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/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2015 Douglas L. Theobald
This file is part of THESEUS.
THESEUS is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as
published by the Free Software Foundation, either version 3 of
the License, or (at your option) any later version.
THESEUS is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public
License along with THESEUS in the file 'COPYING'. If not, see
<http://www.gnu.org/licenses/>.
-/_|:|_|_\-
*/
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <ctype.h>
#include <math.h>
#include <float.h>
#include <errno.h>
#include "DistMat.h"
DISTMAT
*DISTMATalloc(int ntax)
{
int i;
int name_size = 256;
DISTMAT *distmat = NULL;
distmat = (DISTMAT *) malloc(sizeof(DISTMAT));
distmat->taxa = (char **) malloc(ntax * sizeof(char *));
distmat->dist = (double **) malloc(ntax * sizeof(double *));
distmat->flag = (int **) malloc(ntax * sizeof(int *));
for (i = 0; i < ntax; ++i)
{
distmat->dist[i] = (double *) calloc(ntax, sizeof(double));
distmat->flag[i] = (int *) calloc(ntax, sizeof(int));
distmat->taxa[i] = (char *) malloc(name_size * sizeof(char));
}
distmat->ntax = ntax;
return(distmat);
}
void
DISTMATdestroy(DISTMAT **distmat_ptr)
{
DISTMAT *distmat = *distmat_ptr;
int i;
for (i = 0; i < distmat->ntax; ++i)
{
free(distmat->dist[i]);
free(distmat->flag[i]);
free(distmat->taxa[i]);
}
free(distmat->taxa);
free(distmat->dist);
free(distmat->flag);
free(distmat);
*distmat_ptr = NULL;
}
void
print_NX_distmat(DISTMAT *distmat, char *NXfile_name)
{
int i, j;
FILE *NXfile_ptr = NULL;
NXfile_ptr = fopen(NXfile_name, "w");
fprintf(NXfile_ptr, "#NEXUS\n\n");
fprintf(NXfile_ptr, "begin taxa;\n");
fprintf(NXfile_ptr, " dimensions ntax=%d;\n", distmat->ntax);
fprintf(NXfile_ptr, " taxlabels\n");
for (i = 0; i < distmat->ntax; ++i)
fprintf(NXfile_ptr, " %-s\n", distmat->taxa[i]);
fprintf(NXfile_ptr, " ;\nend;\n\n");
fprintf(NXfile_ptr, "begin distances;\n");
fprintf(NXfile_ptr, " format\n");
fprintf(NXfile_ptr, " triangle=lower;\n");
/*fprintf(NXfile_ptr, " missing=?;\n");*/
fprintf(NXfile_ptr, " matrix\n");
fprintf(NXfile_ptr, " [");
for (i = 0; i < distmat->ntax; ++i)
fprintf(NXfile_ptr, " %8.8s", distmat->taxa[i]);
fprintf(NXfile_ptr, "]\n");
for (i = 0; i < distmat->ntax; ++i) /* for all taxa (down the row) */
{
fprintf(NXfile_ptr, " %-12.12s", distmat->taxa[i]);
for (j = 0; j <= i; ++j) /* for each column from 0 up to the diagonal */
{
fprintf(NXfile_ptr, " %8.6f", distmat->dist[i][j]);
}
fprintf(NXfile_ptr, "\n"); /* end the row */
}
fprintf(NXfile_ptr, " [");
for (i = 0; i < distmat->ntax; ++i)
fprintf(NXfile_ptr, " %8.8s", distmat->taxa[i]);
fprintf(NXfile_ptr, "]\n");
fprintf(NXfile_ptr, ";\nend;\n\n");
//fprintf(stdout, "\n\nNEXUS file \'%s\' written out. \n", NXfile_name);
/*fprintf(NXfile_ptr, "begin paup;\n dset distance=user;\n upgma;\nend;\n\n");
*/
fclose(NXfile_ptr);
}
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