try to grab the symbols. nlist=conftest.nm if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist\""; } >&5 (eval $NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT_DLSYM_CONST #else # define LT_DLSYM_CONST const #endif #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ LT_DLSYM_CONST struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_globsym_save_LIBS=$LIBS lt_globsym_save_CFLAGS=$CFLAGS LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS=$lt_globsym_save_LIBS CFLAGS=$lt_globsym_save_CFLAGS else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } fi # Response file support. if test "$lt_cv_nm_interface" = "MS dumpbin"; then nm_file_list_spec='@' elif $NM --help 2>/dev/null | grep '[@]FILE' >/dev/null; then nm_file_list_spec='@' fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sysroot" >&5 $as_echo_n "checking for sysroot... " >&6; } # Check whether --with-sysroot was given. if test "${with_sysroot+set}" = set; then : withval=$with_sysroot; else with_sysroot=no fi lt_sysroot= case ${with_sysroot} in #( yes) if test "$GCC" = yes; then lt_sysroot=`$CC --print-sysroot 2>/dev/null` fi ;; #( /*) lt_sysroot=`echo "$with_sysroot" | sed -e "$sed_quote_subst"` ;; #( no|'') ;; #( *) { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${with_sysroot}" >&5 $as_echo "${with_sysroot}" >&6; } as_fn_error $? "The sysroot must be an absolute path." "$LINENO" 5 ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${lt_sysroot:-no}" >&5 $as_echo "${lt_sysroot:-no}" >&6; } # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then : enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line '$LINENO' "configure"' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) case `/usr/bin/file conftest.o` in *x86-64*) LD="${LD-ld} -m elf32_x86_64" ;; *) LD="${LD-ld} -m elf_i386" ;; esac ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if ${lt_cv_cc_needs_belf+:} false; then : $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_cc_needs_belf=yes else lt_cv_cc_needs_belf=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; *-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) case $host in i?86-*-solaris*) LD="${LD-ld} -m elf_x86_64" ;; sparc*-*-solaris*) LD="${LD-ld} -m elf64_sparc" ;; esac # GNU ld 2.21 introduced _sol2 emulations. Use them if available. if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then LD="${LD-ld}_sol2" fi ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}mt", so it can be a program name with args. set dummy ${ac_tool_prefix}mt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_MANIFEST_TOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$MANIFEST_TOOL"; then ac_cv_prog_MANIFEST_TOOL="$MANIFEST_TOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_MANIFEST_TOOL="${ac_tool_prefix}mt" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi MANIFEST_TOOL=$ac_cv_prog_MANIFEST_TOOL if test -n "$MANIFEST_TOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MANIFEST_TOOL" >&5 $as_echo "$MANIFEST_TOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_MANIFEST_TOOL"; then ac_ct_MANIFEST_TOOL=$MANIFEST_TOOL # Extract the first word of "mt", so it can be a program name with args. set dummy mt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_MANIFEST_TOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_MANIFEST_TOOL"; then ac_cv_prog_ac_ct_MANIFEST_TOOL="$ac_ct_MANIFEST_TOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_MANIFEST_TOOL="mt" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_MANIFEST_TOOL=$ac_cv_prog_ac_ct_MANIFEST_TOOL if test -n "$ac_ct_MANIFEST_TOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_MANIFEST_TOOL" >&5 $as_echo "$ac_ct_MANIFEST_TOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_MANIFEST_TOOL" = x; then MANIFEST_TOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac MANIFEST_TOOL=$ac_ct_MANIFEST_TOOL fi else MANIFEST_TOOL="$ac_cv_prog_MANIFEST_TOOL" fi test -z "$MANIFEST_TOOL" && MANIFEST_TOOL=mt { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $MANIFEST_TOOL is a manifest tool" >&5 $as_echo_n "checking if $MANIFEST_TOOL is a manifest tool... " >&6; } if ${lt_cv_path_mainfest_tool+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_path_mainfest_tool=no echo "$as_me:$LINENO: $MANIFEST_TOOL '-?'" >&5 $MANIFEST_TOOL '-?' 2>conftest.err > conftest.out cat conftest.err >&5 if $GREP 'Manifest Tool' conftest.out > /dev/null; then lt_cv_path_mainfest_tool=yes fi rm -f conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_mainfest_tool" >&5 $as_echo "$lt_cv_path_mainfest_tool" >&6; } if test "x$lt_cv_path_mainfest_tool" != xyes; then MANIFEST_TOOL=: fi case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DSYMUTIL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DSYMUTIL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_NMEDIT+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_NMEDIT+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_LIPO+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_LIPO+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL"; then ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OTOOL="otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL if test -n "$ac_ct_OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5 $as_echo "$ac_ct_OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL" = x; then OTOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL=$ac_ct_OTOOL fi else OTOOL="$ac_cv_prog_OTOOL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. set dummy ${ac_tool_prefix}otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OTOOL64+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL64"; then ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL64=$ac_cv_prog_OTOOL64 if test -n "$OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5 $as_echo "$OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL64"; then ac_ct_OTOOL64=$OTOOL64 # Extract the first word of "otool64", so it can be a program name with args. set dummy otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OTOOL64+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL64"; then ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OTOOL64="otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 if test -n "$ac_ct_OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5 $as_echo "$ac_ct_OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL64" = x; then OTOOL64=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL64=$ac_ct_OTOOL64 fi else OTOOL64="$ac_cv_prog_OTOOL64" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5 $as_echo_n "checking for -single_module linker flag... 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Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs=no fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) case `$LD -v 2>&1` in *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) ld_shlibs=no cat <<_LT_EOF 1>&2 *** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not *** reliably create shared libraries on SCO systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.16.91.0.3 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF ;; *) # For security reasons, it is highly recommended that you always # use absolute paths for naming shared libraries, and exclude the # DT_RUNPATH tag from executables and libraries. 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then lt_cv_aix_libpath_=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$lt_cv_aix_libpath_"; then lt_cv_aix_libpath_="/usr/lib:/lib" fi fi aix_libpath=$lt_cv_aix_libpath_ fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then func_echo_all "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag="-z nodefs" archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. if test "${lt_cv_aix_libpath+set}" = set; 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then # We only use this code for GNU lds that support --whole-archive. whole_archive_flag_spec='${wl}--whole-archive$convenience ${wl}--no-whole-archive' else # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec='$convenience' fi archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. case $cc_basename in cl*) # Native MSVC hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported always_export_symbols=yes file_list_spec='@' # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames=' archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then sed -n -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp; else sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; fi~ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ linknames=' # The linker will not automatically build a static lib if we build a DLL. # _LT_TAGVAR(old_archive_from_new_cmds, )='true' enable_shared_with_static_runtimes=yes exclude_expsyms='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*' export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1,DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' # Don't use ranlib old_postinstall_cmds='chmod 644 $oldlib' postlink_cmds='lt_outputfile="@OUTPUT@"~ lt_tool_outputfile="@TOOL_OUTPUT@"~ case $lt_outputfile in *.exe|*.EXE) ;; *) lt_outputfile="$lt_outputfile.exe" lt_tool_outputfile="$lt_tool_outputfile.exe" ;; esac~ if test "$MANIFEST_TOOL" != ":" && test -f "$lt_outputfile.manifest"; then $MANIFEST_TOOL -manifest "$lt_tool_outputfile.manifest" -outputresource:"$lt_tool_outputfile" || exit 1; $RM "$lt_outputfile.manifest"; fi' ;; *) # Assume MSVC wrapper hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `func_echo_all "$deplibs" | $SED '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_from_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' enable_shared_with_static_runtimes=yes ;; esac ;; darwin* | rhapsody*) archive_cmds_need_lc=no hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported if test "$lt_cv_ld_force_load" = "yes"; then whole_archive_flag_spec='`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`' else whole_archive_flag_spec='' fi link_all_deplibs=yes allow_undefined_flag="$_lt_dar_allow_undefined" case $cc_basename in ifort*) _lt_dar_can_shared=yes ;; *) _lt_dar_can_shared=$GCC ;; esac if test "$_lt_dar_can_shared" = "yes"; then output_verbose_link_cmd=func_echo_all archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else ld_shlibs=no fi ;; dgux*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-L$libdir' hardcode_shlibpath_var=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2.*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$RM $output_objdir/$soname~$CC -shared $pic_flag ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes && test "$with_gnu_ld" = no; then archive_cmds='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes && test "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) # Older versions of the 11.00 compiler do not understand -b yet # (HP92453-01 A.11.01.20 doesn't, HP92453-01 B.11.X.35175-35176.GP does) { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $CC understands -b" >&5 $as_echo_n "checking if $CC understands -b... " >&6; } if ${lt_cv_prog_compiler__b+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_prog_compiler__b=no save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -b" echo "$lt_simple_link_test_code" > conftest.$ac_ext if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then # The linker can only warn and ignore the option if not recognized # So say no if there are warnings if test -s conftest.err; then # Append any errors to the config.log. cat conftest.err 1>&5 $ECHO "$_lt_linker_boilerplate" | $SED '/^$/d' > conftest.exp $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 if diff conftest.exp conftest.er2 >/dev/null; then lt_cv_prog_compiler__b=yes fi else lt_cv_prog_compiler__b=yes fi fi $RM -r conftest* LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler__b" >&5 $as_echo "$lt_cv_prog_compiler__b" >&6; } if test x"$lt_cv_prog_compiler__b" = xyes; then archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. # This should be the same for all languages, so no per-tag cache variable. { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $host_os linker accepts -exported_symbol" >&5 $as_echo_n "checking whether the $host_os linker accepts -exported_symbol... " >&6; } if ${lt_cv_irix_exported_symbol+:} false; then : $as_echo_n "(cached) " >&6 else save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int foo (void) { return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_irix_exported_symbol=yes else lt_cv_irix_exported_symbol=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_irix_exported_symbol" >&5 $as_echo "$lt_cv_irix_exported_symbol" >&6; } if test "$lt_cv_irix_exported_symbol" = yes; then archive_expsym_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' fi else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: inherit_rpath=yes link_all_deplibs=yes ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no hardcode_direct_absolute=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~echo DATA >> $output_objdir/$libname.def~echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $pic_flag $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi archive_cmds_need_lc='no' hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. 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then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; hppa*64*) shrext_cmds='.sl' hardcode_into_libs=yes dynamic_linker="$host_os dld.sl" shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; *) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555, ... postinstall_cmds='chmod 555 $lib' # or fails outright, so override atomically: install_override_mode=555 ;; interix[3-9]*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux # correct to gnu/linux during the next big refactor else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH if ${lt_cv_shlibpath_overrides_runpath+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_shlibpath_overrides_runpath=no save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\"" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : lt_cv_shlibpath_overrides_runpath=yes fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS=$save_LDFLAGS libdir=$save_libdir fi shlibpath_overrides_runpath=$lt_cv_shlibpath_overrides_runpath # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;s/"//g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. Since this was broken with cross compilers, # most powerpc-linux boxes support dynamic linking these days and # people can always --disable-shared, the test was removed, and we # assume the GNU/Linux dynamic linker is in use. dynamic_linker='GNU/Linux ld.so' ;; netbsdelf*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='NetBSD ld.elf_so' ;; netbsd*) version_type=sunos need_lib_prefix=no need_version=no if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' dynamic_linker='NetBSD (a.out) ld.so' else library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='NetBSD ld.elf_so' fi shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes ;; newsos6) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[89] | openbsd2.[89].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5 $as_echo "$dynamic_linker" >&6; } test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5 $as_echo_n "checking how to hardcode library paths into programs... " >&6; } hardcode_action= if test -n "$hardcode_libdir_flag_spec" || test -n "$runpath_var" || test "X$hardcode_automatic" = "Xyes" ; then # We can hardcode non-existent directories. if test "$hardcode_direct" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no && test "$hardcode_minus_L" != no; then # Linking always hardcodes the temporary library directory. hardcode_action=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action=unsupported fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5 $as_echo "$hardcode_action" >&6; } if test "$hardcode_action" = relink || test "$inherit_rpath" = yes; then # Fast installation is not supported enable_fast_install=no elif test "$shlibpath_overrides_runpath" = yes || test "$enable_shared" = no; then # Fast installation is not necessary enable_fast_install=needless fi if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32* | cegcc*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if ${ac_cv_lib_dl_dlopen+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = xyes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load" if test "x$ac_cv_func_shl_load" = xyes; then : lt_cv_dlopen="shl_load" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5 $as_echo_n "checking for shl_load in -ldld... " >&6; } if ${ac_cv_lib_dld_shl_load+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char shl_load (); int main () { return shl_load (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dld_shl_load=yes else ac_cv_lib_dld_shl_load=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5 $as_echo "$ac_cv_lib_dld_shl_load" >&6; } if test "x$ac_cv_lib_dld_shl_load" = xyes; then : lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld" else ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen" if test "x$ac_cv_func_dlopen" = xyes; then : lt_cv_dlopen="dlopen" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if ${ac_cv_lib_dl_dlopen+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = xyes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5 $as_echo_n "checking for dlopen in -lsvld... " >&6; } if ${ac_cv_lib_svld_dlopen+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsvld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_svld_dlopen=yes else ac_cv_lib_svld_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5 $as_echo "$ac_cv_lib_svld_dlopen" >&6; } if test "x$ac_cv_lib_svld_dlopen" = xyes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5 $as_echo_n "checking for dld_link in -ldld... " >&6; } if ${ac_cv_lib_dld_dld_link+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. 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'A' + ((c) - 'a') : (c)) #else # define ISLOWER(c) \ (('a' <= (c) && (c) <= 'i') \ || ('j' <= (c) && (c) <= 'r') \ || ('s' <= (c) && (c) <= 'z')) # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) return 2; return 0; } _ACEOF if ac_fn_c_try_run "$LINENO"; then : else ac_cv_header_stdc=no fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then $as_echo "#define STDC_HEADERS 1" >>confdefs.h fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5 $as_echo_n "checking for an ANSI C-conforming const... 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(char *) 0 : (char const *) 0; *t++ = 0; if (s) return 0; } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this sort of thing, saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; } bx; struct s *b = &bx; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; if (!foo) return 0; } return !cs[0] && !zero.x; #endif ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : ac_cv_c_const=yes else ac_cv_c_const=no fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5 $as_echo "$ac_cv_c_const" >&6; } if test $ac_cv_c_const = no; then $as_echo "#define const /**/" >>confdefs.h fi ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default" if test "x$ac_cv_type_size_t" = xyes; then : else cat >>confdefs.h <<_ACEOF #define size_t unsigned int _ACEOF fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether time.h and sys/time.h may both be included" >&5 $as_echo_n "checking whether time.h and sys/time.h may both be included... 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Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char sqrt (); int main () { return sqrt (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_m_sqrt=yes else ac_cv_lib_m_sqrt=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_sqrt" >&5 $as_echo "$ac_cv_lib_m_sqrt" >&6; } if test "x$ac_cv_lib_m_sqrt" = xyes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBM 1 _ACEOF LIBS="-lm $LIBS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for exp in -lm" >&5 $as_echo_n "checking for exp in -lm... 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" >&6; } if ${ac_cv_lib_m_pow+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char pow (); int main () { return pow (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_m_pow=yes else ac_cv_lib_m_pow=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_pow" >&5 $as_echo "$ac_cv_lib_m_pow" >&6; } if test "x$ac_cv_lib_m_pow" = xyes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBM 1 _ACEOF LIBS="-lm $LIBS" fi GHMM_RNG_BSD=0 GHMM_RNG_GSL=0 GHMM_RNG_MERSENNE_TWISTER=0 # Check whether --enable-gsl was given. if test "${enable_gsl+set}" = set; then : enableval=$enable_gsl; if test "x$enable_gsl" != "xno" ; then $as_echo "#define DO_WITH_GSL 1" >>confdefs.h # Check whether --with-gsl-prefix was given. if test "${with_gsl_prefix+set}" = set; then : withval=$with_gsl_prefix; gsl_prefix="$withval" else gsl_prefix="" fi # Check whether --with-gsl-exec-prefix was given. if test "${with_gsl_exec_prefix+set}" = set; then : withval=$with_gsl_exec_prefix; gsl_exec_prefix="$withval" else gsl_exec_prefix="" fi # Check whether --enable-gsltest was given. if test "${enable_gsltest+set}" = set; then : enableval=$enable_gsltest; else enable_gsltest=yes fi if test x$gsl_exec_prefix != x ; then gsl_args="$gsl_args --exec-prefix=$gsl_exec_prefix" if test x${GSL_CONFIG+set} != xset ; then GSL_CONFIG=$gsl_exec_prefix/bin/gsl-config fi fi if test x$gsl_prefix != x ; then gsl_args="$gsl_args --prefix=$gsl_prefix" if test x${GSL_CONFIG+set} != xset ; then GSL_CONFIG=$gsl_prefix/bin/gsl-config fi fi # Extract the first word of "gsl-config", so it can be a program name with args. set dummy gsl-config; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... 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If gsl-config is correct, then it is\n", major, minor, micro); printf("*** best to upgrade to the required version.\n"); printf("*** If gsl-config was wrong, set the environment variable GSL_CONFIG\n"); printf("*** to point to the correct copy of gsl-config, and remove the file\n"); printf("*** config.cache before re-running configure\n"); exit(1); } } _ACEOF if ac_fn_c_try_run "$LINENO"; then : else no_gsl=yes fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi CFLAGS="$ac_save_CFLAGS" LIBS="$ac_save_LIBS" fi fi if test "x$no_gsl" = x ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } : else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } if test "$GSL_CONFIG" = "no" ; then echo "*** The gsl-config script installed by GSL could not be found" echo "*** If GSL was installed in PREFIX, make sure PREFIX/bin is in" echo "*** your path, or set the GSL_CONFIG environment variable to the" echo "*** full path to gsl-config." else if test -f conf.gsltest ; then : else echo "*** Could not run GSL test program, checking why..." CFLAGS="$CFLAGS $GSL_CFLAGS" LIBS="$LIBS $GSL_LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main () { return 0; ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : echo "*** The test program compiled, but did not run. This usually means" echo "*** that the run-time linker is not finding GSL or finding the wrong" echo "*** version of GSL. If it is not finding GSL, you'll need to set your" echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" echo "*** to the installed location Also, make sure you have run ldconfig if that" echo "*** is required on your system" echo "***" echo "*** If you have an old version installed, it is best to remove it, although" echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH" else echo "*** The test program failed to compile or link. See the file config.log for the" echo "*** exact error that occured. This usually means GSL was incorrectly installed" echo "*** or that you have moved GSL since it was installed. In the latter case, you" echo "*** may want to edit the gsl-config script: $GSL_CONFIG" fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext CFLAGS="$ac_save_CFLAGS" LIBS="$ac_save_LIBS" fi fi # GSL_CFLAGS="" # GSL_LIBS="" as_fn_error $? "\"GSL Version 0.7 or higher required.\"" "$LINENO" 5 fi rm -f conf.gsltest LIBS="$LIBS $GSL_LIBS" CFLAGS="$CFLAGS $GSL_CFLAGS" CXXFLAGS="$CXXFLAGS $GSL_CFLAGS" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gsl_inteval" >&5 $as_echo_n "checking for gsl_inteval... 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" >&6; } if ${ac_cv_lib_m_cos+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. 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|| _lt_function_replace_fail=: sed -e '/^func_append_quoted ()$/,/^} # func_append_quoted /c\ func_append_quoted ()\ {\ \ func_quote_for_eval "${2}"\ \ eval "${1}+=\\\\ \\$func_quote_for_eval_result"\ } # Extended-shell func_append_quoted implementation' "$cfgfile" > $cfgfile.tmp \ && mv -f "$cfgfile.tmp" "$cfgfile" \ || (rm -f "$cfgfile" && cp "$cfgfile.tmp" "$cfgfile" && rm -f "$cfgfile.tmp") test 0 -eq $? || _lt_function_replace_fail=: # Save a `func_append' function call where possible by direct use of '+=' sed -e 's%func_append \([a-zA-Z_]\{1,\}\) "%\1+="%g' $cfgfile > $cfgfile.tmp \ && mv -f "$cfgfile.tmp" "$cfgfile" \ || (rm -f "$cfgfile" && cp "$cfgfile.tmp" "$cfgfile" && rm -f "$cfgfile.tmp") test 0 -eq $? || _lt_function_replace_fail=: else # Save a `func_append' function call even when '+=' is not available sed -e 's%func_append \([a-zA-Z_]\{1,\}\) "%\1="$\1%g' $cfgfile > $cfgfile.tmp \ && mv -f "$cfgfile.tmp" "$cfgfile" \ || (rm -f "$cfgfile" && cp "$cfgfile.tmp" "$cfgfile" && rm -f "$cfgfile.tmp") test 0 -eq $? || _lt_function_replace_fail=: fi if test x"$_lt_function_replace_fail" = x":"; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Unable to substitute extended shell functions in $ofile" >&5 $as_echo "$as_me: WARNING: Unable to substitute extended shell functions in $ofile" >&2;} fi mv -f "$cfgfile" "$ofile" || (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile") chmod +x "$ofile" ;; esac done # for ac_tag as_fn_exit 0 _ACEOF ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. # Unfortunately, on DOS this fails, as config.log is still kept open # by configure, so config.status won't be able to write to it; its # output is simply discarded. So we exec the FD to /dev/null, # effectively closing config.log, so it can be properly (re)opened and # appended to by config.status. When coming back to configure, we # need to make the FD available again. if test "$no_create" != yes; then ac_cs_success=: ac_config_status_args= test "$silent" = yes && ac_config_status_args="$ac_config_status_args --quiet" exec 5>/dev/null $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi ghmm-0.9-rc3/ghmm/sdfoba.h000664 001750 001750 00000004222 12154244034 015245 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/sdfoba.h * Authors: Wasinee Rungsarityotin, Utz Pape, Andrea Weisse * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1713 $ * from $Date: 2006-10-16 10:06:28 -0400 (Mon, 16 Oct 2006) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_SDFOBA_H #define GHMM_SDFOBA_H #ifdef __cplusplus extern "C" { #endif /**@name HMM-Modell */ /*@{ (Doc++-Group: ds_model) */ int ghmm_dsmodel_forward (ghmm_dsmodel * mo, const int *O, int len, double **alpha, double *scale, double *log_p); int ghmm_dsmodel_backward (ghmm_dsmodel * mo, const int *O, int len, double **beta, const double *scale); int ghmm_dsmodel_logp (ghmm_dsmodel * mo, const int *O, int len, double *log_p); #ifdef __cplusplus } #endif #endif ghmm-0.9-rc3/ghmm/viterbi.h000775 001750 001750 00000006135 12154244034 015463 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/viterbi.h * Authors: Bernhard Knab, Wasinee Rungsarityotin, Benjamin Georgi * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1988 $ * from $Date: 2007-12-05 10:48:14 -0500 (Wed, 05 Dec 2007) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_VITERBI_H #define GHMM_VITERBI_H #ifdef __cplusplus extern "C" { #endif #include /**@name Viterbi-Algorithmus */ /*@{ (Doc++-Group: viterbi) */ /** Viterbi algorithm. Calculates the Viterbi path (the optimal path trough the model) and the Viterbi probability to a given model and a given sequence. The matrices in the local_store struct are allocated using stat_matrix_d_alloc. In case of a model with silent states, the length of the viterbi path is not identical with the sequence length. In such a case the end of the state path is marked by a -1 entry in the returned array. deprecated, use the argument pathlen instead @return Viterbi path @param mo: model @param o: sequence @param len: length of the sequence @param pathlen: length of the viterbi path excluding the final "-1" @param log_p: probability of the sequence in the Viterbi path */ int * ghmm_dmodel_viterbi (ghmm_dmodel * mo, int *o, int len, int *pathlen, double *log_p); /** Calculates the logarithmic probability to a given path through the states (does not have to be the Viterbi path), given sequence and a model. @param mo: model @param o: sequence @param len: length of the sequence @param state_seq: path through the states @return log P */ double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq); #ifdef __cplusplus } #endif #endif /*@} (Doc++-Group: viterbi) */ ghmm-0.9-rc3/ghmm/discrime.c000664 001750 001750 00000114342 12154244034 015606 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/discrime.c * Authors: Janne Grunau * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1754 $ * from $Date: 2006-11-03 11:29:44 -0500 (Fri, 03 Nov 2006) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include #include #include "ghmm.h" #include "mes.h" #include "matrix.h" #include "model.h" #include "foba.h" #include "gradescent.h" #include "discrime.h" #include "ghmm_internals.h" #define LAMBDA 0.14 #define TRIM(o, n) ((1-LAMBDA)*(o) + LAMBDA*(n)) #if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) #else #define logl(A) log(A) #define expl(A) exp(A) #endif /* forward declaration */ static int discrime_galloc (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, double ******matrix_b, double *****matrix_a, double *****matrix_pi, long double ***omega, long double ****omegati, double ****log_p); static void discrime_gfree (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, double *****matrix_b, double ****matrix_a, double ****matrix_pi, long double **omega, long double ***omegati, double ***log_p); static void discrime_trim_gradient (double *new, int length); static double discrime_lambda = 0.0; static double discrime_alpha = 1.0; /*----------------------------------------------------------------------------*/ /** allocates memory for m and n matrices: */ static int discrime_galloc (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, double ******matrix_b, double *****matrix_a, double *****matrix_pi, long double ***omega, long double ****omegati, double ****log_p) { #define CUR_PROC "discrime_galloc" int i, k, l, m; /* first allocate memory for matrix_b: */ ARRAY_CALLOC (*matrix_b, noC); for (k = 0; k < noC; k++) { ARRAY_CALLOC ((*matrix_b)[k], sqs[k]->seq_number); for (l = 0; l < sqs[k]->seq_number; l++) { ARRAY_CALLOC ((*matrix_b)[k][l], noC); for (m = 0; m < noC; m++) { ARRAY_CALLOC ((*matrix_b)[k][l][m], mo[m]->N); for (i = 0; i < mo[m]->N; i++) ARRAY_CALLOC ((*matrix_b)[k][l][m][i], ghmm_ipow (mo[m], mo[m]->M, mo[m]->order[i] + 1)); } } } /* matrix_a(k,l,i,j) = matrix_a[k][l][i*mo->N + j] */ ARRAY_CALLOC (*matrix_a, noC); for (k = 0; k < noC; k++) { ARRAY_CALLOC ((*matrix_a)[k], sqs[k]->seq_number); for (l = 0; l < sqs[k]->seq_number; l++) { ARRAY_CALLOC ((*matrix_a)[k][l], noC); for (m = 0; m < noC; m++) ARRAY_CALLOC ((*matrix_a)[k][l][m], mo[m]->N * mo[m]->N); } } /* allocate memory for matrix_pi */ ARRAY_CALLOC (*matrix_pi, noC); for (k = 0; k < noC; k++) { ARRAY_CALLOC ((*matrix_pi)[k], sqs[k]->seq_number); for (l = 0; l < sqs[k]->seq_number; l++) { ARRAY_CALLOC ((*matrix_pi)[k][l], noC); for (m = 0; m < noC; m++) ARRAY_CALLOC ((*matrix_pi)[k][l][m], mo[m]->N); } } /* allocate memory for matrices of likelihoods log_p[k][l][m] = log_prob of l-th sequence of k-th class under the m-th ghmm_dmodel */ ARRAY_CALLOC (*log_p, noC); for (k = 0; k < noC; k++) { ARRAY_CALLOC ((*log_p)[k], sqs[k]->seq_number); for (l = 0; l < sqs[k]->seq_number; l++) ARRAY_CALLOC ((*log_p)[k][l], noC); } /* allocate memory for outer derivatives */ ARRAY_CALLOC (*omega, noC); for (k = 0; k < noC; k++) ARRAY_CALLOC ((*omega)[k], sqs[k]->seq_number); /* allocate memory for omega tilde. NB: size(omega)*noC == size(omegati) */ ARRAY_CALLOC (*omegati, noC); for (k = 0; k < noC; k++) { ARRAY_CALLOC ((*omegati)[k], sqs[k]->seq_number); for (l = 0; l < sqs[k]->seq_number; l++) ARRAY_CALLOC ((*omegati)[k][l], noC); } return 0; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ discrime_gfree (mo, sqs, noC, *matrix_b, *matrix_a, *matrix_pi, *omega, *omegati, *log_p); return -1; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ /** frees memory for expectation matrices for all classes & training sequences*/ static void discrime_gfree (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, double *****matrix_b, double ****matrix_a, double ****matrix_pi, long double **omega, long double ***omegati, double ***log_p) { #define CUR_PROC "discrime_gfree" int i, k, l, m; for (k = 0; k < noC; k++) { for (l = 0; l < sqs[k]->seq_number; l++) { for (m = 0; m < noC; m++) { for (i = 0; i < mo[m]->N; i++) m_free (matrix_b[k][l][m][i]); m_free (matrix_b[k][l][m]); } m_free (matrix_b[k][l]); } m_free (matrix_b[k]); } m_free (matrix_b); for (k = 0; k < noC; k++) { for (l = 0; l < sqs[k]->seq_number; l++) { for (m = 0; m < noC; m++) m_free (matrix_a[k][l][m]); m_free (matrix_a[k][l]); } m_free (matrix_a[k]); } m_free (matrix_a); for (k = 0; k < noC; k++) { for (l = 0; l < sqs[k]->seq_number; l++) { for (m = 0; m < noC; m++) m_free (matrix_pi[k][l][m]); m_free (matrix_pi[k][l]); } m_free (matrix_pi[k]); } m_free (matrix_pi); for (k = 0; k < noC; k++) { for (l = 0; l < sqs[k]->seq_number; l++) m_free (log_p[k][l]); m_free (log_p[k]); } m_free (log_p); for (k = 0; k < noC; k++) m_free (omega[k]); m_free (omega); for (k = 0; k < noC; k++) { for (l = 0; l < sqs[k]->seq_number; l++) m_free (omegati[k][l]); m_free (omegati[k]); } m_free (omegati); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static int discrime_calculate_omega (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, long double **omega, long double ***omegati, double ***log_p) { #define CUR_PROC "discrime_calculate_omega" int k, l, m; int seq_no, argmax = 0; double sum, max; double exponent; long double sigmoid; /* compute outer derivatives */ /* iterate over all classes */ for (k = 0; k < noC; k++) { seq_no = sqs[k]->seq_number; /*iterate over all training sequences */ for (l = 0; l < seq_no; l++) { max = 1.0; /* calculate log(sum[prob]) for logarithmic probabilities first determine the maximum */ for (m = 0; m < noC; m++) { if (m != k && (1.0 == max || max < (log_p[k][l][m] + log (mo[m]->prior)))) { max = log_p[k][l][m] + log (mo[m]->prior); argmax = m; } } /* sum */ sum = 1.0; for (m = 0; m < noC; m++) { if (m != k && m != argmax) sum += exp (log_p[k][l][m] + log (mo[m]->prior) - max); } sum = log (sum) + max; exponent = log_p[k][l][k] + log (mo[k]->prior) - sum; if (exponent < logl (LDBL_MIN)) { printf ("exponent was too large (%g) cut it down!\n", exponent); exponent = (double) logl (LDBL_MIN); } sigmoid = 1.0 / (1.0 + expl ((-discrime_alpha) * exponent)); omega[k][l] = discrime_alpha * sigmoid * (1.0 - sigmoid); /* printf("omega[%d][%d] = %Lg\n",k ,l, omega[k][l]); */ /* omegati is not useful for m==k equation (2.9) */ for (m = 0; m < noC; m++) { if (m == k) omegati[k][l][m] = 0; else omegati[k][l][m] = omega[k][l] * expl (log_p[k][l][m] - sum) * (long double) mo[m]->prior; /* printf("%Lg, ", expl(log_p[k][l][m] - sum) * (long double)mo[m]->prior); */ /* printf("omegati[%d][%d][%d] = %Lg\n",k ,l, m, omegati[k][l][m]); */ } /* printf("\n"); */ } } return 0; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static int discrime_precompute (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, double *****expect_b, double ****expect_a, double ****expect_pi, double ***log_p) { #define CUR_PROC "discrime_precompute" int k, l, m; int seq_len, success = 1; /* forward, backward variables and scaler */ double **alpha, **beta, *scale; ghmm_dseq *sq; /* iterate over all classes */ for (k = 0; k < noC; k++) { sq = sqs[k]; /*iterate over all training sequences */ for (l = 0; l < sq->seq_number; l++) { seq_len = sq->seq_len[l]; /* iterate over all classes */ for (m = 0; m < noC; m++) { if (-1 == ighmm_reestimate_alloc_matvek (&alpha, &beta, &scale, seq_len, mo[m]->N)) return -1; /* calculate forward and backward variables without labels: */ if (-1 == ghmm_dmodel_forward (mo[m], sq->seq[l], seq_len, alpha, scale, &(log_p[k][l][m]))) { success = 0; printf ("forward\n"); goto FREE; } if (-1 == ghmm_dmodel_backward (mo[m], sq->seq[l], seq_len, beta, scale)) { success = 0; printf ("backward\n"); goto FREE; } /* compute expectation matrices expect_*[k][l][m] holds the expected number how ofter a particular parameter of model m is used by l-th training sequence of class k */ ghmm_dmodel_label_gradient_expectations (mo[m], alpha, beta, scale, sq->seq[l], seq_len, expect_b[k][l][m], expect_a[k][l][m], expect_pi[k][l][m]); FREE: ighmm_reestimate_free_matvek (alpha, beta, scale, seq_len); if (!success) return -1; } } } return 0; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ double ghmm_dmodel_label_discrim_perf(ghmm_dmodel** mo, ghmm_dseq** sqs, int noC) { #define CUR_PROC "ghmm_dmodel_label_discrim_perf" int k, l, m, temp; int argmax = 0; double sum, max; double *logp; double exponent; long double sigmoid; double performance = 0.0; ghmm_dseq *sq; ARRAY_CALLOC (logp, noC); /* iterate over all classes */ for (k = 0; k < noC; k++) { sq = sqs[k]; /*iterate over all training sequences */ for (l = 0; l < sq->seq_number; l++) { /* iterate over all classes */ for (m = 0; m < noC; m++) { temp = ghmm_dmodel_logp (mo[m], sq->seq[l], sq->seq_len[l], &(logp[m])); if (0 != temp) printf ("ghmm_dmodel_logp error in sequence[%d][%d] under model %d (%g)\n", k, l, m, logp[m]); /*printf("ghmm_dmodel_logp sequence[%d][%d] under model %d (%g)\n", k, l, m, logp[m]);*/ } max = 1.0; for (m = 0; m < noC; m++) { if (m != k && (1.0 == max || max < (logp[m] + log (mo[m]->prior)))) { max = logp[m] + log (mo[m]->prior); argmax = m; } } /* sum */ sum = 1.0; for (m = 0; m < noC; m++) { if (m != k && m != argmax) sum += exp (logp[m] + log (mo[m]->prior) - max); } sum = log (sum) + max; exponent = logp[k] + log (mo[k]->prior) - sum; if (exponent < logl (LDBL_MIN)) { printf ("exponent was too large (%g) cut it down!\n", exponent); exponent = (double) logl (LDBL_MIN); } sigmoid = 1.0 / (1.0 + expl ((-discrime_alpha) * exponent)); performance += (double) sigmoid; } } m_free (logp); STOP: /* Label STOP from ARRAY_[CM]ALLOC */ return performance; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_print_statistics(ghmm_dmodel** mo, ghmm_dseq** sqs, int noC, int* falseP, int* falseN) { #define CUR_PROC "discrime_print_statistics" int k, l, m; int argmax; double *logp, max; ghmm_dseq *sq; ARRAY_CALLOC (logp, noC); for (k = 0; k < noC; k++) { falseP[k] = 0; falseN[k] = 0; } for (k = 0; k < noC; k++) { sq = sqs[k]; printf ("Looking at training tokens of Class %d\n", k); for (l = 0; l < sq->seq_number; l++) { argmax = 0, max = -DBL_MAX; for (m = 0; m < noC; m++) { ghmm_dmodel_logp (mo[m], sq->seq[l], sq->seq_len[l], &(logp[m])); if (m == 0 || max < logp[m]) { max = logp[m]; argmax = m; } } if (sq->seq_number < 11 && noC < 8) { /* printing fancy statistics */ printf ("%2d: %8.4g", l, logp[0] - logp[argmax]); for (m = 1; m < noC; m++) printf (", %8.4g", logp[m] - logp[argmax]); printf (" \t+(%g)\n", logp[argmax]); } /* counting false positives and false negatives */ if (argmax != k) { falseP[argmax]++; falseN[k]++; } } printf ("%d false negatives in class %d.\n", falseN[k], k); } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (logp); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_trim_gradient (double *new, int length) { #define CUR_PROC "discrime_trim_gradient" int i, argmin = 0; double min, sum = 0; /* printf("unnormalised: %g", new[0]); */ /* for (i=1; iN); ARRAY_CALLOC (pi_new, mo[class]->N); /* itarate over all states of the current model */ for (i = 0; i < mo[class]->N; i++) { /* iterate over all classes */ sum = 0.0; for (m = 0; m < noC; m++) { sq = sqs[m]; /*iterate over all training sequences */ if (m == class) for (l = 0; l < sq->seq_number; l++) sum += omega[class][l] * expect_pi[class][l][class][i]; else for (l = 0; l < sq->seq_number; l++) sum -= omegati[m][l][class] * expect_pi[m][l][class][i]; } /* check for valid new parameter */ pi_old[i] = mo[class]->s[i].pi; if (fabs (pi_old[i]) == 0.0) pi_new[i] = pi_old[i]; else pi_new[i] = pi_old[i] + discrime_lambda * (sum / pi_old[i]); } /* change paramters to fit into valid parameter range */ discrime_trim_gradient (pi_new, mo[class]->N); /* update parameters */ for (i = 0; i < mo[class]->N; i++) { /* printf("update parameter Pi in state %d of model %d with: %5.3g", i, class, pi_new[i]); printf(" (%5.3g) old value.\n", pi_old[i]); */ mo[class]->s[i].pi = pi_new[i]; } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (pi_old); m_free (pi_new); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_update_a_gradient (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int class, double ****expect_a, long double **omega, long double ***omegati) { #define CUR_PROC "discrime_update_a_gradient" int i, j, g, l, m; int j_id; double *a_old = NULL; double *a_new = NULL; double sum; ghmm_dseq *sq = NULL; ARRAY_CALLOC (a_old, mo[class]->N); ARRAY_CALLOC (a_new, mo[class]->N); /* updating current class */ /* itarate over all states of the current model */ for (i = 0; i < mo[class]->N; i++) { for (j = 0; j < mo[class]->s[i].out_states; j++) { j_id = mo[class]->s[i].out_id[j]; sum = 0.0; /* iterate over all classes and training sequences */ for (m = 0; m < noC; m++) { sq = sqs[m]; if (m == class) for (l = 0; l < sq->seq_number; l++) sum += omega[class][l] * expect_a[class][l][+class][i * mo[class]->N + j_id]; else for (l = 0; l < sq->seq_number; l++) sum -= omegati[m][l][class] * expect_a[m][l][class][i * mo[class]->N + j_id]; } /* check for valid new parameter */ a_old[j] = mo[class]->s[i].out_a[j]; if (fabs (a_old[j]) == 0.0) a_new[j] = a_old[j]; else a_new[j] = a_old[j] + discrime_lambda * (sum / a_old[j]); } /* change paramters to fit into valid parameter range */ discrime_trim_gradient (a_new, mo[class]->s[i].out_states); /* update parameter */ for (j = 0; j < mo[class]->s[i].out_states; j++) { /* printf("update parameter A[%d] in state %d of model %d with: %5.3g", j, i, class, a_new[j]); printf(" (%5.3g) old value.\n", a_old[j]); */ mo[class]->s[i].out_a[j] = a_new[j]; /* mirror out_a to corresponding in_a */ j_id = mo[class]->s[i].out_id[j]; for (g = 0; g < mo[class]->s[j_id].in_states; g++) if (i == mo[class]->s[j_id].in_id[g]) { mo[class]->s[j_id].in_a[g] = mo[class]->s[i].out_a[j]; break; } } } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (a_old); m_free (a_new); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_update_b_gradient (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int class, double *****expect_b, long double **omega, long double ***omegati) { #define CUR_PROC "discrime_update_b_gradient" int i, h, l, m; int hist, size; double *b_old = NULL; double *b_new = NULL; double sum; ARRAY_CALLOC (b_old, mo[class]->M); ARRAY_CALLOC (b_new, mo[class]->M); /* updating current class */ /* itarate over all states of the current model */ for (i = 0; i < mo[class]->N; i++) { if (mo[class]->s[i].fix) continue; size = ghmm_ipow (mo[class], mo[class]->M, mo[class]->order[i] + 1); for (hist = 0; hist < size; hist += mo[class]->M) { for (h = hist; h < hist + mo[class]->M; h++) { /* iterate over all classes and training sequences */ sum = 0.0; for (m = 0; m < noC; m++) { if (m == class) for (l = 0; l < sqs[m]->seq_number; l++) sum += omega[class][l] * expect_b[class][l][class][i][h]; else for (l = 0; l < sqs[m]->seq_number; l++) sum -= omegati[m][l][class] * expect_b[m][l][class][i][h]; } /* check for valid new parameters */ b_old[h] = mo[class]->s[i].b[h]; if (fabs (b_old[h]) == 0.0) b_new[h] = b_old[h]; else b_new[h] = b_old[h] + discrime_lambda * (sum / b_old[h]); } /* change parameters to fit into valid parameter range */ discrime_trim_gradient (b_new, mo[0]->M); for (h = hist; h < hist + mo[class]->M; h++) { /* update parameters */ /*printf("update parameter B[%d] in state %d of model %d with: %5.3g", h, i, class, b_new[h]); printf(" (%5.3g) old value.\n", b_old[h]); */ mo[class]->s[i].b[h] = b_new[h]; } } } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (b_old); m_free (b_new); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_update_pi_closed (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int class, double lfactor, double ****expect_pi, long double **omega, long double ***omegati) { #define CUR_PROC "discrime_update_pi_closed" int i, l, m; double *pi_old = NULL; double *pi_new = NULL; double sum, lagrangian; ghmm_dseq *sq = NULL; ARRAY_CALLOC (pi_old, mo[class]->N); ARRAY_CALLOC (pi_new, mo[class]->N); /* updating current class (all or only specified) */ /* itarate over all states of the k-th model to compute lagrangian multiplier */ lagrangian = 0.0; for (i = 0; i < mo[class]->N; i++) { /* iterate over all classes */ for (m = 0; m < noC; m++) { sq = sqs[m]; /* if current class and class of training sequence match, add the first term */ if (m == class) for (l = 0; l < sq->seq_number; l++) lagrangian -= omega[class][l] * expect_pi[class][l][class][i]; /* otherwise the second */ else for (l = 0; l < sq->seq_number; l++) lagrangian += lfactor * omegati[m][l][class] * expect_pi[m][l][class][i]; } } for (i = 0; i < mo[class]->N; i++) { /* iterate over all classes */ sum = 0.0; for (m = 0; m < noC; m++) { sq = sqs[m]; /*iterate over all training sequences */ if (m == class) for (l = 0; l < sq->seq_number; l++) sum -= omega[class][l] * expect_pi[class][l][class][i]; else for (l = 0; l < sq->seq_number; l++) sum += lfactor * omegati[m][l][class] * expect_pi[m][l][class][i]; } /* check for valid new parameter */ pi_old[i] = mo[class]->s[i].pi; if (fabs (lagrangian) == 0.0) pi_new[i] = pi_old[i]; else pi_new[i] = sum / lagrangian; } /* update parameters */ for (i = 0; i < mo[class]->N; i++) { /* printf("update parameter Pi in state %d of model %d with: %5.3g", i, class, pi_new[i]); printf(" (%5.3g) old value.\n", pi_old[i]); */ mo[class]->s[i].pi = TRIM (pi_old[i], pi_new[i]); } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (pi_old); m_free (pi_new); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_update_a_closed (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int class, double lfactor, double ****expect_a, long double **omega, long double ***omegati) { #define CUR_PROC "discrime_update_a_closed" int i, j, g, l, m; int j_id; double *a_old = NULL; double *a_new = NULL; double sum, lagrangian; ghmm_dseq *sq = NULL; ARRAY_CALLOC (a_old, mo[class]->N); ARRAY_CALLOC (a_new, mo[class]->N); /* updating current class (all or only specified) */ /* itarate over all states of the k-th model */ for (i = 0; i < mo[class]->N; i++) { /* compute lagrangian multiplier */ lagrangian = 0.0; for (j = 0; j < mo[class]->s[i].out_states; j++) { j_id = mo[class]->s[i].out_id[j]; /* iterate over all classes and training sequences */ for (m = 0; m < noC; m++) { sq = sqs[m]; if (m == class) for (l = 0; l < sq->seq_number; l++) lagrangian -= omega[class][l] * expect_a[class][l][class][i * mo[class]->N + j_id]; else for (l = 0; l < sq->seq_number; l++) lagrangian += lfactor * omegati[m][l][class] * expect_a[m][l][class][i * mo [class]-> N + j_id]; } } for (j = 0; j < mo[class]->s[i].out_states; j++) { j_id = mo[class]->s[i].out_id[j]; sum = 0.0; /* iterate over all classes and training sequences */ for (m = 0; m < noC; m++) { sq = sqs[m]; if (m == class) for (l = 0; l < sq->seq_number; l++) sum -= omega[class][l] * expect_a[class][l][+class][i * mo[class]->N + j_id]; else for (l = 0; l < sq->seq_number; l++) sum += lfactor * omegati[m][l][class] * expect_a[m][l][class][i * mo [class]-> N + j_id]; } /* check for valid new parameter */ a_old[j] = mo[class]->s[i].out_a[j]; if (fabs (lagrangian) == 0.0) a_new[j] = a_old[j]; else a_new[j] = sum / lagrangian; } /* update parameter */ for (j = 0; j < mo[class]->s[i].out_states; j++) { mo[class]->s[i].out_a[j] = TRIM (a_old[j], a_new[j]); /*printf("update parameter A[%d] in state %d of model %d with: %5.3g", j, i, class, mo[class]->s[i].out_a[j]); printf(" (%5.3g) old value, %5.3g estimted\n", a_old[j], a_new[j]); */ /* mirror out_a to corresponding in_a */ j_id = mo[class]->s[i].out_id[j]; for (g = 0; g < mo[class]->s[j_id].in_states; g++) if (i == mo[class]->s[j_id].in_id[g]) { mo[class]->s[j_id].in_a[g] = mo[class]->s[i].out_a[j]; break; } } } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (a_old); m_free (a_new); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_update_b_closed (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int class, double lfactor, double *****expect_b, long double **omega, long double ***omegati) { #define CUR_PROC "discrime_update_b_closed" int i, h, l, m; int hist, size; double *b_old = NULL; double *b_new = NULL; double sum, lagrangian; ARRAY_CALLOC (b_old, mo[class]->M); ARRAY_CALLOC (b_new, mo[class]->M); /* itarate over all states of the k-th model */ for (i = 0; i < mo[class]->N; i++) { if (mo[class]->s[i].fix) continue; size = ghmm_ipow (mo[class], mo[class]->M, mo[class]->order[i] + 1); for (hist = 0; hist < size; hist += mo[class]->M) { /* compute lagrangian multiplier */ lagrangian = 0.0; for (h = hist; h < hist + mo[class]->M; h++) { /* iterate over all classes and training sequences */ for (m = 0; m < noC; m++) { if (m == class) for (l = 0; l < sqs[m]->seq_number; l++) lagrangian -= omega[class][l] * expect_b[class][l][class][i][h]; else for (l = 0; l < sqs[m]->seq_number; l++) lagrangian += lfactor * omegati[m][l][class] * expect_b[m][l][class][i][h]; } } for (h = hist; h < hist + mo[class]->M; h++) { /* iterate over all classes and training sequences */ sum = 0.0; for (m = 0; m < noC; m++) { if (m == class) for (l = 0; l < sqs[m]->seq_number; l++) sum -= omega[class][l] * expect_b[class][l][class][i][h]; else for (l = 0; l < sqs[m]->seq_number; l++) sum += lfactor * omegati[m][l][class] * expect_b[m][l][class][i][h]; } /* check for valid new parameters */ b_old[h] = mo[class]->s[i].b[h]; if (fabs (lagrangian) == 0.0) b_new[h] = b_old[h]; else b_new[h] = sum / lagrangian; } /* update parameters */ for (h = hist; h < hist + mo[class]->M; h++) { mo[class]->s[i].b[h] = TRIM (b_old[h], b_new[h]); /*printf("update parameter B[%d] in state %d of model %d with: %5.3g", h, i, class, mo[class]->s[i].b[h]); printf(" (%5.3g) old value, estimate %5.3g\n", b_old[h], b_new[h]); */ } } } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (b_old); m_free (b_new); return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static void discrime_find_factor (ghmm_dmodel * mo, ghmm_dseq ** sqs, int noC, int k, double lfactor, double ****expect_pi, double ****expect_a, double *****expect_b, long double **omega, long double ***omegati) { #define CUR_PROC "discrime_find_factor" int h, i, j, l, m; int size, hist, j_id; double self, other; ghmm_dseq *sq; /* itarate over all states of the k-th model */ for (i = 0; i < mo->N; i++) { /* PI */ /* iterate over all classes */ self = other = 0.0; for (m = 0; m < noC; m++) { sq = sqs[m]; /* if current class and class of training sequence match, add the first term */ if (m == k) for (l = 0; l < sq->seq_number; l++) self += omega[k][l] * expect_pi[k][l][k][i]; /* otherwise the second */ else for (l = 0; l < sq->seq_number; l++) other += lfactor * omegati[m][l][k] * expect_pi[m][l][k][i]; } if (self < other) lfactor *= self / other; /*printf("PI[%d]: %g - %g = %g \t %g\n", k, self, other, self-other, lfactor);*/ /* A */ for (j = 0; j < mo->s[i].out_states; j++) { j_id = mo->s[i].out_id[j]; /* iterate over all classes and training sequences */ self = other = 0.0; for (m = 0; m < noC; m++) { sq = sqs[m]; if (m == k) for (l = 0; l < sq->seq_number; l++) self += omega[k][l] * expect_a[k][l][k][i * mo->N + j_id]; else for (l = 0; l < sq->seq_number; l++) other += lfactor * omegati[m][l][k] * expect_a[m][l][k][i * mo->N + j_id]; } if (self < other) lfactor *= self / other; /*printf(" A[%d]: %g - %g = %g \t %g\n", k, self, other, self-other, lfactor);*/ } /* B */ if (mo->s[i].fix) continue; size = ghmm_ipow(mo, mo->M, mo->order[i] + 1); for (hist = 0; hist < size; hist += mo->M) { for (h = hist; h < hist + mo->M; h++) { self = other = 0.0; /* iterate over all classes and training sequences */ for (m = 0; m < noC; m++) { if (m == k) for (l = 0; l < sqs[m]->seq_number; l++) self += omega[k][l] * expect_b[k][l][k][i][h]; else for (l = 0; l < sqs[m]->seq_number; l++) other += lfactor * omegati[m][l][k] * expect_b[m][l][k][i][h]; } if (self < other) lfactor *= self / other; /*printf(" B[%d]: %g - %g = %g \t %g\n", k, self, other, self-other, lfactor);*/ } } } return; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static int discrime_onestep (ghmm_dmodel ** mo, ghmm_dseq ** sqs, int noC, int grad, int class) { #define CUR_PROC "discrime_onestep" int j, l, retval = -1; /* expected use of parameter (for partial derivatives) */ double *****expect_b, ****expect_a, ****expect_pi; /* matrix of log probabilities */ double ***log_p; /* matrix of outer derivatives */ long double **omega, ***omegati; long double psum = 0, nsum = 0; double lfactor; if (-1 == discrime_galloc (mo, sqs, noC, &expect_b, &expect_a, &expect_pi, &omega, &omegati, &log_p)) { printf ("Allocation Error.\n"); return -1; } if (-1 == discrime_precompute (mo, sqs, noC, expect_b, expect_a, expect_pi, log_p)) { printf ("precompute Error.\n"); goto FREE; } if (-1 == discrime_calculate_omega (mo, sqs, noC, omega, omegati, log_p)) { printf ("omega Error.\n"); goto FREE; } if (grad) { /* updateing parameters */ discrime_update_pi_gradient (mo, sqs, noC, class, expect_pi, omega, omegati); discrime_update_a_gradient (mo, sqs, noC, class, expect_a, omega, omegati); discrime_update_b_gradient (mo, sqs, noC, class, expect_b, omega, omegati); } else { /* calculate a pleaseant lfactor */ for (j = 0; j < noC; j++) { for (l = 0; l < sqs[j]->seq_number; l++) { if (j == class) psum += omega[class][l]; else nsum += omegati[j][l][class]; } } if (fabs (nsum) > 1e-200 && psum < nsum) lfactor = (psum / nsum); else lfactor = 1.0; /* determing maximum lfactor */ discrime_find_factor (mo[class], sqs, noC, class, lfactor, expect_pi, expect_a, expect_b, omega, omegati); lfactor *= .99; printf ("Calculated L: %g\n", lfactor); /* updating parameters */ discrime_update_pi_closed (mo, sqs, noC, class, lfactor, expect_pi, omega, omegati); discrime_update_a_closed (mo, sqs, noC, class, lfactor, expect_a, omega, omegati); discrime_update_b_closed (mo, sqs, noC, class, lfactor, expect_b, omega, omegati); } retval = 0; FREE: discrime_gfree (mo, sqs, noC, expect_b, expect_a, expect_pi, omega, omegati, log_p); return retval; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ int ghmm_dmodel_label_discriminative(ghmm_dmodel** mo, ghmm_dseq** sqs, int noC, int max_steps, int gradient) { #define CUR_PROC "ghmm_dmodel_label_discriminative" double last_perf, cur_perf; int retval=-1, last_cer, cur_cer; double lambda=0.0; double noiselevel = 0.0667; int fp, fn, totalseqs = 0, totalsyms = 0; int *falseP=NULL, *falseN=NULL; double * prior_backup=NULL; int i, k, step; ghmm_dmodel * last; ARRAY_CALLOC (falseP, noC); ARRAY_CALLOC (falseN, noC); ARRAY_CALLOC (prior_backup, noC); for (i = 0; i < noC; i++) { totalseqs += sqs[i]->seq_number; for (k = 0; k < sqs[i]->seq_number; k++) totalsyms += sqs[i]->seq_len[k]; } /* setting priors from number of training sequences and remember the old values */ for (i=0; iprior; mo[i]->prior = (double)sqs[i]->seq_number / totalseqs; printf("original prior: %g \t new prior %g\n", prior_backup[i], mo[i]->prior); } last_perf = ghmm_dmodel_label_discrim_perf (mo, sqs, noC); cur_perf = last_perf; discrime_print_statistics (mo, sqs, noC, falseP, falseN); fp = fn = 0; for (i = 0; i < noC; i++) { printf ("Model %d likelihood: %g, \t false positives: %d\n", i, ghmm_dmodel_likelihood (mo[i], sqs[i]), falseP[i]); fn += falseN[i]; fp += falseP[i]; } printf ("\n%d false positives and %d false negatives after ML-initialisation; Performance: %g.\n", fp, fn, last_perf); last_cer = cur_cer = fp; for (k = 0; k < noC; k++) { last = NULL; step = 0; if (gradient) lambda = .3; do { if (last) ghmm_dmodel_free (&last); /* save a copy of the currently trained model */ last = ghmm_dmodel_copy (mo[k]); last_cer = cur_cer; last_perf = cur_perf; noiselevel /= 1.8; discrime_lambda = lambda / totalsyms; printf ("==============================================================\n"); printf ("Optimising class %d, current step %d, lambda: %g noise: %g, gradient: %d\n", k, step, discrime_lambda, noiselevel, gradient); /* if (gradient) */ /* ghmm_dmodel_add_noise(mo[k], noiselevel, 0); */ discrime_onestep (mo, sqs, noC, gradient, k); cur_perf = ghmm_dmodel_label_discrim_perf (mo, sqs, noC); discrime_print_statistics (mo, sqs, noC, falseP, falseN); fp = fn = 0; for (i = 0; i < noC; i++) { printf ("Model %d likelihood: %g, \t false positives: %d\n", i, ghmm_dmodel_likelihood (mo[i], sqs[i]), falseP[i]); fn += falseN[i]; fp += falseP[i]; } cur_cer = fp; printf ("MAP=%12g -> training -> MAP=%12g", last_perf, cur_perf); printf (" %d false positives, %d false negatives\n", fp, fn); printf ("==============================================================\n"); } while ((last_perf < cur_perf || cur_cer < last_cer) && (step++ < max_steps)); mo[k] = ghmm_dmodel_copy (last); ghmm_dmodel_free (&last); cur_perf = last_perf; cur_cer = last_cer; } /* resetting priors to old values */ for (i = 0; i < noC; i++) mo[i]->prior = prior_backup[i]; retval = 0; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (prior_backup); m_free (falseP); m_free (falseN); return retval; #undef CUR_PROC } ghmm-0.9-rc3/acinclude.m4000775 001750 001750 00000013665 12154244040 015112 0ustar00ericeric000000 000000 dnl author : Achim Gaedke dnl filename : ghmm/acinclude.m4 dnl created : DATE: 2001-04-04 dnl $Id: acinclude.m4 2254 2009-04-20 12:06:19Z grunau $ # Configure path for the GNU Scientific Library # Christopher R. Gabriel , April 2000 AC_DEFUN([AM_PATH_GSL], [ AC_ARG_WITH(gsl-prefix,[ --with-gsl-prefix=PFX Prefix where GSL is installed (optional)], gsl_prefix="$withval", gsl_prefix="") AC_ARG_WITH(gsl-exec-prefix,[ --with-gsl-exec-prefix=PFX Exec prefix where GSL is installed (optional)], gsl_exec_prefix="$withval", gsl_exec_prefix="") AC_ARG_ENABLE(gsltest, [ --disable-gsltest Do not try to compile and run a test GSL program], , enable_gsltest=yes) if test x$gsl_exec_prefix != x ; then gsl_args="$gsl_args --exec-prefix=$gsl_exec_prefix" if test x${GSL_CONFIG+set} != xset ; then GSL_CONFIG=$gsl_exec_prefix/bin/gsl-config fi fi if test x$gsl_prefix != x ; then gsl_args="$gsl_args --prefix=$gsl_prefix" if test x${GSL_CONFIG+set} != xset ; then GSL_CONFIG=$gsl_prefix/bin/gsl-config fi fi AC_PATH_PROG(GSL_CONFIG, gsl-config, no) min_gsl_version=ifelse([$1], ,0.2.5,$1) AC_MSG_CHECKING(for GSL - version >= $min_gsl_version) no_gsl="" if test "$GSL_CONFIG" = "no" ; then no_gsl=yes else GSL_CFLAGS=`$GSL_CONFIG $gslconf_args --cflags` GSL_LIBS=`$GSL_CONFIG $gslconf_args --libs` dnl append flags for gsl if test -z "`echo $GSL_LIBS | grep l.*blas`" ; then GSL_LIBS="$GSL_LIBS -lgslblas" fi gsl_major_version=`$GSL_CONFIG $gsl_args --version | \ sed 's/^\([[0-9]]*\).*/\1/'` if test "x${gsl_major_version}" = "x" ; then gsl_major_version=0 fi gsl_minor_version=`$GSL_CONFIG $gsl_args --version | \ sed 's/^\([[0-9]]*\)\.\{0,1\}\([[0-9]]*\).*/\2/'` if test "x${gsl_minor_version}" = "x" ; then gsl_minor_version=0 fi gsl_micro_version=`$GSL_CONFIG $gsl_config_args --version | \ sed 's/^\([[0-9]]*\)\.\{0,1\}\([[0-9]]*\)\.\{0,1\}\([[0-9]]*\).*/\3/'` if test "x${gsl_micro_version}" = "x" ; then gsl_micro_version=0 fi if test "x$enable_gsltest" = "xyes" ; then ac_save_CFLAGS="$CFLAGS" ac_save_LIBS="$LIBS" CFLAGS="$CFLAGS $GSL_CFLAGS" LIBS="$LIBS $GSL_LIBS" rm -f conf.gsltest AC_TRY_RUN([ #include #include #include char* my_strdup (const char *str) { char *new_str; if (str) { new_str = (char *)malloc ((strlen (str) + 1) * sizeof(char)); strcpy (new_str, str); } else new_str = NULL; return new_str; } int main (void) { int major = 0, minor = 0, micro = 0; int n; char *tmp_version; system ("touch conf.gsltest"); /* HP/UX 9 (%@#!) writes to sscanf strings */ tmp_version = my_strdup("$min_gsl_version"); n = sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) ; if (n != 2 && n != 3) { printf("%s, bad version string\n", "$min_gsl_version"); exit(1); } if (($gsl_major_version > major) || (($gsl_major_version == major) && ($gsl_minor_version > minor)) || (($gsl_major_version == major) && ($gsl_minor_version == minor) && ($gsl_micro_version >= micro))) { exit(0); } else { printf("\n*** 'gsl-config --version' returned %d.%d.%d, but the minimum version\n", $gsl_major_version, $gsl_minor_version, $gsl_micro_version); printf("*** of GSL required is %d.%d.%d. If gsl-config is correct, then it is\n", major, minor, micro); printf("*** best to upgrade to the required version.\n"); printf("*** If gsl-config was wrong, set the environment variable GSL_CONFIG\n"); printf("*** to point to the correct copy of gsl-config, and remove the file\n"); printf("*** config.cache before re-running configure\n"); exit(1); } } ],, no_gsl=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"]) CFLAGS="$ac_save_CFLAGS" LIBS="$ac_save_LIBS" fi fi if test "x$no_gsl" = x ; then AC_MSG_RESULT(yes) ifelse([$2], , :, [$2]) else AC_MSG_RESULT(no) if test "$GSL_CONFIG" = "no" ; then echo "*** The gsl-config script installed by GSL could not be found" echo "*** If GSL was installed in PREFIX, make sure PREFIX/bin is in" echo "*** your path, or set the GSL_CONFIG environment variable to the" echo "*** full path to gsl-config." else if test -f conf.gsltest ; then : else echo "*** Could not run GSL test program, checking why..." CFLAGS="$CFLAGS $GSL_CFLAGS" LIBS="$LIBS $GSL_LIBS" AC_TRY_LINK([ #include ], [ return 0; ], [ echo "*** The test program compiled, but did not run. This usually means" echo "*** that the run-time linker is not finding GSL or finding the wrong" echo "*** version of GSL. If it is not finding GSL, you'll need to set your" echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" echo "*** to the installed location Also, make sure you have run ldconfig if that" echo "*** is required on your system" echo "***" echo "*** If you have an old version installed, it is best to remove it, although" echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"], [ echo "*** The test program failed to compile or link. See the file config.log for the" echo "*** exact error that occured. This usually means GSL was incorrectly installed" echo "*** or that you have moved GSL since it was installed. In the latter case, you" echo "*** may want to edit the gsl-config script: $GSL_CONFIG" ]) CFLAGS="$ac_save_CFLAGS" LIBS="$ac_save_LIBS" fi fi # GSL_CFLAGS="" # GSL_LIBS="" ifelse([$3], , :, [$3]) fi AC_SUBST(GSL_CFLAGS) AC_SUBST(GSL_LIBS) rm -f conf.gsltest ]) ghmm-0.9-rc3/ghmm/smap_classify.h000775 001750 001750 00000006544 12154244034 016660 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/smap_classify.h * Authors: Bernd Wichern * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2275 $ * from $Date: 2009-04-28 08:21:57 -0400 (Tue, 28 Apr 2009) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_SMAP_CLASSIFY_H #define GHMM_SMAP_CLASSIFY_H #include "ghmmconfig.h" #ifdef GHMM_OBSOLETE #include "smodel.h" #ifdef __cplusplus extern "C" { #endif /** Maximum A Posteriori Classification Algorithm (MAPCA). \obsolete given a field of models and one sequence and suppose the sequence has been produced by one of these models. This algorithm calculates for each model the probability, that the seq. comes from the model. This bayesian approach uses a prior for the models. If none is specified equal prob. is assumed. The maps are copied into "result", which has to be of dimension "smo_number" Ref.: A. Kehagias: Bayesian Classification of HMM, Math. Comp. Modelling (1995) @return number of the model, that fits best to the sequence @param smo vector of models @param result gives the probability for all the models @param smo_number number of models @param O sequence @param T length of the sequence */ int ghmm_smap_classify (ghmm_cmodel ** smo, double *result, int smo_number, double *O, int T); /** Alternative to MAPCA (smap_classify) using Bayes' theorem. \obsolete calculate p[m] directly using Bayes' theorem, instead of recursive over t. p(m | O) = p(O | m) * p(m) / (sum_i p(O | i) * p(i)) @return number of the model, that fits best to the sequence @param smo vector of models @param result gives the probability for all the models @param smo_number number of models @param O sequence @param T length of the sequence */ int ghmm_smap_bayes (ghmm_cmodel ** smo, double *result, int smo_number, double *O, int T); #ifdef __cplusplus } #endif #endif /* GHMM_OBSOLETE */ #endif /* GHMM_SMAP_CLASSIFY_H */ ghmm-0.9-rc3/ghmm/linkedlist.c000775 001750 001750 00000007016 12154244034 016153 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/linkedlist.c * Authors: Matthias Heinig * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1442 $ * from $Date: 2005-10-12 13:09:41 -0400 (Wed, 12 Oct 2005) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include "mes.h" #include "ghmm_internals.h" void ighmm_list_append(i_list * list, int val){ i_el * last; i_el * el; el = ighmm_list_init_el(val); if (list->first == NULL) { list->first = el; list->last = el; } else { last = list->last; last->next = el; list->last = el; } list->length++; } void ighmm_list_insert(i_list * list, int val) { i_el * first; i_el * el; el = ighmm_list_init_el(val); if (list->first == NULL) { list->first = el; list->last = el; } else { first = list->first; el->next = first; list->first = el; } list->length++; } void ighmm_list_print(i_list * list) { i_el * el = list->first; printf("LIST : "); while(el != NULL) { printf("%i, ", el->val); el = el->next; } printf("\n"); } int * ighmm_list_to_array(i_list * list) { #define CUR_PROC "ighmm_list_to_array" int counter = 0; int * array; i_el * el; ARRAY_CALLOC (array, list->length); el = list->first; while(el != NULL) { array[counter] = el->val; el = el->next; counter++; } return array; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free(array); return NULL; #undef CUR_PROC } i_list * ighmm_list_init_list() { #define CUR_PROC "ighmm_list_init_list" i_list * list; ARRAY_CALLOC (list, 1); list->first = NULL; list->last = NULL; list->length = 0; return list; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ ighmm_list_free(list); return NULL; #undef CUR_PROC } i_el * ighmm_list_init_el(int val) { #define CUR_PROC "ighmm_list_init_el" i_el * el; ARRAY_CALLOC (el, 1); el->next = NULL; el->val = val; return el; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ free(el); return NULL; #undef CUR_PROC } int ighmm_list_free(i_list * list) { i_el * el; i_el * next; el = list->first; while(el != NULL) { next = el->next; free(el); el = next; } return 0; } ghmm-0.9-rc3/ghmmwrapper/wrapper_dmodel.i000664 001750 001750 00000030350 12176563435 020433 0ustar00ericeric000000 000000 %{ #include #include #include #include #include #include #include #include #include %} /*========================================================================== ===== discrete background distribution =================================== */ typedef struct { /** Number of distributions */ int n; /** Number of symbols in alphabet */ int m; /** Order of the respective distribution */ int *order; /** The probabilities */ double **b; /** string ids of the background distributions */ char * * name; } ghmm_dbackground; ghmm_dbackground* ghmm_dbackground_alloc (int n, int m, int* orders, double** B); %extend ghmm_dbackground { ghmm_dbackground(int n, int m, int* orders, double** B) { return ghmm_dbackground_alloc(n, m, orders, B); } ~ghmm_dbackground() { ghmm_dbackground_free(self); } ghmm_dbackground *copy(); int getOrder(size_t index) { return self->order[index]; } double *getWeights(size_t index) { return self->b[index]; } char *getName (size_t index) { return self->name[index]; } void setName (size_t index, char *value) { if(index < self->n){ self->name[index] = (char*) malloc(sizeof(char) * (strlen(value)+1)); strcpy(self->name[index], value); }//todo error handleing } } /*========================================================================== ===== discrete emission states =========================================== */ typedef struct { /** Initial probability */ double pi; /** Output probability */ double *b; /** IDs of the following states */ int *out_id; /** IDs of the previous states */ int *in_id; /** transition probabilities to successor states. */ double *out_a; /** transition probabilities from predecessor states. */ double *in_a; /** Number of successor states */ int out_states; /** Number of precursor states */ int in_states; /** if fix == 1 --> b stays fix during the training */ int fix; /** contains a description of the state (null terminated utf-8)*/ char * desc; /** x coordinate position for graph representation plotting **/ int xPosition; /** y coordinate position for graph representation plotting **/ int yPosition; } ghmm_dstate; %extend ghmm_dstate { void clean(); int getInState(size_t index) { return self->in_id[index]; } int getOutState(size_t index) { return self->out_id[index]; } double getInProb(size_t index) { return self->in_a[index]; } double getOutProb(size_t index) { return self->out_a[index]; } char* getDesc(){return self->desc;} void setDesc(char* name){ self->desc = (char*) malloc(sizeof(char) * (strlen(name)+1)); strcpy(self->desc, name); } } STRUCT_ARRAY(ghmm_dstate, dstate) REFERENCE_ARRAY(ghmm_dstate, dstate_ptr) /*========================================================================== ===== discrete emission models =========================================== */ %newobject ghmm_dmodel::generate_sequences; typedef struct { /** Number of states */ int N; /** Number of outputs */ int M; /** Vector of the states */ ghmm_dstate *s; /** The a priori probability for the model. A value of -1 indicates that no prior is defined. Note: this is not to be confused with priors on emission distributions*/ double prior; /* contains a arbitrary name for the model (null terminated utf-8) */ /*unsigned */char * name; /** Contains bit flags for varios model extensions such as kSilentStates, kTiedEmissions (see ghmm.h for a complete list) */ int model_type; /** Flag variables for each state indicating whether it is emitting or not. Note: silent != NULL iff (model_type & kSilentStates) == 1 */ int *silent; /*AS*/ /** Int variable for the maximum level of higher order emissions */ int maxorder; /** saves the history of emissions as int, the nth-last emission is (emission_history * |alphabet|^n+1) % |alphabet| see ...*/ int emission_history; /** Flag variables for each state indicating whether the states emissions are tied to another state. Groups of tied states are represented by their tie group leader (the lowest numbered member of the group). tied_to[s] == kUntied : s is not a tied state tied_to[s] == s : s is a tie group leader tied_to[t] == s : t is tied to state s (t>s) Note: tied_to != NULL iff (model_type & kTiedEmissions) != 0 */ int *tied_to; /** Note: State store order information of the emissions. Classic HMMS have emission order 0, that is the emission probability is conditioned only on the state emitting the symbol. For higher order emissions, the emission are conditioned on the state s as well as the previous emission_order[s] observed symbols. The emissions are stored in the state's usual double* b. The order is set order. Note: order != NULL iff (model_type & kHigherOrderEmissions) != 0 */ int * order; /** ghmm_dbackground is a pointer to a ghmm_dbackground structure, which holds (essentially) an array of background distributions (which are just vectors of floating point numbers like state.b). For each state the array background_id indicates which of the background distributions to use in parameter estimation. A value of kNoBackgroundDistribution indicates that none should be used. Note: background_id != NULL iff (model_type & kHasBackgroundDistributions) != 0 */ int *background_id; ghmm_dbackground *bp; /** (WR) added these variables for topological ordering of silent states Condition: topo_order != NULL iff (model_type & kSilentStates) != 0 */ int *topo_order; int topo_order_length; /** pow_lookup is a array of precomputed powers It contains in the i-th entry M (alphabet size) to the power of i The last entry is maxorder+1 */ int *pow_lookup; /** Store for each state a class label. Limits the possibly state sequence Note: label != NULL iff (model_type & kLabeledStates) != 0 */ int* label; ghmm_alphabet* label_alphabet; ghmm_alphabet* alphabet; } ghmm_dmodel; extern int ghmm_dmodel_free(ghmm_dmodel **mo); %extend ghmm_dmodel { ghmm_dmodel() { return calloc(1, sizeof(ghmm_dmodel)); } ghmm_dmodel(int no_states, int no_emissions) { ghmm_dmodel *mo = calloc(1, sizeof(ghmm_dmodel)); mo->N = no_states; mo->M = no_emissions; mo->model_type = GHMM_kDiscreteHMM; mo->prior = -1; return mo; } ~ghmm_dmodel() { ghmm_dmodel_free(&self); } int write_xml(char* filename) { return ghmm_dmodel_xml_write(&self, filename, 1); } int forward_init(double *alpha_1, int symb, double *scale); int forward(const int *O, int len, double **alpha, double *scale, double *log_p); int backward(const int *O, int len, double **beta, const double *scale); int backward_termination(const int *O, int length, double **beta, double *scale, double *log_p); int logp(const int *O, int len, double *log_p); int logp_joint(const int *O, int len, const int *S, int slen, double *log_p); int forward_lean(const int *O, int len, double *log_p); //int check_compatibility(ghmm_dmodel **mo, int model_number); ghmm_dseq* generate_sequences(int seed, int global_len, long seq_number, int Tmax); double likelihood(ghmm_dseq *sq); double get_transition(int i, int j); int check_transition(int i, int j); void set_transition(int i, int j, double prob); double prob_distance(ghmm_dmodel *m, int maxT, int symmetric, int verbose); int normalize(void); int add_noise(double level, int seed); int duration_apply(int cur, int times); int background_apply(double *background_weight); int get_uniform_background(ghmm_dseq *sq); void order_topological(void); void update_tie_groups(void); int baum_welch(ghmm_dseq *sq); int baum_welch_nstep(ghmm_dseq *sq, int max_step, double likelihood_delta); int** fbgibbs(ghmm_dseq* seq, double **pA, double **pB, double *pPi, int burnIn, int seed); int** cfbgibbs (ghmm_dseq* seq, double **pA, double **pB, double *pPi, int R, int burnIn, int seed); int* viterbi(int *o, int len, int *pathlen, double *log_p); double viterbi_logp(int *o, int len, int *state_seq); ghmm_dstate* getState(size_t index) { return self->s + index; } int getSilent(size_t index) { return self->silent[index]; } void setSilent(size_t index, int value) { self->silent[index] = value; } int getTiedTo(size_t index) { return self->tied_to[index]; } void setTiedTo(size_t index, int value) { self->tied_to[index] = value; } int getOrder(size_t index) { return self->order[index]; } void setOrder(size_t index, int value) { self->order[index] = value; } int getBackgroundID(size_t index) { return self->background_id[index]; } void setBackgroundID(size_t index, int value) { self->background_id[index] = value; } int getStateLabel(size_t index) { return self->label[index]; } void setStateLabel(size_t index, int value) { self->label[index] = value; } void addModelTypeFlags(unsigned int flags) { self->model_type |= flags; return; } void removeModelTypeFlags(unsigned int flags) { self->model_type &= ~flags; return; } char* getStateName(size_t index){ if((self->s + index) && index < self->N) return (self->s + index)->desc; else return NULL; } void setStateName(size_t index, char* name){ (self->s+index)->desc = (char*) malloc(sizeof(char) * (strlen(name)+1)); strcpy((self->s+index)->desc, name); } } STRUCT_ARRAY(ghmm_dmodel, dmodel) REFERENCE_ARRAY(ghmm_dmodel, dmodel_ptr) %newobject ghmm_dmodel::label_generate_sequences; /* ====== labeled =========================================================== */ %extend ghmm_dmodel{ int label_forward(const int *O, const int *label, int len, double **alpha, double *scale, double *log_p); int label_logp(const int *O, const int *label, int len, double *log_p); int label_backward(const int *O, const int *label, int len, double **beta, double *scale, double *log_p); //int label_forward_lean(const int *O, const int *label, int len, double *log_p); ghmm_dmodel *label_gradient_descent(ghmm_dseq *sq, double eta, int no_steps); int* label_kbest(int *o_seq, int seq_len, int k, double *log_p); int label_baum_welch(ghmm_dseq *sq); int label_baum_welch_nstep(ghmm_dseq *sq, int max_step, double likelihood_delta); ghmm_dseq* label_generate_sequences(int seed, int global_len, long seq_number, int Tmax); int getLabel(size_t index) { return self->label[index]; } } extern double ghmm_dmodel_label_discrim_perf(ghmm_dmodel** mo, ghmm_dseq** sqs, int noC); extern int ghmm_dmodel_label_discriminative(ghmm_dmodel** mo, ghmm_dseq** sqs, int noC, int max_steps, int gradient); /* obsolete stuff */ #ifdef GHMM_OBSOLETE // ignore the input value for ghmm_dmodel array to python list conversion %typemap(in, numinputs=0) int *mo_number (int temp) { $1 = &temp; } // convert array of ghmm_dmodels to python list %typemap(argout) (int *mo_number) { int i; PyObject *obj; Py_XDECREF($result); /* Blow away any previous result */ if (result) { $result = PyList_New(*$1); for (i=0; i<*$1; i++) { obj = SWIG_NewPointerObj(result[i], SWIGTYPE_p_ghmm_dmodel, SWIG_POINTER_NEW); PyList_SetItem($result, i, obj); } free(result); } else { PyErr_SetString(PyExc_ValueError,"got a null pointer"); return NULL; } } extern ghmm_dmodel **ghmm_dmodel_read(char *filename, int *mo_number); #endif /* GHMM_OBSOLETE */ ghmm-0.9-rc3/ghmm/scanner.h000775 001750 001750 00000012561 12154244034 015450 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/scanner.h * Authors: Frank Nuebel * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2275 $ * from $Date: 2009-04-28 08:21:57 -0400 (Tue, 28 Apr 2009) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_SCANNER_H #define GHMM_SCANNER_H #include "ghmmconfig.h" #ifdef GHMM_OBSOLETE #include #ifdef __cplusplus extern "C" { #endif /** Structure for reading files. \obsolete The functions handle memory and read in the input file, which contains the structure and the methods. */ /*@{ */ /* */ typedef struct scanner_t { /** Input file with parameters */ FILE *fp; /** Name of the input file */ char *filename; /** Current line */ int line; /** Position in the current text line */ int pos; /** Maximal length of the identifier */ int idlen; /** Identifier */ char *id; /** Maximal length of the text line */ int txtlen; /** Contains the current line text (used for error message) */ char *txt; /** Current char */ char c; /** Current char is escaped by '\' */ char esc; /** err == 0 : OK */ char err; /** eof == 1 : end of file reached */ char eof; /** Is set after the first use of length units */ int resolution_used; /** x-size of one dot in inch; */ float x_resolution; /** y-size of one dot in inch; */ float y_resolution; float x_scale; float y_scale; } scanner_t; /** */ scanner_t *ighmm_scanner_alloc (const char *filename); /** */ int ighmm_scanner_consume (scanner_t * s, char ch); /** */ int ighmm_scanner_consume_block (scanner_t * s); /** */ int ighmm_scanner_error (scanner_t * s, char *message); /** */ int ighmm_scanner_free (scanner_t ** s); /** */ int ighmm_scanner_free_array (int *len, void ***arr); /** */ void *ighmm_scanner_get_array (scanner_t * s, int *len, char *type); /** */ double ighmm_scanner_get_double (scanner_t * s); /** */ double ighmm_scanner_get_edouble (scanner_t * s); /** */ int ighmm_scanner_get_id (scanner_t * s); /** */ int ighmm_scanner_get_int (scanner_t * s); /** */ int ighmm_scanner_get_name (scanner_t * s); /** */ char *ighmm_scanner_get_path (scanner_t * s); /** */ char *ighmm_scanner_get_str (scanner_t * s, int *len, int cmode); /** */ double **ighmm_scanner_get_d_matrix (scanner_t * s, int *rows, int *cols); /**************************/ /** */ int ighmm_scanner_get_index (scanner_t * s, int n); /** */ int ighmm_scanner_get_length_x (scanner_t * s); /** */ int ighmm_scanner_get_length_y (scanner_t * s); /** */ double ighmm_scanner_get_resolution (scanner_t * s); /** */ #define scanner_get_boolean( s ) (!!ighmm_scanner_get_int( s )) /** */ #define scanner_get_char( s ) ((char)(ighmm_scanner_get_int( s ))) /** */ #define scanner_get_cchar( s ) ((char)(ighmm_scanner_get_int( s ))) /** */ #define scanner_get_cstring( s ) ighmm_scanner_get_str( (s), NULL, 1 ) /** */ #define scanner_get_string( s ) ighmm_scanner_get_str( (s), NULL, 0 ) /** */ #define scanner_get_char_array(s,len) ighmm_scanner_get_array((s),(len),"char" ) /** */ #define scanner_get_cstring_array(s,len) ighmm_scanner_get_array((s),(len),"cstring" ) /** */ #define scanner_get_double_array(s,len) ighmm_scanner_get_array((s),(len),"double" ) /** */ #define scanner_get_double_earray(s,len) ighmm_scanner_get_array((s),(len),"edouble" ) /** */ #define scanner_get_int_array(s,len) ighmm_scanner_get_array((s),(len),"int" ) /** */ #define scanner_get_string_array(s,len) ighmm_scanner_get_array((s),(len),"string" ) /*@} scanner section */ #ifdef __cplusplus } #endif #endif /* GHMM_OBSOLETE */ #endif /* GHMM_SCANNER_H */ ghmm-0.9-rc3/ghmm/sfoba.c000775 001750 001750 00000030470 12154244034 015103 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/sfoba.c * Authors: Bernhard Knab, Benjamin Georgi * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2243 $ * from $Date: 2008-11-05 08:05:05 -0500 (Wed, 05 Nov 2008) $ * last change by $Author: christoph_mpg $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include "ghmm.h" #include "mprintf.h" #include "mes.h" #include "sfoba.h" #include "matrix.h" #include "randvar.h" #include "ghmm_internals.h" /*----------------------------------------------------------------------------*/ static int sfoba_initforward (ghmm_cmodel * smo, double *alpha_1, double *omega, double *scale, double **b) { # define CUR_PROC "sfoba_initforward" int i; double c_0; scale[0] = 0.0; if (b == NULL){ for (i = 0; i < smo->N; i++) { alpha_1[i] = smo->s[i].pi * ghmm_cmodel_calc_b(smo->s+i, omega); scale[0] += alpha_1[i]; } } else { for (i = 0; i < smo->N; i++) { alpha_1[i] = smo->s[i].pi * b[i][smo->M]; scale[0] += alpha_1[i]; } } if (scale[0] > DBL_MIN) { /* >= EPS_PREC */ c_0 = 1 / scale[0]; for (i = 0; i < smo->N; i++) alpha_1[i] *= c_0; } return (0); # undef CUR_PROC } /* sfoba_initforward */ /*----------------------------------------------------------------------------*/ static double sfoba_stepforward (ghmm_cstate * s, double *alpha_t, int osc, double b_omega) { int i, id; double value = 0.0; for (i = 0; i < s->in_states; i++) { id = s->in_id[i]; value += s->in_a[osc][i] * alpha_t[id]; } value *= b_omega; /* b_omega outside the sum */ return (value); } /* sfoba_stepforward */ /*============================================================================*/ int ghmm_cmodel_forward (ghmm_cmodel * smo, double *O, int T, double ***b, double **alpha, double *scale, double *log_p) { # define CUR_PROC "ghmm_cmodel_forward" int res = -1; int i, t = 0, osc = 0; double c_t; int pos; /* T is length of sequence; divide by dimension to represent the number of time points */ T /= smo->dim; /* calculate alpha and scale for t = 0 */ if (b == NULL) sfoba_initforward(smo, alpha[0], O, scale, NULL); else sfoba_initforward(smo, alpha[0], O, scale, b[0]); if (scale[0] <= DBL_MIN) { /* means f(O[0], mue, u) << 0, first symbol very unlikely */ /* GHMM_LOG(LCONVERTED, "scale[0] == 0.0!\n"); */ goto STOP; } else { *log_p = -log (1 / scale[0]); if (smo->cos == 1) { osc = 0; } else { if (!smo->class_change->get_class) { printf ("ERROR: get_class not initialized\n"); return (-1); } /* printf("1: cos = %d, k = %d, t = %d\n",smo->cos,smo->class_change->k,t); */ osc = smo->class_change->get_class (smo, O, smo->class_change->k, t); if (osc >= smo->cos){ printf("ERROR: get_class returned index %d but model has only %d classes !\n",osc,smo->cos); goto STOP; } } for (t = 1; t < T; t++) { scale[t] = 0.0; pos = t * smo->dim; /* b not calculated yet */ if (b == NULL) { for (i = 0; i < smo->N; i++) { alpha[t][i] = sfoba_stepforward(smo->s+i, alpha[t-1], osc, ghmm_cmodel_calc_b(smo->s+i, O+pos)); scale[t] += alpha[t][i]; } } /* b precalculated */ else { for (i = 0; i < smo->N; i++) { alpha[t][i] = sfoba_stepforward (smo->s+i, alpha[t - 1], osc, b[t][i][smo->M]); scale[t] += alpha[t][i]; } } if (scale[t] <= DBL_MIN) { /* seq. can't be build */ goto STOP; break; } c_t = 1 / scale[t]; /* scale alpha */ for (i = 0; i < smo->N; i++) alpha[t][i] *= c_t; /* summation of log(c[t]) for calculation of log( P(O|lambda) ) */ *log_p -= log (c_t); if (smo->cos == 1) { osc = 0; } else { if (!smo->class_change->get_class) { printf ("ERROR: get_class not initialized\n"); return (-1); } /* printf("1: cos = %d, k = %d, t = %d\n",smo->cos,smo->class_change->k,t); */ osc = smo->class_change->get_class (smo, O, smo->class_change->k, t); if (osc >= smo->cos){ printf("ERROR: get_class returned index %d but model has only %d classes !\n",osc,smo->cos); goto STOP; } } } } /* log_p should not be smaller than value used for seqs. that can't be build ??? if (*log_p < (double)PENALTY_LOGP) *log_p = (double)PENALTY_LOGP; */ return 0; STOP: *log_p = (double) -DBL_MAX; return (res); # undef CUR_PROC } /* ghmm_cmodel_forward */ #define LOWER_SCALE_BOUND 3.4811068399043105e-57 /* exp(-130) */ /*============================================================================*/ int ghmm_cmodel_backward (ghmm_cmodel * smo, double *O, int T, double ***b, double **beta, const double *scale) { # define CUR_PROC "ghmm_cmodel_backward" double *beta_tmp, sum, c_t; int i, j, j_id, t, osc; int res = -1; int pos; /* T is length of sequence; divide by dimension to represent the number of time points */ T /= smo->dim; ARRAY_CALLOC (beta_tmp, smo->N); for (t = 0; t < T; t++) { /* try differenent bounds here in case of problems like beta[t] = NaN */ if (scale[t] < LOWER_SCALE_BOUND) { /* printf("backward scale(%d) = %e\n", t , scale[t]); */ goto STOP; } } /* initialize */ c_t = 1 / scale[T - 1]; for (i = 0; i < smo->N; i++) { beta[T - 1][i] = 1; beta_tmp[i] = c_t; } /* Backward Step for t = T-2, ..., 0 */ /* beta_tmp: Vector for storage of scaled beta in one time step */ if (smo->cos == 1) { osc = 0; } else { if (!smo->class_change->get_class) { printf ("ERROR: get_class not initialized\n"); goto STOP; } osc = smo->class_change->get_class (smo, O, smo->class_change->k, T - 2); /* printf("osc(%d) = %d\n",T-2,osc); */ if (osc >= smo->cos){ printf("ERROR: get_class returned index %d but model has only %d classes !\n",osc,smo->cos); goto STOP; } } for (t = T - 2; t >= 0; t--) { pos = t * smo->dim; if (b == NULL) for (i = 0; i < smo->N; i++) { sum = 0.0; for (j = 0; j < smo->s[i].out_states; j++) { j_id = smo->s[i].out_id[j]; sum += smo->s[i].out_a[osc][j] * ghmm_cmodel_calc_b(smo->s+j_id, O+pos+smo->dim) * beta_tmp[j_id]; } beta[t][i] = sum; } else for (i = 0; i < smo->N; i++) { sum = 0.0; for (j = 0; j < smo->s[i].out_states; j++) { j_id = smo->s[i].out_id[j]; sum += smo->s[i].out_a[osc][j] * b[t + 1][j_id][smo->M] * beta_tmp[j_id]; /*printf(" smo->s[%d].out_a[%d][%d] * b[%d] * beta_tmp[%d] = %f * %f * %f\n",i,osc,j,t+1,j_id,smo->s[i].out_a[osc][j], b[t + 1][j_id][smo->M], beta_tmp[j_id]); */ } beta[t][i] = sum; /* printf(" -> beta[%d][%d] = %f\n",t,i,beta[t][i]); */ } c_t = 1 / scale[t]; for (i = 0; i < smo->N; i++) beta_tmp[i] = beta[t][i] * c_t; if (smo->cos == 1) { osc = 0; } else { if (!smo->class_change->get_class) { printf ("ERROR: get_class not initialized\n"); goto STOP; } /* if t=1 the next iteration will be the last */ if (t >= 1){ osc = smo->class_change->get_class (smo, O, smo->class_change->k, t-1); /* printf("osc(%d) = %d\n",t-1,osc); */ if (osc >= smo->cos){ printf("ERROR: get_class returned index %d but model has only %d classes !\n",osc,smo->cos); goto STOP; } } } } res = 0; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (beta_tmp); return (res); # undef CUR_PROC } /* ghmm_cmodel_backward */ /*============================================================================*/ int ghmm_cmodel_logp (ghmm_cmodel * smo, double *O, int T, double *log_p) { # define CUR_PROC "ghmm_cmodel_logp" int res = -1; double **alpha, *scale = NULL; alpha = ighmm_cmatrix_stat_alloc (T, smo->N); if (!alpha) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_CALLOC (scale, T); /* run forward alg. */ if (ghmm_cmodel_forward (smo, O, T, NULL, alpha, scale, log_p) == -1) { /* GHMM_LOG_QUEUED(LCONVERTED); */ goto STOP; } res = 0; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ ighmm_cmatrix_stat_free (&alpha); m_free (scale); return (res); # undef CUR_PROC } /* ghmm_cmodel_logp */ /*============================================================================*/ int ghmm_cmodel_logp_joint(ghmm_cmodel *mo, const double *O, int len, const int *S, int slen, double *log_p) { # define CUR_PROC "ghmm_cmodel_logp_joint" int prevstate, state, state_pos=0, pos=0, j, osc=0; int dim = mo->dim; prevstate = state = S[0]; *log_p = log(mo->s[state].pi); if (!(mo->model_type & GHMM_kSilentStates) || 1 /* XXX !mo->silent[state] */ ) { *log_p += log(ghmm_cmodel_calc_b(mo->s+state, O+pos)); pos+=dim; } for (state_pos=1; state_pos < slen || pos+dim <= len; state_pos++) { state = S[state_pos]; for (j=0; j < mo->s[state].in_states; ++j) { if (prevstate == mo->s[state].in_id[j]) break; } if (mo->cos > 1) { if (!mo->class_change->get_class) { GHMM_LOG(LERROR, "get_class not initialized"); goto STOP; } osc = mo->class_change->get_class(mo, O, mo->class_change->k, pos); if (osc >= mo->cos) { GHMM_LOG_PRINTF(LERROR, LOC, "get_class returned index %d " "but model has only %d classes!", osc, mo->cos); goto STOP; } } if (j == mo->s[state].in_states || fabs(mo->s[state].in_a[osc][j]) < GHMM_EPS_PREC) { GHMM_LOG_PRINTF(LERROR, LOC, "Sequence can't be built. There is no " "transition from state %d to %d.", prevstate, state); goto STOP; } *log_p += log(mo->s[state].in_a[osc][j]); if (!(mo->model_type & GHMM_kSilentStates) || 1 /* XXX !mo->silent[state] */) { *log_p += log(ghmm_cmodel_calc_b(mo->s+state, O+pos)); pos+=dim; } prevstate = state; } if (pos < len) GHMM_LOG_PRINTF(LINFO, LOC, "state sequence too short! processed only %d symbols", pos/dim); if (state_pos < slen) GHMM_LOG_PRINTF(LINFO, LOC, "sequence too short! visited only %d states", state_pos); return 0; STOP: return -1; # undef CUR_PROC } ghmm-0.9-rc3/tools/scluster.c000644 000000 000000 00000006302 12154244036 016127 0ustar00rootroot000000 000000 /******************************************************************************* author : Bernhard Knab filename : ghmm/tools/scluster.c created : 2001-04-20 by Achim Gaedke from hmm/src/scluster.c $Id: scluster.c 2267 2009-04-24 15:01:58Z grunau $ Copyright (C) 1998-2005 Alexander Schliep Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln Copyright (C) 2002-2005 Max-Planck-Institut fuer Molekulare Genetik, Berlin This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details. You should have received a copy of the GNU Library General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA ******************************************************************************* Parts of the library are Copyright of Sun Microsystems, Inc. and re distributed under following license * ==================================================== * Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved. * * Developed at SunPro, a Sun Microsystems, Inc. business. * Permission to use, copy, modify, and distribute this * software is freely granted, provided that this notice * is preserved. * ==================================================== *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include #include int main(int argc, char* argv[]) { #define CUR_PROC "scluster_main" #ifdef GHMM_OBSOLETE int exitcode = -1; ghmm_rng_init(); if (argc == 5 || argc == 6) { if (argc == 6) GHMM_RNG_SET(RNG,atoi(argv[5])); else { /* random init */ ghmm_rng_timeseed(RNG); } printf("Clustering Sequences with start partition\n"); switch(atoi(argv[4])) { case 0: printf("SP_BEST (best model)\n"); break; case 1: printf("NO_SP (no start partition)\n"); break; case 2: printf("SP_KM (partition from k-means)\n"); break; case 3: printf("SP_ZUF (random start partition)\n"); break; default: printf("argv[4] %d not valid. must be in [0, 3]\n", atoi(argv[4])); return exitcode; } exitcode = ghmm_scluster_hmm(argv); } else { GHMM_LOG(LCONVERTED, "Insufficient arguments. \ Usage: scluster [sequence file][model file][outfile][labels]\n"); } /*------------------------------------------------------------------------*/ ighmm_mes(MES_WIN, "\n(%2.2T): Program finished with exitcode %d.\n", exitcode ); ighmm_mes_exit(); return(exitcode); #else /* GHMM_OBSOLETE */ fprintf (stderr, "cluster is obsolete. If you need it rebuild the GHMM with \"GHMM_OBSOLETE\".\n"); return 0; #endif /* GHMM_OBSOLETE */ # undef CUR_PROC } /* main */ ghmm-0.9-rc3/ghmm/gauss_tail.c000775 001750 001750 00000010311 12154244034 016134 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/gauss_tail.c * Authors: Bernhard Knab * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1453 $ * from $Date: 2005-11-20 08:33:04 -0500 (Sun, 20 Nov 2005) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include "ghmm.h" #include "randvar.h" #include "ghmm_internals.h" /*============================================================================*/ double ighmm_gtail_pmue (double mue, double A, double B, double eps) { double feps, u, Atil, Btil; Atil = A + eps; Btil = B + eps * A; u = Btil - mue * Atil; /* if (u < EPS_U) u = (double)EPS_U; DANGEROUS: would fudge the function value! */ if (u <= DBL_MIN) return (mue - A); feps = ighmm_rand_normal_density_trunc (-eps, mue, u, -eps); return (A - mue - u * feps); } /*============================================================================*/ /* To avoid numerical ocillation: Interpolate p(\mu) between 2 sampling points for PHI NOTA BENE: This Version is very expensive and exact. */ double ighmm_gtail_pmue_interpol (double mue, double A, double B, double eps) { double u, Atil, Btil, z, z1, z2, m1, m2, u1, u2, p1, p2, pz; int i1, i2; Atil = A + eps; Btil = B + eps * A; u = Btil - mue * Atil; /*if (u < EPS_U) u = (double)EPS_U; DANGEROUS: would fudge the function value! */ if (u <= DBL_MIN) return (mue - A); /* Compute like normally where mue positiv. */ if (mue >= 0.0) return (A - mue - u * ighmm_rand_normal_density_trunc (-eps, mue, u, -eps)); /* Otherwise: Interpolate the function itself between 2 sampling points. */ z = (eps + mue) / sqrt (u); i1 = (int) (fabs (z) * ighmm_rand_get_xfaktphi ()); if (i1 >= ighmm_rand_get_philen () - 1) { i1 = (int) ighmm_rand_get_philen () - 1; i2 = i1; } else i2 = i1 + 1; z1 = i1 / ighmm_rand_get_xfaktphi (); z2 = i2 / ighmm_rand_get_xfaktphi (); m1 = -z1 * sqrt (Btil + eps * Atil + Atil * Atil * z1 * z1 * 0.25) -(eps + Atil * z1 * z1 * 0.5); m2 = -z2 * sqrt (Btil + eps * Atil + Atil * Atil * z2 * z2 * 0.25) -(eps + Atil * z2 * z2 * 0.5); u1 = Btil - m1 * Atil; u2 = Btil - m2 * Atil; p1 = A - m1 - u1 * ighmm_rand_normal_density_trunc (-eps, m1, u1, -eps); p2 = A - m1 - u1 * ighmm_rand_normal_density_trunc (-eps, m2, u2, -eps); if (i1 >= ighmm_rand_get_philen () - 1) pz = p1; else { pz = p1 + (fabs (z) - i1 * ighmm_rand_get_xstepphi ()) *(p2 - p1) / ighmm_rand_get_xstepphi (); /* pz = p1; */ } return (pz); } /*============================================================================*/ double ighmm_gtail_pmue_umin (double mue, double A, double B, double eps) { double feps, u; u = GHMM_EPS_U; feps = ighmm_rand_normal_density_trunc (-eps, mue, u, -eps); return (A - mue - u * feps); } ghmm-0.9-rc3/ghmm/sdfoba.c000775 001750 001750 00000030547 12154244034 015254 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/sdfoba.c * Authors: Utz J. Pape * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1713 $ * from $Date: 2006-10-16 10:06:28 -0400 (Mon, 16 Oct 2006) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include "ghmm.h" #include "sdmodel.h" #include "matrix.h" #include "mes.h" #include "ghmm_internals.h" static int sdfoba_initforward (ghmm_dsmodel * mo, double *alpha_1, int symb, double *scale) { # define CUR_PROC "sdfoba_initforward" int i, j, id, in_id; int class = 0; double c_0; scale[0] = 0.0; /*iterate over non-silent states*/ for (i = 0; i < mo->N; i++) { if (!(mo->silent[i])) { if (symb != mo->M) { alpha_1[i] = mo->s[i].pi * mo->s[i].b[symb]; /* printf("\nalpha1[%i]=%f\n",i,alpha_1[i]);*/ } else { alpha_1[i] = mo->s[i].pi; } scale[0] += alpha_1[i]; } } /*iterate over silent states*/ for (i = 0; i < mo->topo_order_length; i++) { id = mo->topo_order[i]; alpha_1[id] = mo->s[id].pi; /* printf("\nsilent_start alpha1[%i]=%f\n",id,alpha_1[id]);*/ for (j = 0; j < mo->s[id].in_states; j++) { in_id = mo->s[id].in_id[j]; alpha_1[id] += mo->s[id].in_a[class][j] * alpha_1[in_id]; } /* printf("\n\tsilent_run alpha1[%i]=%f\n",id,alpha_1[id]);*/ scale[0] += alpha_1[id]; } /* printf("\n%f\n",scale[0]);*/ if (scale[0] >= GHMM_EPS_PREC) { c_0 = 1 / scale[0]; for (i = 0; i < mo->N; i++) alpha_1[i] *= c_0; } return (0); /* attention scale[0] might be 0 */ # undef CUR_PROC } /* sdfoba_initforward */ /*----------------------------------------------------------------------------*/ static double sdfoba_stepforward (ghmm_dsstate * s, double *alpha_t, const double b_symb, int class) { int i, id; double value = 0.0; for (i = 0; i < s->in_states; i++) { id = s->in_id[i]; /* printf("state:\t%s, instate:\t%d, prob:\t%f\n", s->label, id, s->in_a[class][i]);*/ value += s->in_a[class][i] * alpha_t[id]; } value *= b_symb; return (value); } /* sdfoba_stepforward */ /*============================================================================*/ int ghmm_dsmodel_forward (ghmm_dsmodel * mo, const int *O, int len, double **alpha, double *scale, double *log_p) { # define CUR_PROC "ghmm_dsmodel_forward" int i, t, id; double c_t, dblems; int class = 0; /*if (mo->model_type & kSilentStates) ghmm_dsmodel_topo_order(mo); */ sdfoba_initforward (mo, alpha[0], O[0], scale); if (scale[0] < GHMM_EPS_PREC) { /* means: first symbol can't be generated by hmm */ printf ("\nnach init gestoppt\n"); *log_p = +1; } else { *log_p = -log (1 / scale[0]); for (t = 1; t < len; t++) { scale[t] = 0.0; /* printf("\nStep t=%i mit len=%i, O[i]=%i\n",t,len,O[t]);*/ if (mo->cos > 1) class = mo->get_class (&(mo->N), t-1); /*iterate over non-silent states*/ /*printf("\nnach Class\n");*/ for (i = 0; i < mo->N; i++) { if (!(mo->model_type & GHMM_kSilentStates) || !(mo->silent[i])) { if (O[t] != mo->M) { dblems = mo->s[i].b[O[t]]; } else { dblems = 1.0; } alpha[t][i] = sdfoba_stepforward (&mo->s[i], alpha[t - 1], dblems, class); /* printf("alpha[%i][%i] = %f\n", t, i, alpha[t][i]);*/ scale[t] += alpha[t][i]; /*printf("\nalpha[%d][%d] = %e, scale[%d] = %e", t,i, alpha[t][i], t, scale[t]);*/ /*printf("scale[%i] = %f\n", t, scale[t]);*/ } } /*printf("\nvor silent states\n");*/ /*iterate over silent state*/ if (mo->model_type & GHMM_kSilentStates) { for (i = 0; i < mo->topo_order_length; i++) { /*printf("\nget id\n");*/ id = mo->topo_order[i]; /*printf("\nin stepforward\n");*/ alpha[t][id] = sdfoba_stepforward (&mo->s[id], alpha[t], 1, class); /* printf("alpha[%i][%i] = %f\n", t, id, alpha[t][id]);*/ /*printf("\nnach stepforward\n");*/ scale[t] += alpha[t][id]; /*printf("\nalpha[%d][%d] = %e, scale[%d] = %e", t,id, alpha[t][id], t, scale[t]);*/ /*printf("silent state: %d\n", id);*/ } } /*printf("\nnach silent states\n");*/ if (scale[t] < GHMM_EPS_PREC) { /*char *str = */ printf ("numerically questionable: "); /*GHMM_LOG(LCONVERTED, str);*/ /*printf("\neps = %e\n", EPS_PREC);*/ /*printf("\nscale kleiner als eps HUHU, Zeit t = %d, scale = %e\n", t, scale[t]);*/ /*printf("\nlabel: %s, char: %d, ems: %f\n", mo->s[92].label,O[t], mo->s[4].b[O[t]]);*/ /*ighmm_cvector_print(stdout, alpha[t],mo->N, "\t", " ", "\n");*/ /* O-string can't be generated by hmm */ /* *log_p = +1.0;*/ /*break;*/ } c_t = 1 / scale[t]; for (i = 0; i < mo->N; i++) alpha[t][i] *= c_t; /* sum log(c[t]) to get log( P(O|lambda) ) */ *log_p -= log (c_t); } } return 0; # undef CUR_PROC } /* ghmm_dsmodel_forward */ #if 0 /* unused */ /*============================================================================*/ static int sdfobau_initforward (ghmm_dsmodel * mo, double *alpha_1, int symb, double *scale) { # define CUR_PROC "sdfoba_initforward" int i, j, id, in_id; int class = 0; double c_0; scale[0] = 0.0; /*iterate over non-silent states*/ for (i = 0; i < mo->N; i++) { if (!(mo->silent[i])) { alpha_1[i] = mo->s[i].pi * mo->s[i].b[symb]; /*printf("\nalpha1[%i]=%f\n",i,alpha_1[i]);*/ scale[0] += alpha_1[i]; } } /*iterate over silent states*/ for (i = 0; i < mo->topo_order_length; i++) { id = mo->topo_order[i]; alpha_1[id] = mo->s[id].pi; /*printf("\nsilent_start alpha1[%i]=%f\n",id,alpha_1[id]);*/ for (j = 0; j < mo->s[id].in_states; j++) { in_id = mo->s[id].in_id[j]; alpha_1[id] += mo->s[id].in_a[class][j] * alpha_1[in_id]; /*printf("\n\tsilent_run alpha1[%i]=%f\n",id,alpha_1[id]);*/ } /*scale[0] += alpha_1[id];*/ } /*printf("\n%f\n",scale[0]);*/ if (scale[0] >= EPS_PREC) { c_0 = 1 / scale[0]; for (i = 0; i < mo->N; i++) alpha_1[i] *= c_0; } return (0); /* attention scale[0] might be 0 */ # undef CUR_PROC } /* sdfoba_initforward */ /*----------------------------------------------------------------------------*/ int sdfobau_forward (ghmm_dsmodel * mo, const int *O, int len, double **alpha, double *scale, double *log_p) { # define CUR_PROC "ghmm_dsmodel_forward" int i, t, id; double c_t; int class = 0; if (mo->model_type & kSilentStates) ghmm_dsmodel_topo_order (mo); sdfobau_initforward (mo, alpha[0], O[0], scale); if (scale[0] < EPS_PREC) { /* means: first symbol can't be generated by hmm */ *log_p = +1; } else { *log_p = -log (1 / scale[0]); for (t = 1; t < len; t++) { scale[t] = 0.0; if (mo->cos > 1) class = mo->get_class (&(mo->N), t - 1); /*iterate over non-silent states*/ for (i = 0; i < mo->N; i++) { if (!(mo->model_type & kSilentStates) || !(mo->silent[i])) { alpha[t][i] = sdfoba_stepforward (&mo->s[i], alpha[t - 1], mo->s[i].b[O[t]], class); scale[t] += alpha[t][i]; } } /*iterate over silent state */ if (mo->model_type & kSilentStates) { for (i = 0; i < mo->topo_order_length; i++) { id = mo->topo_order[i]; alpha[t][id] = sdfoba_stepforward (&mo->s[id], alpha[t], 1, class); /*scale[t] += alpha[t][id];*/ } } if (scale[t] < EPS_PREC) { /* O-string can't be generated by hmm */ *log_p = +1.0; break; } c_t = 1 / scale[t]; for (i = 0; i < mo->N; i++) alpha[t][i] *= c_t; /* sum log(c[t]) to get log( P(O|lambda) ) */ *log_p -= log (c_t); } } return 0; # undef CUR_PROC } /* sdfobau_forward */ #endif /* unused */ /*============================================================================*/ int ghmm_dsmodel_forward_descale (double **alpha, double *scale, int t, int n, double **newalpha) { # define CUR_PROC "ghmm_dsmodel_forward_descale" int i, j, k; /*printf("\nAngekommen, t=%i, n=%i\n",t,n);*/ for (i = 0; i < t; i++) { /*printf("i=%i\n",i);*/ for (j = 0; j < n; j++) { /*printf("\tj=%i\n",j);*/ newalpha[i][j] = alpha[i][j]; /*newalpha[i][j] *= scale[j];*/ /*printf(".");*/ for (k = 0; k <= i; k++) { /*printf(",");*/ newalpha[i][j] *= scale[k]; } } } /*printf("\ndescale geschafft\n");*/ return 0; # undef CUR_PROC } /* ghmm_dsmodel_forward_descale */ /*============================================================================*/ int ghmm_dsmodel_backward (ghmm_dsmodel * mo, const int *O, int len, double **beta, const double *scale) { # define CUR_PROC "ghmm_dsmodel_backward" double *beta_tmp, sum; int i, j, j_id, t; int res = -1; ARRAY_CALLOC (beta_tmp, mo->N); for (t = 0; t < len; t++) mes_check_0 (scale[t], goto STOP); /* initialize */ for (i = 0; i < mo->N; i++) { beta[len - 1][i] = 1; beta_tmp[i] = 1 / scale[len - 1]; } /* Backward Step for t = T-2, ..., 0 */ /* beta_tmp: Vector for storage of scaled beta in one time step */ for (t = len - 2; t >= 0; t--) { for (i = 0; i < mo->N; i++) { sum = 0.0; for (j = 0; j < mo->s[i].out_states; j++) { j_id = mo->s[i].out_id[j]; /*sum += mo->s[i].out_a[j] * mo->s[j_id].b[O[t+1]] * beta_tmp[j_id];*/ } beta[t][i] = sum; } for (i = 0; i < mo->N; i++) beta_tmp[i] = beta[t][i] / scale[t]; } res = 0; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (beta_tmp); return (res); # undef CUR_PROC } /* ghmm_dsmodel_backward */ /*============================================================================*/ int ghmm_dsmodel_logp (ghmm_dsmodel * mo, const int *O, int len, double *log_p) { #define CUR_PROC "ghmm_dsmodel_logp" int res = -1; double **alpha, *scale = NULL; alpha = ighmm_cmatrix_alloc (len, mo->N); if (!alpha) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_CALLOC (scale, len); /* run ghmm_dsmodel_forward */ if (ghmm_dsmodel_forward (mo, O, len, alpha, scale, log_p) == -1) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } res = 0; ighmm_cmatrix_free (&alpha, len); m_free (scale); return (res); STOP: /* Label STOP from ARRAY_[CM]ALLOC */ ighmm_cmatrix_free (&alpha, len); m_free (scale); return (res); # undef CUR_PROC } /* ghmm_dsmodel_logp */ ghmm-0.9-rc3/ghmmwrapper/testdata/discrete.xml000664 001750 001750 00000005052 12154244036 021400 0ustar00ericeric000000 000000 C1 a c g t 0 -1 1.0 1 0 0 1 -1 0 0.0, 0.5, 0.5, 0.0 0 -1 0.0 1 0 0 1 -1 0 0.1, 0.0, 0.8, 0.1 0 -1 0.0 1 0 0 1 -1 0 0.0, 0.0, 0.0, 0.0 0.3 0.3 0.4 0.6 0.1 0.3 1.0 ghmm-0.9-rc3/tests/Makefile.am000644 000000 000000 00000005440 12163055540 016157 0ustar00rootroot000000 000000 # author : Achim Gaedke # filename : ghmm/tests/Makefile.am # created : DATE: April 2001 # $Id: Makefile.am 2314 2013-06-24 15:06:51Z ejb177 $ # # Copyright (C) 1998-2005 Alexander Schliep # Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln # Copyright (C) 2002-2005 Max-Planck-Institut fuer Molekulare Genetik, Berlin # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Library General Public # License as published by the Free Software Foundation; either # version 2 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # Library General Public License for more details. # # You should have received a copy of the GNU Library General Public # License along with this library; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA # # # # # ******************************************************************************* # Parts of the library are Copyright of Sun Microsystems, Inc. # and re distributed under following license # # * ==================================================== # * Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved. # * # * Developed at SunPro, a Sun Microsystems, Inc. business. # * Permission to use, copy, modify, and distribute this # * software is freely granted, provided that this notice # * is preserved. # * ==================================================== # include $(top_srcdir)/dist_hook.mak SUBDIRS = data # tests and examples CLEANFILES = ghmm.log ghmm.sum site.exp site.bak MAINTAINERCLEANFILES = Makefile.in # stuff from dejagnu INCLUDES=-I$(top_srcdir) #these tests will not be installed # in progress: test_sdfoba nullmodel ciscreen test_sdmodel noinst_PROGRAMS = randvar_test \ root_finder_test \ coin_toss_test \ two_states_three_symbols \ libxml-test \ chmm \ chmm_test \ shmm_viterbi_test \ test_gsl_ran_gaussian_tail \ sequences_test \ sequences_old_format \ label_higher_order_test \ read_fa \ mcmc LDADD = $(top_builddir)/ghmm/.libs/libghmm.a TESTS_ENVIRONMENT = GHMM_SILENT_TESTS TESTS = root_finder_test \ coin_toss_test \ two_states_three_symbols \ libxml-test \ chmm \ chmm_test \ shmm_viterbi_test \ test_gsl_ran_gaussian_tail \ sequences_test \ sequences_old_format \ label_higher_order_test \ read_fa \ mcmc ghmm-0.9-rc3/tests/two_states_three_symbols.c000775 001750 001750 00000010553 12154244037 021361 0ustar00ericeric000000 000000 /******************************************************************************* author : Achim Gaedke filename : ghmm/tests/two_states_three_symbols.c created : DATE: 2001-04-25 $Id: two_states_three_symbols.c 2267 2009-04-24 15:01:58Z grunau $ *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include #include #include /* model with two states and three symbols transition probability: 0->0: 0.9, 0->1: 0.1, 1->0: 0.1 and 1->1:0.9 state 0 has symbol 0 (probability 0.5) and 1 (probability 0.5) state 1 has symbol 2 */ int my_model() { /* model structure, that contains states */ ghmm_dmodel my_model; /* array of states */ ghmm_dstate model_states[2]; /* first state */ /* probability of emmission of 0,1 or 2 */ double symbols_0_state[3]={0.5,0.5,0.0}; /* transition to which state is given in the following arrays */ int trans_id_0_state[2]={0,1}; /* transition probability from here to 0-state (self) and 1-state */ double trans_prob_0_state[2]={0.9,0.1}; /* transition probability from 0-state (self) and 1-state to this state */ double trans_prob_0_state_rev[2]={0.9,0.1}; /* second state , comments see above */ double symbols_1_state[3]={0.0,0.0,1.0}; int trans_id_1_state[2]={0,1}; double trans_prob_1_state[2]={0.1,0.9}; double trans_prob_1_state_rev[2]={0.1,0.9}; ghmm_dseq* my_output; int pow_look[2] = {1,3}; /* flags indicating whether a state is silent */ /*int silent_array[2] = {0,0};*/ /* initialise state 0 */ /* start probability for this state */ model_states[0].pi = 0.5; /* array with emission probabilities */ model_states[0].b=symbols_0_state; /* number of fields in out_a and out_id */ model_states[0].out_states=2; /* transition probability from this state */ model_states[0].out_a=trans_prob_0_state; /* state ids belonging to the probability */ model_states[0].out_id=trans_id_0_state; /* transition probability to this state */ /* in_states,in_id and in_a have the same function as above*/ model_states[0].in_states=2; model_states[0].in_id=trans_id_0_state; model_states[0].in_a=trans_prob_0_state_rev; /* should emission probabilities be changed during reestimation? 1: no, else: yes*/ model_states[0].fix=0; /* initialise state 1 */ /* same meaning as above */ model_states[1].pi = 0.5; model_states[1].b=symbols_1_state; model_states[1].out_states=2; model_states[1].out_a=trans_prob_1_state; model_states[1].out_id=trans_id_1_state; model_states[1].in_states=2; model_states[1].in_id=trans_id_0_state; model_states[1].in_a=trans_prob_1_state_rev; model_states[1].fix=0; /* initialise model */ my_model.N=2; /* number of states, dimension of model.s */ my_model.M=3; /* number of symbols, dimension of states.b */ my_model.s=model_states; /* array of states */ my_model.prior=-1; /* probability of this model, used in a model array */ /*my_model.silent = silent_array;*/ my_model.pow_lookup = pow_look; my_model.maxorder = 0; my_model.model_type =0; /* consistency check */ fprintf(stdout,"checking model:\n"); if (ghmm_dmodel_check(&my_model)) { fprintf(stderr,"ghmm_dmodel_check failed!\n"); return 1; } fprintf(stdout,"model is ok\n"); /* print model parameters */ fprintf(stdout,"two_states_three_symbols model:\n"); ghmm_dmodel_print(stdout,&my_model); /* generate sequences */ fprintf(stdout,"generating sequences:..."); my_output=ghmm_dmodel_generate_sequences(&my_model, /* model */ 0, /* random seed */ 100, /* length of each sequence */ 100, /* no of sequences */ 100); /* maxT */ fprintf(stdout,"Done\n"); /*ghmm_dseq_print(stdout,my_output);*/ /* slight change of emission probabilities in state 0 */ symbols_0_state[0] = 0.6; symbols_0_state[1] = 0.4; symbols_0_state[2] = 0.0; /* reestimation */ fprintf(stdout,"reestimating with Baum-Welch-algorithm..."); ghmm_dmodel_baum_welch(&my_model,my_output); /* print the result */ fprintf(stdout,"Done\nthe result is:\n"); ghmm_dmodel_print(stdout,&my_model); ghmm_dseq_free(&my_output); return 0; } int main() { /* Important! initialise rng */ ghmm_rng_init(); return my_model(); } ghmm-0.9-rc3/ghmm/scanner.c000775 001750 001750 00000072676 12154244034 015460 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/scanner.c * Authors: Frank Nübel * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1977 $ * from $Date: 2007-11-16 10:49:06 -0500 (Fri, 16 Nov 2007) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include "ghmmconfig.h" #ifdef GHMM_OBSOLETE #include #include #include #include #include "mprintf.h" #include "mes.h" #include "scanner.h" #include "ghmm_internals.h" #define SCANNER_TYPE_CHAR 1 #define SCANNER_TYPE_INT 2 #define SCANNER_TYPE_DOUBLE 3 #define SCANNER_TYPE_EDOUBLE 4 #define SCANNER_TYPE_STRING 5 #define SCANNER_TYPE_CSTRING 6 #define m_scanner_isdigit( c ) ( (c)>= '0' && (c) <= '9' ) #define m_scanner_isxdigit( c ) \ ( m_scanner_isdigit(c) || ((c) >= 'a' && (c) <= 'f') || ((c)>='A' && (c)<= 'F') ) #define m_scanner_isalpha( c ) \ ( ((c)>='a' && (c)<='z') || ((c)>='A' && (c)<='Z') ) #define m_scanner_isxalpha( c )\ (m_scanner_isalpha(c)||((c)&0x80 || (c)=='_')) /*----------------------------------------------------------------------------*/ static int scanner_type (char *type, int *size) { if (!strcmp (type, "char")) { *size = sizeof (char); return (SCANNER_TYPE_CHAR); } if (!strcmp (type, "int")) { *size = sizeof (int); return (SCANNER_TYPE_INT); } if (!strcmp (type, "double")) { *size = sizeof (double); return (SCANNER_TYPE_DOUBLE); } if (!strcmp (type, "edouble")) { *size = sizeof (double); return (SCANNER_TYPE_EDOUBLE); } if (!strcmp (type, "string")) { *size = sizeof (char *); return (SCANNER_TYPE_STRING); } if (!strcmp (type, "cstring")) { *size = sizeof (char *); return (SCANNER_TYPE_CSTRING); } *size = 0; return (0); } /* scanner_type */ /*----------------------------------------------------------------------------*/ static int scanner_digit (int *val, scanner_t * s, int radix, int expect) { switch (radix) { case 10: if ('0' <= s->c && s->c <= '9') *val = *val * 10 + s->c - '0'; else if (expect) { ighmm_scanner_error (s, "decimal digit expected"); return (-1); } else return (1); break; case 16: if (s->c >= '0' && s->c <= '9') *val = *val * 16 + s->c - '0'; else if ('A' <= s->c && s->c <= 'F') *val = *val * 16 + s->c - 'A' + 10; else if ('a' <= s->c && s->c <= 'f') *val = *val * 16 + s->c - 'a' + 10; else if (expect) { ighmm_scanner_error (s, "decimal digit expected"); return (-1); } else return (1); break; case 2: if (s->c >= '0' && s->c <= '1') *val = *val * 2 + s->c - '0'; else if (expect) { ighmm_scanner_error (s, "binary digit expected"); return (-1); } else return (1); break; case 8: if (s->c >= '0' && s->c <= '7') *val = *val * 8 + s->c - '0'; else if (expect) { ighmm_scanner_error (s, "octal digit expected"); return (-1); } else return (1); break; default: return (1); } return (0); } /* scanner_digit */ /*----------------------------------------------------------------------------*/ static int scanner_virtual_fgetc (scanner_t * s) { int c; if (!s) return (EOF); c = fgetc (s->fp); /* Don't use the mes-functions here */ if (c == EOF) return (c); ungetc (c, s->fp); return (c); } /* scanner_virtual_fgetc */ /*----------------------------------------------------------------------------*/ static void scanner_fgetc (scanner_t * s) { int c; if (!s) return; c = fgetc (s->fp); /* Don't use the mes-functions here */ if (c == EOF) { s->c = 0; s->eof = 1; } else s->c = c; } /* scanner_fgetc */ /*----------------------------------------------------------------------------*/ static int scanner_nextchar (scanner_t * s, int expect) { if (!s || s->err || s->eof) return (0); while (s->pos + 1 >= s->txtlen) { int mes_stat = ighmm_mes_ability (0); int err = ighmm_realloc ((void**)&(s->txt), sizeof(*(s->txt))*(s->txtlen + 256)); ighmm_mes_ability (mes_stat); if (err) { ighmm_scanner_error (s, "line too long"); return (-1); } else s->txtlen += 256; } s->txt[s->pos] = s->c; if (s->c == '\n') { s->pos = 0; s->line++; } else s->pos++; s->txt[s->pos] = 0; scanner_fgetc (s); if (s->eof && expect) { ighmm_scanner_error (s, "unexpected end of file"); return (-1); } return (0); } /* scanner_nextchar */ /*----------------------------------------------------------------------------*/ static int scanner_nextcchar (scanner_t * s) { if (!s || s->eof || s->err) return (0); if (s) s->esc = 0; if (scanner_nextchar (s, 1)) return (-1); if (s->c - '\\') return (0); else { int radix = 0; int digits = 0; int val = 0; if (scanner_nextchar (s, 1)) return (-1); s->esc = 1; if ('0' <= s->c && s->c <= '7') { radix = 8; val = s->c - '0'; digits = 2; } else { switch (s->c) { case 'a': s->c = '\a'; break; case 'b': s->c = '\b'; break; case 'f': s->c = '\f'; break; case 'n': s->c = '\n'; break; case 'r': s->c = '\r'; break; case 't': s->c = '\t'; break; case 'v': s->c = '\v'; break; case '\\': s->c = '\\'; break; case '\'': s->c = '\''; break; case '"': s->c = '\"'; break; case '?': s->c = '\?'; break; case 'd': radix = 10; digits = 3; break; case 'x': radix = 16; digits = 2; break; case '_': radix = 2; digits = 8; break; default: return (0); } if (!radix) return (0); } while (digits--) { if (scanner_nextchar (s, 1)) return (-1); if (scanner_digit (&val, s, radix, 1)) return (-1); } s->c = val; } return (0); } /* scanner_nextcchar */ /*----------------------------------------------------------------------------*/ static int scanner_skipspace (scanner_t * s) { if (s->eof || s->err) return (0); while (!s->eof) { if (s->c == '#') { /* skip comment */ do { if (scanner_nextchar (s, 0)) return (-1); } while (!s->eof && s->c - '\n'); } /* New : C-Comment allowed */ else if (s->c == '/' && scanner_virtual_fgetc (s) == '*') { do { if (scanner_nextchar (s, 0)) return (-1); } while (!s->eof && (s->c - '*' || scanner_virtual_fgetc (s) - '/')); if (!s->eof && scanner_nextchar (s, 0)) return (-1); if (!s->eof && scanner_nextchar (s, 0)) return (-1); } /* FN: 22.10.97 */ else if (strchr (" \n\r\t\f\v\b\a", s->c)) { if (scanner_nextchar (s, 0)) return (-1); } else break; } return (0); } /* scanner_skipspace */ /*----------------------------------------------------------------------------*/ static double scanner_get_length (scanner_t * s, double resolution) { double val = ighmm_scanner_get_double (s); if (!s || s->err) return (0); if (s->eof) { ighmm_scanner_error (s, "length expected"); return (0); } if (s->c - ';') { if (resolution <= 0.0) { ighmm_scanner_error (s, "resolution not set"); return (0); } s->resolution_used = 1; if (ighmm_scanner_get_id (s)) return (0); if (!strcmp (s->id, "INCH")) val *= resolution; else if (!strcmp (s->id, "CM")) val *= (resolution / 2.54); else if (!strcmp (s->id, "MM")) val *= (resolution / 25.4); else { ighmm_scanner_error (s, "unknown length unit"); return (0); } } return val; } /* scanner_get_length */ /*============================================================================*/ /*============================================================================*/ /*============================================================================*/ int ighmm_scanner_free (scanner_t ** s) { # define CUR_PROC "ighmm_scanner_free" mes_check_ptr (s, return (-1)); if (!*s) return (0); m_free ((*s)->filename); m_free ((*s)->id); m_free ((*s)->txt); m_fclose ((*s)->fp); m_free (*s); return (0); # undef CUR_PROC } /* ighmm_scanner_free */ /*============================================================================*/ scanner_t *ighmm_scanner_alloc (const char *filename) { #define CUR_PROC "ighmm_scanner_alloc" scanner_t *s = NULL; mes_check_ptr (filename, return (NULL)); ARRAY_CALLOC (s, 1); s->txtlen = 256; s->idlen = 256; if (!(s->fp = ighmm_mes_fopen (filename, "rt"))) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_MALLOC (s->txt, s->txtlen); ARRAY_MALLOC (s->id, s->txtlen); ARRAY_CALLOC (s->filename, strlen (filename) + 1); memcpy (s->filename, filename, strlen (filename) + 1); s->line = 1; s->pos = 0; s->c = ' '; s->err = 0; /****************/ s->resolution_used = 0; s->x_resolution = 0.0; s->y_resolution = 0.0; s->x_scale = 1.0; s->y_scale = 1.0; scanner_fgetc (s); if (scanner_skipspace (s)) goto STOP; return (s); STOP: /* Label STOP from ARRAY_[CM]ALLOC */ ighmm_scanner_free (&s); return (NULL); #undef CUR_PROC } /* ighmm_scanner_alloc */ /*============================================================================*/ int ighmm_scanner_error (scanner_t * s, char *message) { int i, j; if (!s || s->err) return (0); j = s->pos; while (!s->eof && s->c - '\n' && !scanner_nextchar (s, 0)); ighmm_mes_time (); mes_file_win (s->txt); mes_file_win ("\n"); for (i = 0; i < j; i++) { if (s->txt[i] - '\t') s->txt[i] = ' '; } s->txt[j] = 0; mes_file_win (s->txt); mes_file_win ("^\n"); if (message) { ighmm_mes (MES_FILE_WIN, "Error in file %s, line %d : %s\n", s->filename, s->line + 1, message); } else { ighmm_mes (MES_FILE_WIN, "Syntax error in file %s, line %d\n", s->filename, s->line + 1, message); } s->err = 1; s->c = 0; return (0); } /* ighmm_scanner_error */ /*============================================================================*/ int ighmm_scanner_consume (scanner_t * s, char ch) { if (s->err) return (0); if (s->eof || ch - s->c) { char txt[] = "' ' expected!"; txt[1] = ch; ighmm_scanner_error (s, txt); return (-1); } else if (scanner_nextchar (s, 0)) return (-1); if (scanner_skipspace (s)) return (-1); return (0); } /* ighmm_scanner_consume */ /*============================================================================*/ /* Reads over a block, that's enclosed in '{' and '}'. Other blocks, lying within this one will be skipped */ int ighmm_scanner_consume_block (scanner_t * s) { int open_brackets = 0; if (s->err) return (0); ighmm_scanner_consume (s, '{'); if (s->err) return (-1); open_brackets++; while (!s->eof && open_brackets) { if (!('{' - s->c)) open_brackets++; else if (!('}' - s->c)) open_brackets--; if (scanner_nextchar (s, 0)) return (-1); if (scanner_skipspace (s)) return (-1); } if (open_brackets) { ighmm_scanner_error (s, "Unexpected EOF! '}'expected"); return (-1); } return (0); } /* ighmm_scanner_consume_block */ /*============================================================================*/ int ighmm_scanner_get_name (scanner_t * s) { int pos = 0; if (!s || s->err) return (0); while (m_scanner_isxalpha (s->c) || m_scanner_isdigit (s->c)) { while (pos + 1 >= s->idlen) { int mes_stat = ighmm_mes_ability (0); int err = ighmm_realloc ((void**)&(s->txt), sizeof(*(s->txt))*(s->txtlen + 256)); ighmm_mes_ability (mes_stat); if (err) { ighmm_scanner_error (s, "identifier too long"); return (-1); } else s->idlen += 256; } s->id[pos++] = s->c; if (scanner_nextchar (s, 0)) return (-1); } if (!pos || m_scanner_isdigit (s->id[0])) ighmm_scanner_error (s, "identifier expected"); s->id[pos] = 0; if (scanner_skipspace (s)) return (-1); return (0); } /* ighmm_scanner_get_name */ /*============================================================================*/ int ighmm_scanner_get_id (scanner_t * s) { char *str; if (!s || s->err) return (0); if (ighmm_scanner_get_name (s)) return (0); str = s->id; while (*str) { if ('a' <= *str && *str <= 'z') *str += 'A' - 'a'; str++; } return (0); } /* ighmm_scanner_get_id */ /*============================================================================*/ char *ighmm_scanner_get_str (scanner_t * s, int *len, int cmode) { # define CUR_PROC "scanner_get_string" int i = 0; int maxlen = 128; char *val = NULL; if (!s || s->err) return (NULL); if (s->eof || s->c - '"') { ighmm_scanner_error (s, "string expected"); goto STOP; } ARRAY_MALLOC (val, maxlen); while (!s->eof && s->c == '"') { if (cmode) { if (scanner_nextcchar (s)) goto STOP; } else { if (scanner_nextchar (s, 1)) goto STOP; } while (s->c - '"' || s->esc) { if (s->eof || ((!s->c || s->c == '\n') && !s->esc)) { ighmm_scanner_error (s, "String not closed"); goto STOP; } if (i + 1 == maxlen) { ARRAY_REALLOC (val, maxlen + 128); maxlen += 128; } if (s->c || len) val[i++] = s->c; if (cmode) { if (scanner_nextcchar (s)) goto STOP; } else { if (scanner_nextchar (s, 1)) goto STOP; } } if (ighmm_scanner_consume (s, '"')) goto STOP; if (scanner_skipspace (s)) goto STOP; } val[i++] = 0; ARRAY_REALLOC (val, i); if (len) *len = i; return (val); STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (val); return (NULL); # undef CUR_PROC } /* ighmm_scanner_get_str */ /*============================================================================*/ char *ighmm_scanner_get_path (scanner_t * s) { #define CUR_PROC "ighmm_scanner_get_path" char *res = scanner_get_string (s); char *p; # if defined(_PPC) || defined(_DOS) || defined(_WINDOWS) if (res) for (p = res; *p; p++) if (*p == '/') *p = '\\'; # else if (res) for (p = res; *p; p++) if (*p == '\\') *p = '/'; # endif return (res); #undef CUR_PROC } /* ighmm_scanner_get_path */ /*============================================================================*/ int ighmm_scanner_get_int (scanner_t * s) { int val = 0; int sign = 0; if (!s || s->err) return (0); if (s->eof) { ighmm_scanner_error (s, "integer expected"); return (0); } if (s->c == '-') { if (scanner_nextchar (s, 1)) return (0); sign = 1; } else if (s->c == '+') { if (scanner_nextchar (s, 1)) return (0); } if (scanner_skipspace (s)) return (0); if (s->c == '\'') { if (scanner_nextcchar (s)) return (0); val = (unsigned char) (s->c); if (scanner_nextchar (s, 1)) return (0); if (s->c - '\'') { if (!s->esc) { ighmm_scanner_error (s, " \' expected"); return (0); } val = (unsigned char) '\\'; } else if (scanner_nextchar (s, 1)) return (0); } else if (!m_scanner_isdigit (s->c)) { if (ighmm_scanner_get_id (s)) return (0); if (!strcmp (s->id, "TRUE")) return (sign ? 0 : 1); else if (!strcmp (s->id, "FALSE")) return (sign ? 1 : 0); if (!strcmp (s->id, "ON")) return (sign ? 0 : 1); else if (!strcmp (s->id, "OFF")) return (sign ? 1 : 0); ighmm_scanner_error (s, "integer value expected"); return (0); } else { int radix = 10; if (s->c == '0') { if (scanner_nextchar (s, 1)) return (0); if (m_scanner_isdigit (s->c)) { val = s->c - '0'; if (scanner_nextchar (s, 1)) return (0); } else switch (s->c) { case 'x': case 'X': radix = 16; break; case '_': radix = 2; break; case 'o': radix = 8; break; } if (radix - 10) { if (scanner_nextchar (s, 1)) return (0); if (scanner_digit (&val, s, radix, 1)) return (0); if (scanner_nextchar (s, 1)) return (0); } } while (!scanner_digit (&val, s, radix, 0)) { if (scanner_nextchar (s, 1)) return (0); } } if (scanner_skipspace (s)) return (0); return (sign ? -val : val); # undef CUR_PROC } /* ighmm_scanner_get_int */ /*============================================================================*/ double ighmm_scanner_get_double (scanner_t * s) { double val = 0; int sign = 0; if (!s || s->err) return (0); if (s->eof) { ighmm_scanner_error (s, "real number expected"); return (0); } if (s->c == '-') { if (scanner_nextchar (s, 1)) return (0); sign = 1; } else if (s->c == '+' && scanner_nextchar (s, 1)) return (0); if (scanner_skipspace (s)) return (0); if (!m_scanner_isdigit (s->c) && s->c - '.') { ighmm_scanner_error (s, "real number expected"); return (0); } while (m_scanner_isdigit (s->c)) { val = 10 * val + (double) (s->c - '0'); if (scanner_nextchar (s, 1)) return (0); } if (s->c == '.') { double factor = 1; if (scanner_nextchar (s, 1)) return (0); while (m_scanner_isdigit (s->c)) { val = 10 * val + (double) (s->c - '0'); if (scanner_nextchar (s, 1)) return (0); factor *= 10; } val /= factor; } if (scanner_skipspace (s)) return (0); return (sign ? -val : val); } /* ighmm_scanner_get_double */ /*============================================================================*/ double ighmm_scanner_get_edouble (scanner_t * s) { double val = 0; int sign = 0; if (!s || s->err) return (0); if (s->eof) { ighmm_scanner_error (s, "real number expected"); return (0); } if (s->c == '-') { if (scanner_nextchar (s, 1)) return (0); sign = 1; } else if (s->c == '+' && scanner_nextchar (s, 1)) return (0); if (scanner_skipspace (s)) return (0); if (!m_scanner_isdigit (s->c) && s->c - '.') { ighmm_scanner_error (s, "real number expected"); return (0); } while (m_scanner_isdigit (s->c)) { val = 10 * val + (double) (s->c - '0'); if (scanner_nextchar (s, 1)) return (0); } if (s->c == '.') { double factor = 1; if (scanner_nextchar (s, 1)) return (0); while (m_scanner_isdigit (s->c)) { val = 10 * val + (double) (s->c - '0'); if (scanner_nextchar (s, 1)) return (0); factor *= 10; } val /= factor; } if (s->c == 'e' || s->c == 'E') { int i; double eval; double efactor = 1; int esign = 0; if (scanner_nextchar (s, 1)) return (0); if (s->c == '-') { if (scanner_nextchar (s, 1)) return (0); esign = 1; } else if (s->c == '+' && scanner_nextchar (s, 1)) return (0); eval = ighmm_scanner_get_int (s); if (eval < 0) return (0); for (i = 0; i < eval; i++) efactor *= 10; if (esign) val /= efactor; else val *= efactor; } if (scanner_skipspace (s)) return (0); return (sign ? -val : val); } /* ighmm_scanner_get_edouble */ /*============================================================================*/ void *ighmm_scanner_get_array (scanner_t * s, int *len, char *type) { #define CUR_PROC "ighmm_scanner_get_array" int size = 0; int typ = scanner_type (type, &size); int maxlen = 16 * size; char *val = NULL; int i = 0; char txt[256]; int err; int mes_stat; if (!s || !type || !len || s->err) goto STOP; if (!typ) { ighmm_scanner_error (s, ighmm_mprintf (txt, sizeof (txt), "unknown type %s ", type)); goto STOP; } if (!len || !s || s->err) goto STOP; if (s->eof) { ighmm_scanner_error (s, ighmm_mprintf (txt, sizeof (txt), "%s array expected ", type)); goto STOP; } if (s->c == ';') { *len = 0; goto STOP; } mes_stat = ighmm_mes_ability (0); val = ighmm_malloc (sizeof (char *) * maxlen); err = !val; ighmm_mes_ability (mes_stat); if (err) { ighmm_mprintf (txt, sizeof (txt), "Not enough memory to read %s array", type); ighmm_scanner_error (s, txt); goto STOP; } while (s->c - ';') { /* Originally: if( i && ighmm_scanner_consume( s, ',' ) ) goto STOP; */ /* Changed: read array without seperator now possible */ if (s->c == ',') ighmm_scanner_consume (s, ','); switch (typ) { case SCANNER_TYPE_CHAR: val[i] = ighmm_scanner_get_int (s); break; case SCANNER_TYPE_INT: *(int *) (val + i) = ighmm_scanner_get_int (s); break; case SCANNER_TYPE_DOUBLE: *(double *) (val + i) = ighmm_scanner_get_double (s); break; case SCANNER_TYPE_EDOUBLE: *(double *) (val + i) = ighmm_scanner_get_edouble (s); break; case SCANNER_TYPE_STRING: *(char **) (val + i) = scanner_get_string (s); break; case SCANNER_TYPE_CSTRING: *(char **) (val + i) = scanner_get_cstring (s); break; default: goto STOP; } i += size; if (s->err) goto STOP; if (i == maxlen) { mes_stat = ighmm_mes_ability (0); err = ighmm_realloc ((void**)&val, sizeof (*val) * (maxlen + 16 * size)); ighmm_mes_ability (mes_stat); if (err) { ighmm_mprintf (txt, sizeof (txt), "Not enough memory to read %s array", type); ighmm_scanner_error (s, txt); goto STOP; } maxlen += 16 * size; } } mes_stat = ighmm_mes_ability (0); ighmm_realloc ((void**)&val, sizeof (*val) * i);/* Do'nt worry if this fails!*/ ighmm_mes_ability (mes_stat); *len = i / size; return (val); STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (val); if (len) *len = 0; return (NULL); # undef CUR_PROC } /* ighmm_scanner_get_array */ /*============================================================================*/ int ighmm_scanner_free_array (int *len, void ***arr) { # define CUR_PROC "ighmm_scanner_free_array" mes_check_ptr (len, return (-1)); mes_check_ptr (arr, return (-1)); while ((*len)-- > 0) { m_free ((*arr)[*len]); } free (*arr); *len = 0; return (0); # undef CUR_PROC } /* ighmm_scanner_free_array */ /*============================================================================*/ int ighmm_scanner_get_index (scanner_t * s, int n) { int index = n - 1; if (!s || s->err) return (0); if (s->eof || s->c - '@') { ighmm_scanner_error (s, "index expected"); return (0); } if (ighmm_scanner_consume (s, '@')) return (0); index = ighmm_scanner_get_int (s); if (s->err) return (0); if (index >= n) ighmm_scanner_error (s, "index too high"); if (ighmm_scanner_consume (s, ';')) return (0); return (index); } /* ighmm_scanner_get_index */ /*============================================================================*/ double ighmm_scanner_get_resolution (scanner_t * s) { double val; if (!s || s->err) return (0); val = ighmm_scanner_get_double (s); if (s->err) return (0); if (ighmm_scanner_get_id (s)) return (0); if (strcmp (s->id, "DPI")) { ighmm_scanner_error (s, "dpi expected"); return (0); } return (val); } /* ighmm_scanner_get_resolution */ /*============================================================================*/ int ighmm_scanner_get_length_x (scanner_t * s) { return (s->x_scale * scanner_get_length (s, s->x_resolution) + 0.5); } /* ighmm_scanner_get_length_x */ /*============================================================================*/ int ighmm_scanner_get_length_y (scanner_t * s) { return (s->y_scale * scanner_get_length (s, s->y_resolution) + 0.5); } /* ighmm_scanner_get_length_y */ #if defined( TEST ) /*============================================================================*/ int scanner_tst (void) { # define CUR_PROC "scanner_tst" scanner_t *s = ighmm_scanner_alloc ("scanner.cfg"); char *char_arr = NULL; int char_len = 0; int *int_arr = NULL; int int_len = 0; double *double_arr = NULL; int double_len = 0; char **string_arr = NULL; int string_len = 0; int res = -1; int i; if (!s) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } while (!s->err && !s->eof) { if (ighmm_scanner_get_name (s)) break; if (ighmm_scanner_consume (s, '=')) break; else if (!strcmp (s->id, "char")) { m_free (char_arr); char_arr = scanner_get_char_array (s, &char_len); } else if (!strcmp (s->id, "int")) { m_free (int_arr); int_arr = scanner_get_int_array (s, &int_len); } else if (!strcmp (s->id, "string")) { m_free (string_arr); string_arr = scanner_get_cstring_array (s, &string_len); } else if (!strcmp (s->id, "double")) { m_free (double_arr); double_arr = scanner_get_double_array (s, &double_len); } else ighmm_scanner_error (s, "unknown identifyer"); if (ighmm_scanner_consume (s, ';')) break; } if (char_arr) { mes_win ("\nchar:\n"); for (i = 0; i < char_len; i++) ighmm_mes (MES_WIN, " '%c'\n", char_arr[i]); } if (int_arr) { mes_win ("\nint:\n"); for (i = 0; i < int_len; i++) ighmm_mes (MES_WIN, " %d\n", int_arr[i]); } if (double_arr) { mes_win ("\ndouble:\n"); for (i = 0; i < double_len; i++) ighmm_mes (MES_WIN, " %f\n", double_arr[i]); } if (string_arr) { mes_win ("\nstring:\n"); for (i = 0; i < string_len; i++) ighmm_mes (MES_WIN, " \"%s\"\n", string_arr[i]); } res = 0; STOP: ighmm_scanner_free (&s); m_free (char_arr); m_free (int_arr); m_free (double_arr); if (string_arr) for (i = 0; i < string_len; i++) m_free (string_arr[i]); m_free (string_arr); return (res); # undef CUR_PROC } /* scanner_tst */ #endif /* defined( TEST ) */ /*----------------------------------------------------------------------------*/ static int scanner_free_d_matrix (double ***matrix, long rows) { # define CUR_PROC "scanner_free_d_matrix" long i; mes_check_ptr (matrix, return (-1)); if (!*matrix) return (0); for (i = 0; i < rows; i++) m_free ((*matrix)[i]); m_free (*matrix); return (0); # undef CUR_PROC } /* scanner_free_d_matrix */ /*============================================================================*/ double **ighmm_scanner_get_d_matrix (scanner_t * s, int *rows, int *cols) { #define CUR_PROC "ighmm_scanner_get_d_matrix" double **matrix = NULL; int local_cols = 0; *rows = *cols = 0; while (!s->eof && !s->err && s->c - '}') { (*rows)++; ARRAY_REALLOC (matrix, *rows); matrix[*rows - 1] = scanner_get_double_array (s, &local_cols); ighmm_scanner_consume (s, ';'); if (s->err) goto STOP; if (*rows > 1) if (local_cols != *cols) { ighmm_scanner_error (s, "rows of variing length in matrix"); goto STOP; } *cols = local_cols; } /* while ... */ return matrix; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ scanner_free_d_matrix (&matrix, *rows); return NULL; #undef CUR_PROC } /* ighmm_scanner_get_d_matrix */ #endif /* GHMM_OBSOLETE */ ghmm-0.9-rc3/ghmm/viterbi.c000775 001750 001750 00000026323 12154244034 015457 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/viterbi.c * Authors: Wasinee Rungsarityotin, Benjamin Georgi * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1991 $ * from $Date: 2007-12-05 11:39:04 -0500 (Wed, 05 Dec 2007) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include #include "ghmm.h" #include "mes.h" #include "mprintf.h" #include "matrix.h" #include "sdmodel.h" #include "ghmm_internals.h" typedef struct local_store_t { double **log_in_a; double **log_b; double *phi; double *phi_new; int **psi; int *path_len; int *topo_order; int topo_order_length; } local_store_t; /*----------------------------------------------------------------------------*/ static int viterbi_free(local_store_t **v, int n, int len) { #define CUR_PROC "viterbi_free" int j; mes_check_ptr(v, return -1); if (!*v) return 0; for (j = 0; j < n; j++) m_free((*v)->log_in_a[j]); m_free((*v)->log_in_a); ighmm_cmatrix_free(&((*v)->log_b), n); m_free((*v)->phi); m_free((*v)->phi_new); /*ighmm_dmatrix_free( &((*v)->psi), len ); */ ighmm_dmatrix_stat_free(&((*v)->psi)); m_free((*v)->path_len); m_free((*v)->topo_order); m_free(*v); return 0; #undef CUR_PROC } /* viterbi_free */ /*----------------------------------------------------------------------------*/ static local_store_t *viterbi_alloc(ghmm_dmodel *mo, int len) { #define CUR_PROC "sdviterbi_alloc" local_store_t *v = NULL; int j; ARRAY_CALLOC(v, 1); /* Allocate the log_in_a's -> individal lenghts */ ARRAY_CALLOC(v->log_in_a, mo->N); for (j = 0; j < mo->N; j++) { ARRAY_CALLOC(v->log_in_a[j], mo->s[j].in_states); } v->log_b = ighmm_cmatrix_alloc(mo->N, mo->M); if (!(v->log_b)) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_CALLOC(v->phi, mo->N); ARRAY_CALLOC(v->phi_new, mo->N); v->psi = ighmm_dmatrix_stat_alloc(len, mo->N); if (!(v->psi)) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_CALLOC(v->path_len, mo->N); v->topo_order_length = 0; ARRAY_CALLOC(v->topo_order, mo->N); return v; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ viterbi_free(&v, mo->N, len); return NULL; #undef CUR_PROC } /* viterbi_alloc */ /*----------------------------------------------------------------------------*/ static void Viterbi_precompute(ghmm_dmodel *mo, int *o, int len, local_store_t *v) { #define CUR_PROC "viterbi_precompute" int i, j, t; /* Precomputing the log(a_ij) */ for (j = 0; j < mo->N; j++) { for (i = 0; i < mo->s[j].in_states; i++) { if (mo->s[j].in_a[i] == 0.0) /* DBL_EPSILON ? */ v->log_in_a[j][i] = +1; /* Not used any further in the calculations */ else v->log_in_a[j][i] = log(mo->s[j].in_a[i]); } } /* Precomputing the log(bj(ot)) */ for (j = 0; j < mo->N; j++) { for (t = 0; t < mo->M; t++) { if (mo->s[j].b[t] == 0.0) /* DBL_EPSILON ? */ v->log_b[j][t] = +1; else v->log_b[j][t] = log(mo->s[j].b[t]); } } #undef CUR_PROC } /* viterbi_precompute */ /*----------------------------------------------------------------------------*/ static void viterbi_silent(ghmm_dmodel *mo, int t, local_store_t *v) { #define CUR_PROC "viterbi_silent" int topocount; int i, St, i_id, max_id; double max_value, value; for (topocount=0; topocount < mo->topo_order_length; topocount++) { St = mo->topo_order[topocount]; if (mo->silent[St]) { /* Silent states */ /* Determine the maximum */ /* max_phi = phi[i] + log_in_a[j][i] ... */ max_value = -DBL_MAX; max_id = -1; for (i = 0; i < mo->s[St].in_states; i++) { i_id = mo->s[St].in_id[i]; if (v->phi[i_id] != +1 && v->log_in_a[St][i] != +1) { value = v->phi[i_id] + v->log_in_a[St][i]; if (value > max_value) { max_value = value; max_id = i_id; } } } /* No maximum found (that is, state never reached) or the output O[t] = 0.0: */ if (max_id < 0) { v->phi[St] = +1; } else { v->phi[St] = max_value; v->psi[t][St] = max_id; v->path_len[St] = v->path_len[max_id] + 1; } } } #undef CUR_PROC } /*============================================================================*/ /** Return the viterbi path of the sequence. */ int *ghmm_dmodel_viterbi(ghmm_dmodel * mo, int *o, int len, int *pathlen, double *log_p) { #define CUR_PROC "ghmm_dmodel_viterbi" int *state_seq = NULL; int t, j, i, i_id, St, max_id; int end_state, next_state, prev_state; int len_path, state_seq_index; int *plen, *exchange; double value, max_value, *temp; local_store_t *v; /* for silent states: initializing path length with a multiple of the sequence length and sort the silent states topological */ if (mo->model_type & GHMM_kSilentStates) { ghmm_dmodel_order_topological(mo); } /* Allocate the matrices log_in_a, log_b,Vektor phi, phi_new, Matrix psi */ v = viterbi_alloc(mo, len); if (!v) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_CALLOC(plen, mo->N); /* Precomputing the log(a_ij) and log(bj(ot)) */ Viterbi_precompute(mo, o, len, v); /* Initialization, that is t = 0 */ for (j = 0; j < mo->N; j++) { if (mo->s[j].pi == 0.0 || v->log_b[j][o[0]] == +1) /* instead of 0, DBL_EPS.? */ v->phi[j] = +1; else { v->phi[j] = log(mo->s[j].pi) + v->log_b[j][o[0]]; v->path_len[j] = 1; } } if (mo->model_type & GHMM_kSilentStates) { /* could go into silent state at t=0 */ viterbi_silent(mo, t = 0, v); } /* t > 0 */ for (t = 1; t < len; t++) { for (j = 0; j < mo->N; j++) { /* initialization of phi, psi */ v->phi_new[j] = +1; v->psi[t][j] = -1; } for (St=0; St < mo->N; St++) { /* Determine the maximum */ /* max_phi = phi[i] + log_in_a[j][i] ... */ if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[St]) { max_value = -DBL_MAX; max_id = -1; for (i = 0; i < mo->s[St].in_states; i++) { i_id = mo->s[St].in_id[i]; if (v->phi[i_id] != +1 && v->log_in_a[St][i] != +1) { value = v->phi[i_id] + v->log_in_a[St][i]; if (value > max_value) { max_value = value; max_id = i_id; } } } /* No maximum found (that is, state never reached) or the output O[t] = 0.0: */ if (max_id >= 0 && v->log_b[St][o[t]] != +1) { v->phi_new[St] = max_value + v->log_b[St][o[t]]; v->psi[t][St] = max_id; plen[St] = v->path_len[max_id] + 1; } } } /* complete time step for emitting states */ /* Exchange pointers */ temp = v->phi; v->phi = v->phi_new; v->phi_new = temp; exchange = v->path_len; v->path_len = plen; plen = exchange; /* complete time step for silent states */ if (mo->model_type & GHMM_kSilentStates) { viterbi_silent(mo, t, v); } } /* Next observation , increment time-step */ /* Termination - find end state */ max_value = -DBL_MAX; end_state = -1; for (j=0; j < mo->N; j++) { if (v->phi[j] != +1 && v->phi[j] > max_value) { max_value = v->phi[j]; end_state = j; } } if (end_state < 0) { /* Sequence can't be generated from the model! */ *log_p = +1; len_path = 1; } else { *log_p = max_value; len_path = v->path_len[end_state]; } /* allocating state_seq array */ ARRAY_CALLOC(state_seq, len_path+1); t = len-1; state_seq_index = len_path-1; state_seq[len_path] = -1; state_seq[state_seq_index--] = end_state; prev_state = end_state; /* backtrace is simple if the path length is known */ for (; state_seq_index >= 0; state_seq_index--) { next_state = v->psi[t][prev_state]; state_seq[state_seq_index] = prev_state = next_state; if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[next_state]) t--; } *pathlen = len_path; if (state_seq_index >= 0 || t > 0) GHMM_LOG_PRINTF(LERROR, LOC, "state_seq_index = %d, t = %d", state_seq_index, t); /* Free the memory space */ viterbi_free(&v, mo->N, len); m_free(plen); return state_seq; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ /* Free the memory space */ *pathlen = -1; viterbi_free(&v, mo->N, len); m_free(plen); m_free(state_seq); return NULL; #undef CUR_PROC } /* ghmm_dmodel_viterbi */ /*============================================================================*/ double ghmm_dmodel_viterbi_logp(ghmm_dmodel * mo, int *o, int len, int *state_seq) { #define CUR_PROC "ghmm_dmodel_viterbi_logp" double log_p = 0.0; int unused; int *vpath = ghmm_dmodel_viterbi(mo, o, len, &unused, &log_p); m_free(vpath); return log_p; #undef CUR_PROC } /* ghmm_dmodel_viterbi_logp */ ghmm-0.9-rc3/NEWS000775 001750 001750 00000000000 12154244040 013373 0ustar00ericeric000000 000000 ghmm-0.9-rc3/ghmmwrapper/ghmmwrapper.i000775 001750 001750 00000016613 12154244034 017754 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmmwrapper.i * Authors: Wasinee Rungsarityotin, Benjamin Georgi, Janne Grunau * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2205 $ * from $Date: 2008-03-18 11:36:40 -0400 (Tue, 18 Mar 2008) $ * last change by $Author: grunau $. * *******************************************************************************/ %module ghmmwrapper %include carrays.i %include cmalloc.i %include cpointer.i %include cstring.i %include constraints.i %include exception.i %include typemaps.i /* include ../ghmm/ghmmconfig.h twice, once for swig and once for CC */ %{ #include "../ghmm/ghmmconfig.h" #include "../ghmm/randvar.h" #include "sclass_change.h" #include "pclasschange.h" %} %include "../ghmm/ghmmconfig.h" %include "sclass_change.h" %include "pclasschange.h" // Constraints on GHMM date types - no NULL pointers as function arguments %apply Pointer NONNULL { ghmm_cmodel * }; %apply Pointer NONNULL { ghmm_cmodel ** }; %apply Pointer NONNULL { ghmm_dmodel * }; %apply Pointer NONNULL { ghmm_dmodel ** }; %apply Pointer NONNULL { ghmm_dpmodel * }; %apply Pointer NONNULL { ghmm_dpmodel ** }; %apply Pointer NONNULL { ghmm_dsmodel * }; %apply Pointer NONNULL { ghmm_dsmodel ** }; %apply Pointer NONNULL { ghmm_cstate * }; %apply Pointer NONNULL { ghmm_dstate * }; %apply Pointer NONNULL { ghmm_dpstate * }; %apply Pointer NONNULL { ghmm_dsstate * }; %apply Pointer NONNULL { ghmm_c_emission * }; %apply Pointer NONNULL { ghmm_cseq * }; %apply Pointer NONNULL { ghmm_cseq ** }; %apply Pointer NONNULL { ghmm_dseq * }; %apply Pointer NONNULL { ghmm_dseq ** }; %apply Pointer NONNULL { ghmm_dpseq * }; %apply Pointer NONNULL { ghmm_dpseq ** }; /*========================================================================== ========================== test for obsolete features ==================== */ #ifdef GHMM_OBSOLETE #define SMO_FILE_SUPPORT 1 #define ASCI_SEQ_FILE 1 #define SEQ_LABEL_FIELD 1 #else #define SMO_FILE_SUPPORT 0 #define ASCI_SEQ_FILE 0 #define SEQ_LABEL_FIELD 0 #endif /* GHMM_OBSOLETE */ /*========================================================================== ========================== constants for model types ===================== */ #define kNotSpecified (0) /** Model is a left-right */ #define kLeftRight (1) /** Model contains silent states (i.e., states without emissions) */ #define kSilentStates (1 << 2) /** Model has states with tied emission probabilities */ #define kTiedEmissions (1 << 3) #define kUntied (-1) /** Model has states emission probabilities conditioned on previous orders */ #define kHigherOrderEmissions (1 << 4) /** Model has background distributions */ #define kBackgroundDistributions (1 << 5) #define kNoBackgroundDistribution (-1) /** Model is a class HMM with labeled states */ #define kLabeledStates (1 << 6) #define kTransitionClasses (1 << 7) #define kDiscreteHMM (1 << 8) #define kContinuousHMM (1 << 9) #define kPairHMM (1 << 10) #define kMultivariate (1 << 11) /* ============== constants ================================================= */ /** Convergence: Halt criterium for Baum-Welch reestimation if the difference of log(P) in two consecutive iterations is smaller than (EPS\_ITER\_BW * log(P)).. */ #define EPS_ITER_BW 0.0001 /** Maximum number of iterations in reestimate */ #define MAX_ITER_BW 500 /*============================================================================ =============== Logging Function Callbacks ================================= */ // Grab a Python function object as a Python object. #if defined(SWIGPYTHON) %typemap(in) PyObject *pyfunc { if (!PyCallable_Check($input)) { PyErr_SetString(PyExc_TypeError, "Need a callable object!"); return NULL; } $1 = $input; } %{ /* This function matches the prototype of the normal C callback function for our widget. However, we use the clientdata pointer for holding a reference to a Python callable object. */ static void PythonCallBack(int level, const char *message, void *clientdata) { PyObject *func, *arglist; // Get Python function func = (PyObject *) clientdata; // Build Python arguments arglist = Py_BuildValue("(is)", level, message); // Call Python PyEval_CallObject(func, arglist); // Trash arguments Py_DECREF(arglist); } %} %inline %{ // Set a Python function object as a callback function // Note : PyObject *pyfunc is remapped with a typemap void set_pylogging(PyObject *pyfunc) { ghmm_set_logfunc(PythonCallBack, (void *) pyfunc); Py_INCREF(pyfunc); } %} #endif /* defined(SWIGPYTHON) */ /*========================================================================== ===== Random Number Generator (RNG) ====================================== */ /* Important! initialise rng */ extern void ghmm_rng_init(void); /* Initialise random timeseed */ extern void ghmm_rng_timeseed(GHMM_RNG * r); %inline %{ void time_seed(void){ ghmm_rng_timeseed(RNG); } %} /* for truncated gaussian pdf */ extern double ighmm_rand_normal_density_trunc(double x, double mean, double u, double a); /*========================================================================== ===== import C structs as shadow classes ================================= */ %define STRUCT_ARRAY(type, name) %inline %{ type* name ## _array_alloc(size_t number) { return calloc(number, sizeof(type)); } type* name ## _array_getRef(type* self, size_t index) { return self+index; } %} %enddef %define REFERENCE_ARRAY(type, name) %inline %{ type** name ## _array_alloc(size_t number) { return calloc(number, sizeof(type*)); } type* name ## _array_getitem(type** self, size_t index) { return self[index]; } void name ## _array_setitem(type** self, size_t index, type* value) { self[index] = value; } %} %enddef // double *log_p is used as additional return value %apply double* OUTPUT {double *log_p}; %apply int* OUTPUT {int *pathlen}; %include wrapper_alphabet.i %include wrapper_cseq.i %include wrapper_dseq.i %include wrapper_dpseq.i %include wrapper_cmodel.i %include wrapper_dmodel.i %include wrapper_dpmodel.i %include wrapper_xmlfile.i %include wrapper_arrays.i ghmm-0.9-rc3/ghmm/smap_classify.c000775 001750 001750 00000023333 12154244034 016646 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/smap_classify.c * Authors: Bernd Wichern * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 1977 $ * from $Date: 2007-11-16 10:49:06 -0500 (Fri, 16 Nov 2007) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include "ghmmconfig.h" #ifdef GHMM_OBSOLETE #include #include #include "ghmm.h" #include "mes.h" #include "sfoba.h" #include "matrix.h" #include "smap_classify.h" #include "ghmm_internals.h" typedef struct local_store_t { double ***alpha; double **scale; double *prob; double **p; double **sum_alpha; double *alpha_1; double *prior; int *error; } local_store_t; /*----------------------------------------------------------------------------*/ static local_store_t *smap_classify_alloc (int mo_number, int states, int T) { #define CUR_PROC "smap_classify_alloc" int i; local_store_t *map = NULL; ARRAY_CALLOC (map, 1); ARRAY_CALLOC (map->alpha, mo_number); for (i = 0; i < mo_number; i++) { map->alpha[i] = ighmm_cmatrix_alloc (T, states); if (!map->alpha[i]) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } } map->scale = ighmm_cmatrix_alloc (mo_number, T); if (!map->scale) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } map->p = ighmm_cmatrix_alloc (mo_number, T + 1); if (!map->p) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } map->sum_alpha = ighmm_cmatrix_alloc (mo_number, T); if (!map->sum_alpha) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } ARRAY_CALLOC (map->prob, mo_number); ARRAY_CALLOC (map->alpha_1, mo_number); ARRAY_CALLOC (map->error, mo_number); ARRAY_CALLOC (map->prior, mo_number); return map; STOP: /* Label STOP from ARRAY_[CM]ALLOC */ return NULL; #undef CUR_PROC } /*----------------------------------------------------------------------------*/ static int smap_classify_free (local_store_t ** map, int mo_number, int T) { # define CUR_PROC "smap_classify_free" int i; mes_check_ptr (map, return (-1)); if (!*map) return (0); m_free ((*map)->prob); m_free ((*map)->alpha_1); m_free ((*map)->error); m_free ((*map)->prior); ighmm_cmatrix_free (&((*map)->scale), mo_number); ighmm_cmatrix_free (&((*map)->p), mo_number); ighmm_cmatrix_free (&((*map)->sum_alpha), mo_number); for (i = 0; i < mo_number; i++) ighmm_cmatrix_free (&((*map)->alpha[i]), T); m_free (*map); return 0; #undef CUR_PROC } /*============================================================================*/ /* Maximum A Posteriori Classification Algorithm (MAPCA): given a field of models and one sequence and suppose the sequence has been produced by one of these models. This algorithm calculates for each model the probability, that the seq. comes from the model. This bayesian approach uses a prior for the models. If none is specified equal prob. is assumed. The maps are copied into "result", which has to be of dimension "smo_number" Ref.: A. Kehagias: Bayesian Classification of HMM, Math. Comp. Modelling (1995) */ int ghmm_smap_classify (ghmm_cmodel ** smo, double *result, int smo_number, double *O, int T) { #define CUR_PROC "ghmm_smap_classify" int t, n, m, max_model = -1, build = 0; /* time, states, models */ double log_p, denom_26, sum = 0.0, max_result = 0; local_store_t *map = NULL; if (smo == NULL || smo_number <= 0 || O == NULL || T < 0) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } map = smap_classify_alloc (smo_number, smo[0]->N, T); /* no prior defined --> same prior for all models */ for (m = 0; m < smo_number; m++) if (smo[m]->prior == -1) map->prior[m] = 1 / (double) smo_number; else map->prior[m] = smo[m]->prior; for (m = 0; m < smo_number; m++) sum += map->prior[m]; if (fabs (1 - sum) > 0.0001) { GHMM_LOG(LCONVERTED, "Sum of model priors != 1 or mixing of priors and non-priors \n"); goto STOP; } /* for all models */ for (m = 0; m < smo_number; m++) { map->p[m][0] = map->prior[m]; /* (22) */ map->alpha_1[m] = 1 / (double) smo_number; /* (23) */ /* forward alg. (24) */ if (ghmm_cmodel_forward (smo[m], O, T, NULL, map->alpha[m], map->scale[m], &log_p) == -1) { /* The sequence can't be generated from this model. */ map->error[m] = 1; continue; } build = 1; for (t = 0; t < T; t++) { for (n = 0; n < smo[0]->N; n++) map->sum_alpha[m][t] += map->alpha[m][t][n]; /* Sums (25) */ if (map->sum_alpha[m][t] == 0) { GHMM_LOG(LCONVERTED, "sum_alpha = 0\n"); goto STOP; } /* Another solution ??? */ } } if (!build) { GHMM_LOG(LCONVERTED, "Prob. = 0 for all models\n"); goto STOP; } for (t = 0; t < T; t++) { denom_26 = 0.0; for (m = 0; m < smo_number; m++) { if (!map->error[m]) { if (t != 0) map->prob[m] = map->sum_alpha[m][t] * map->scale[m][t] / /* (25) */ map->sum_alpha[m][t - 1]; else map->prob[m] = map->sum_alpha[m][t] * map->scale[m][t]; /* (25) */ denom_26 += map->prob[m] * map->p[m][t]; } else map->prob[m] = 0.0; /* Seq. cannot be generated by this model */ } for (m = 0; m < smo_number; m++) { if (denom_26 != 0) map->p[m][t + 1] = map->prob[m] * map->p[m][t] / denom_26; /* (26) */ else { GHMM_LOG(LCONVERTED, "denom_26 == 0!\n"); goto STOP; } } } /* copy into result and find best model */ max_result = 0.0; for (m = 0; m < smo_number; m++) { result[m] = map->p[m][T]; if (result[m] > max_result) { max_result = result[m]; max_model = m; } } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ smap_classify_free (&map, smo_number, T); return max_model; #undef CUR_PROC } /* Alternative to MAPCA (smap_classify); calculate p[m] directly using Bayes' theorem, instead of recursive over t. p(m | O) = p(O | m) * p(m) / (sum_i p(O | i) * p(i)) Same result? */ int ghmm_smap_bayes (ghmm_cmodel ** smo, double *result, int smo_number, double *O, int T) { #define CUR_PROC "ghmm_smap_bayes" double *prior, *log_p; double sum = 0.0, p_von_O = 0.0, max_result = 0.0; int *error=NULL; int found_model = 0, err = 0; int m, max_model = -1; /* nothing to do here */ if (smo_number == 1) { result[0] = 1.0; return 0; } for (m = 0; m < smo_number; m++) result[m] = 0; ARRAY_CALLOC (prior, smo_number); ARRAY_CALLOC (log_p, smo_number); ARRAY_CALLOC (error, smo_number); if (smo == NULL || smo_number <= 0 || O == NULL || T < 0) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; } /* no prior defined --> same prior for all models */ for (m = 0; m < smo_number; m++) if (smo[m]->prior == -1) prior[m] = 1 / (double) smo_number; else prior[m] = smo[m]->prior; for (m = 0; m < smo_number; m++) sum += prior[m]; if (fabs (1 - sum) > 0.0001) { GHMM_LOG(LCONVERTED, "Sum of model priors != 1 or mixing of priors and non-priors \n"); for (m = 0; m < smo_number; m++) printf ("%.6f ", prior[m]); printf ("\n"); goto STOP; } /* Calculate log_p for every model; combined with prior gives the likelihood for O, given all models */ for (m = 0; m < smo_number; m++) if (ghmm_cmodel_logp (smo[m], O, T, &log_p[m]) == -1) { error[m] = 1; } else { error[m] = 0; p_von_O += exp (log_p[m]) * prior[m]; found_model = 1; } if (p_von_O == 0) { GHMM_LOG(LCONVERTED, "P(O) = 0!\n"); err = 1; } if (!found_model) { GHMM_LOG(LCONVERTED, "-1 from ghmm_cmodel_logp for all models\n"); err = 1; } if (err) goto STOP; /* Likelihood for the models, given O */ for (m = 0; m < smo_number; m++) { if (!error[m]) { result[m] = exp (log_p[m]) * prior[m] / p_von_O; if (result[m] > max_result) { max_model = m; max_result = result[m]; } } } /* TEST */ if (max_model == -1) { printf ("smap_bayes: max_model == -1\n"); for (m = 0; m < smo_number; m++) if (!error[m]) printf ("%f %.4f %.4f; ", log_p[m], prior[m], p_von_O); printf ("\n"); } STOP: /* Label STOP from ARRAY_[CM]ALLOC */ m_free (prior); m_free (log_p); m_free (error); return max_model; #undef CUR_PROC } #endif /* GHMM_OBSOLETE */ ghmm-0.9-rc3/HMMEd/000755 000000 000000 00000000000 12201221260 013633 5ustar00rootroot000000 000000 ghmm-0.9-rc3/Makefile.in000644 000000 000000 00000072213 12176776667 015060 0ustar00rootroot000000 000000 # Makefile.in generated by automake 1.11.6 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software # Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ # author : Achim Gaedke # filename : ghmm/Makefile.am # created : DATE: April 2001 # $Id: Makefile.am 2270 2009-04-27 14:29:38Z grunau $ # # Copyright (C) 1998-2005 Alexander Schliep # Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln # Copyright (C) 2002-2005 Max-Planck-Institut fuer Molekulare Genetik, Berlin # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Library General Public # License as published by the Free Software Foundation; either # version 2 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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Generated from configure.in by autoheader. */ /* use matrix operations from lapack */ #undef DO_WITH_ATLAS /* use GSL functions instead of ghmm equivalents */ #undef DO_WITH_GSL /* use hack to estimate only diagonal covariance matrix */ #undef DO_WITH_GSL_DIAGONAL_HACK /* gsl_histogram_set_ranges_uniform is defined */ #undef GSL_HISTOGRAM_SET_RANGES_UNIFORM /* root solver allocation takes only one argument */ #undef GSL_ROOT_FSLOVER_ALLOC_WITH_ONE_ARG /* clapack_dgetrf exists */ #undef HAVE_CLAPACK_DGETRF /* clapack_dgetri exists */ #undef HAVE_CLAPACK_DGETRI /* clapack_dpotrf exists */ #undef HAVE_CLAPACK_DPOTRF /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* struct gsl_interval exists */ #undef HAVE_GSL_INTERVAL /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the `bsd' library (-lbsd). */ #undef HAVE_LIBBSD /* Define to 1 if you have the `m' library (-lm). */ #undef HAVE_LIBM /* Define to 1 if you have the `pthread' library (-lpthread). */ #undef HAVE_LIBPTHREAD /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to the sub-directory in which libtool stores uninstalled libraries. */ #undef LT_OBJDIR /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Define to 1 if you can safely include both and . */ #undef TIME_WITH_SYS_TIME /* Define to 1 if your declares `struct tm'. */ #undef TM_IN_SYS_TIME /* Version number of package */ #undef VERSION /* Define to empty if `const' does not conform to ANSI C. */ #undef const /* Define to `unsigned int' if does not define. */ #undef size_t ghmm-0.9-rc3/ghmm/rng.h000775 001750 001750 00000006553 12154244034 014611 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/rng.h * Authors: Alexander Schliep, Ben Rich * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2087 $ * from $Date: 2008-02-28 17:36:54 -0500 (Thu, 28 Feb 2008) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_RNG_H #define GHMM_RNG_H #include "ghmmconfig.h" /* use mersenne twister as default */ #ifndef GHMM_RNG_BSD #ifndef GHMM_RNG_GSL #ifndef GHMM_RNG_MERSENNE_TWISTER #define GHMM_RNG_MERSENNE_TWISTER #endif #endif #endif /* ----- Mersenne Twister -------------------------------------------------- */ #ifdef GHMM_RNG_MERSENNE_TWISTER typedef char ghmm_rng_state_t; typedef ghmm_rng_state_t GHMM_RNG; #endif /* GHMM_RNG_MERSENNE_TWISTER */ /* ----- BSD --------------------------------------------------------------- */ #ifdef GHMM_RNG_BSD #include typedef char ghmm_rng_state_t[8]; typedef ghmm_rng_state_t GHMM_RNG; #endif /* GHMM_RNG_BSD */ /* ----- GSL --------------------------------------------------------------- */ #ifdef GHMM_RNG_GSL #include #include /* Types defined in GSL */ typedef gsl_rng GHMM_RNG; #endif /* GHMM_RNG_GSL */ /** @name rng Initialization for the random number generator */ /** */ extern GHMM_RNG *RNG; #ifdef __cplusplus extern "C" { #endif /** */ void ghmm_rng_init (void); /** */ void ghmm_rng_timeseed (GHMM_RNG * r); /* ----- Mersenne Twister and BSD RNG -------------------------------------- */ #ifdef GHMM_RNG_GSL /* Functions defined in GSL */ #define GHMM_RNG_SET gsl_rng_set #define GHMM_RNG_UNIFORM gsl_rng_uniform #define GHMM_RNG_NAME gsl_rng_name #else /* Functions */ #define GHMM_RNG_SET ghmm_rng_set #define GHMM_RNG_UNIFORM ghmm_rng_uniform #define GHMM_RNG_NAME ghmm_rng_name void ghmm_rng_set (GHMM_RNG * aState, unsigned long int seed); double ghmm_rng_uniform (GHMM_RNG * r); const char *ghmm_rng_name (GHMM_RNG * r); #endif /* not GHMM_RNG_GSL */ #ifdef __cplusplus } #endif #endif /* GHMM_RNG_H */ ghmm-0.9-rc3/install-sh000755 000000 000000 00000033256 12026454250 014772 0ustar00rootroot000000 000000 #!/bin/sh # install - install a program, script, or datafile scriptversion=2011-01-19.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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See the GNU # Library General Public License for more details. # # You should have received a copy of the GNU Library General Public # License along with this library; if not, write to the Free # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # # # # This file is version $Revision: 1.29 $ # from $Date: 2005/02/22 11:12:56 $ # last change by $Author: schliep $. # ################################################################################ import HMMEditor import Tkinter if __name__ == '__main__': # Overide default colors for widgets ... maybe shouldnt be doing that for Windows? tk = Tkinter.Tk() tk.option_add('*ActiveBackground','#EEEEEE') tk.option_add('*background','#DDDDDD') tk.option_add('Tk*Scrollbar.troughColor','#CACACA') HMMEditor = HMMEditor.HMMGraphEditor(tk) HMMEditor.NewGraph() import logging log = logging.getLogger("HMMEd") HMMEditor.mainloop() ghmm-0.9-rc3/ghmm/rng.c000775 001750 001750 00000006602 12154244034 014577 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/rng.c * Authors: Alexander Schliep * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2267 $ * from $Date: 2009-04-24 11:01:58 -0400 (Fri, 24 Apr 2009) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifdef HAVE_CONFIG_H # include "../config.h" #endif #include #include #include "rng.h" #include "math.h" #include "time.h" /* The global RNG */ GHMM_RNG *RNG; /* ----- Mersenne Twister -------------------------------------------------- */ #ifdef GHMM_RNG_MERSENNE_TWISTER #include "mt19937ar.c" static ghmm_rng_state_t *ighmm_rng_state; static char ighmm_rng_name[] = "Mersenne Twister"; void ghmm_rng_set(GHMM_RNG * r, unsigned long int seed) { init_genrand(seed); } double ghmm_rng_uniform(GHMM_RNG * r) { return genrand_real2(); } const char *ghmm_rng_name(GHMM_RNG * r) { return ighmm_rng_name; } void ghmm_rng_init(void) { initstate(1, ighmm_rng_state, sizeof(ghmm_rng_state_t)); RNG = ighmm_rng_state; } #endif /* GHMM_RNG_MERSENNE_TWISTER */ /* ----- BSD --------------------------------------------------------------- */ #ifdef GHMM_RNG_BSD static ghmm_rng_state_t ighmm_rng_state; static char ighmm_rng_name[] = "random"; void ghmm_rng_set(GHMM_RNG * r, unsigned long int seed) { srandom(seed); } double ghmm_rng_uniform(GHMM_RNG * r) { return ((double)random()) / (RAND_MAX + 1.0); } const char *ghmm_rng_name(GHMM_RNG * r) { return ighmm_rng_name; } void ghmm_rng_init(void) { initstate(1, ighmm_rng_state, sizeof(ghmm_rng_state_t)); RNG = &ighmm_rng_state; } #endif /* "GHMM_RNG_BSD */ /* ----- GSL --------------------------------------------------------------- */ #ifdef GHMM_RNG_GSL void ghmm_rng_init(void) { gsl_rng_env_setup(); RNG = gsl_rng_alloc(gsl_rng_default); } #endif /* GHMM_RNG_GSL */ void ghmm_rng_timeseed(GHMM_RNG * r) { unsigned long tm; /* Time seed */ unsigned int timeseed; timeseed = time(NULL); srand(timeseed); tm = rand(); GHMM_RNG_SET(r, tm); /*printf("# using rng '%s' seed=%ld\n", GHMM_RNG_NAME(r), tm); */ fflush(stdout); } ghmm-0.9-rc3/ghmm/ghmm.h000664 001750 001750 00000013757 12154244034 014754 0ustar00ericeric000000 000000 /******************************************************************************* * * This file is part of the General Hidden Markov Model Library, * GHMM version __VERSION__, see http://ghmm.org * * Filename: ghmm/ghmm/ghmm.h * Authors: Alexander Schliep, Janne Grunau * * Copyright (C) 1998-2004 Alexander Schliep * Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln * Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, * Berlin * * Contact: schliep@ghmm.org * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the Free * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * * * This file is version $Revision: 2277 $ * from $Date: 2009-04-28 08:44:31 -0400 (Tue, 28 Apr 2009) $ * last change by $Author: grunau $. * *******************************************************************************/ #ifndef GHMM_H #define GHMM_H #ifdef __cplusplus extern "C" { #endif #include "ghmmconfig.h" /*! \mainpage GHMM library * * The General Hidden Markov Model library (GHMM) is a freely available * LGPL-ed C library implementing efficient data structures and algorithms * for basic and extended HMMs. The development is hosted at * Sourceforge, * where you have access to the Subversion repository, mailing lists and forums. * * The GHMM is developed by the * Algorithmics group at the * Max Planck Institute for Molecular Genetics. * * \par Features: * - Discrete and continous emissions * - Mixtures of PDFs for continous emissions * - Non-homogenous Markov chains * - Pair HMMs (contributed by Genoscope) * - Clustering and mixture modelling for HMMs * - Graphical Editor HMMEd * - Python bindings * - XML-based file format * * \author Achim Gaedke * \author Alexander Riemer * \author Alexander Schliep * \author Andrea Weisse * \author Barthel Steckemetz * \author Benjamin Georgi * \author Berhard Knab * \author Bernd Wichern * \author Christoph Hafemeister * \author Ivan Costa Filho * \author Janne Grunau * \author Mathias Heinig * \author Peter Pipenbacher * \author Sebastian Meller * \author Thordis Linda Thorarinsdottir * \author Utz Pape * \author Wasinee Rungsarityotin * */ /**@name GHMM-Globals */ /*@{ (Doc++-Group: globals) */ /** @name type_constants Constants giving model variations */ #define GHMM_kNotSpecified (0) /** Model is a left-right */ #define GHMM_kLeftRight (1) /** Model contains silent states (i.e., states without emissions) */ #define GHMM_kSilentStates (1 << 2) /** Model has states with tied emission probabilities */ #define GHMM_kTiedEmissions (1 << 3) #define GHMM_kUntied (-1) /** Model has states emission probabilities conditioned on previous orders */ #define GHMM_kHigherOrderEmissions (1 << 4) /** Model has background distributions */ #define GHMM_kBackgroundDistributions (1 << 5) #define GHMM_kNoBackgroundDistribution (-1) /** Model is a class HMM with labeled states */ #define GHMM_kLabeledStates (1 << 6) #define GHMM_kTransitionClasses (1 << 7) #define GHMM_kDiscreteHMM (1 << 8) #define GHMM_kContinuousHMM (1 << 9) #define GHMM_kPairHMM (1 << 10) #define GHMM_kMultivariate (1 << 11) /*@} (Doc++-Group: GHMM-Globals) */ /*@{ (Doc++-Group: Konstanten) */ /** Convergence: Halt criterium for Baum-Welch reestimation if the difference of log(P) in two consecutive iterations is smaller than (GHMM_EPS_ITER_BW * log(P)) */ #define GHMM_EPS_ITER_BW 0.0001 /** If the absolute difference of two numbers is smaller the GHMM_EPS_PREC, then the numbers are equal. (Instead of using zero ) */ #define GHMM_EPS_PREC 1E-8 /** Minimum value for U */ #define GHMM_EPS_U 1E-4 /** Maximum number of iterations in reestimate */ #define GHMM_MAX_ITER_BW 500 /** Maximum length of a sequence */ #define GHMM_MAX_SEQ_LEN 1000000 /** Maximum number of sequences */ #define GHMM_MAX_SEQ_NUMBER 1500000 /** A value that is put in for log_p in the calculation of the objective function if ghmm_cmodel_logp returns -1 (error). */ #define GHMM_PENALTY_LOGP -500.0 /** The left limit for the normal density */ #define GHMM_EPS_NDT 0.1 /*@} (Doc++-Group: Constants) */ /*@{ (Doc++-Group: Logging) */ void ghmm_set_logfunc(void (* fptr)(int, const char *, void *), void * clientdata); void ghmm_set_loglevel(int level); /*@} (Doc++-Group: Logging) */ /*@{ (Doc++-Group: Common data structures) */ /** Mapping between symbols of the distribution and integers [0,M) */ typedef struct { int id; char* description; unsigned int size; char** symbols; } ghmm_alphabet; /** A container for background distributions to be used in the reestimation. * * Model has an ID (== index) to be used for the arrays * background_distributions.order and background_distributions.b */ typedef struct { /** Number of distributions */ int n; /** Number of symbols in alphabet */ int m; /** Order of the respective distribution */ int *order; /** The probabilities */ double **b; /** string ids of the background distributions */ char **name; } ghmm_dbackground; /*@} (Doc++-Group: Common data structures) */ #ifdef __cplusplus } #endif #endif /* GHMM_H */ ghmm-0.9-rc3/HMMEd/Makefile.in000644 000000 000000 00000050221 12176776667 015745 0ustar00rootroot000000 000000 # Makefile.in generated by automake 1.11.6 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software # Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ # filename : /zpr/bspk/src/hmm/ghmm/ghmm/Makefile.am # created : DATE: April 2001 # $Id: Makefile.am 1828 2007-05-16 12:27:49Z grunau $ # # Copyright (C) 1998-2005 Alexander Schliep # Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln # Copyright (C) 2002-2005 Max-Planck-Institut fuer Molekulare Genetik, Berlin # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Library General Public # License as published by the Free Software Foundation; either # version 2 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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// typemap to convert a python list of integers to array of ints %typemap(in) (int *pylist, size_t length) { int i; if (PySequence_Check($input)) { $2 = PySequence_Size($input); $1 = int_array_alloc($2); if (!$1) { PyErr_SetString(PyExc_TypeError,"Could not allocate a int_array with $2 entries"); return NULL; } for (i = 0; i < $2; i++) { PyObject *o = PySequence_GetItem($input,i); if (!PyInt_Check(o)) { Py_XDECREF(o); PyErr_SetString(PyExc_ValueError,"Expecting a sequence of integers"); free($1); return NULL; } $1[i] = (int)PyInt_AsLong(o); Py_DECREF(o); } } else { PyErr_SetString(PyExc_TypeError,"Expecting a sequence"); return NULL; } } // ignore the input value for int array to python list conversion %typemap(in, numinputs=0) size_t *int_array_length (size_t temp) { $1 = &temp; } // convert array of ints to python list %typemap(argout) (size_t *int_array_length) { int i; Py_XDECREF($result); /* Blow away any previous result */ if (result) { $result = PyList_New(*$1); for (i=0; i<*$1; i++) { PyList_SetItem($result, i, PyInt_FromLong(result[i])); } } else { PyErr_SetString(PyExc_ValueError,"got a null pointer"); return NULL; } } // typemap to convert a python list of floats to array of doubles %typemap(in) (double *pylist, size_t length) { int i; if (PySequence_Check($input)) { $2 = PySequence_Size($input); $1 = double_array_alloc($2); if (!$1) { PyErr_SetString(PyExc_TypeError,"Could not allocate a double_array with $2 entries"); return NULL; } for (i = 0; i < $2; i++) { PyObject *o = PySequence_GetItem($input,i); if (PyFloat_Check(o)) { $1[i] = PyFloat_AsDouble(o); Py_DECREF(o); } // conversion from int to double is without loss else if (PyInt_Check(o)) { $1[i] = (double)PyInt_AsLong(o); Py_DECREF(o); } else { Py_XDECREF(o); PyErr_SetString(PyExc_ValueError,"Expecting a sequence of numbers"); free($1); return NULL; } } } else { PyErr_SetString(PyExc_TypeError,"Expecting a sequence"); return NULL; } } // ignore the input value for double array to python list conversion %typemap(in, numinputs=0) size_t *double_array_length (size_t temp) { $1 = &temp; } // convert array of doubles to python list %typemap(argout) (size_t *double_array_length) { int i; Py_XDECREF($result); /* Blow away any previous result */ if (result) { $result = PyList_New(*$1); for (i=0; i<*$1; i++) { PyList_SetItem($result, i, PyFloat_FromDouble(result[i])); } } else { PyErr_SetString(PyExc_ValueError,"got a null pointer"); return NULL; } } %define ARRAY(type) %inline %{ type* type ## _array_alloc(size_t length) { return malloc(length*sizeof(type)); } type type ## _array_getitem(type* self, size_t index) { return self[index]; } void type ## _array_setitem(type* self, size_t index, type value) { self[index] = value; } /* type* list2 ## type ## _array(type* pylist, size_t length) { return pylist; } type* type ## _array2list(type* array, size_t length, size_t* type ## _array_lentgh) { *type ## _array_lentgh = length; return array; } */ %} %enddef ARRAY(int) ARRAY(long) ARRAY(double) %inline %{ int *list2int_array(int *pylist, size_t length) { return pylist; } int *int_array2list(int *array, size_t length, size_t *int_array_length) { *int_array_length = length; return array; } double *list2double_array(double *pylist, size_t length) { return pylist; } double *double_array2list(double *array, size_t length, size_t *double_array_length) { *double_array_length = length; return array; } %} %define MATRIX(type) %inline %{ type** type ## _matrix_alloc(size_t rows, size_t cols) { int i; type** mat = malloc(rows * sizeof(type*)); for (i=0; i