1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
|
/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2014 Douglas L. Theobald
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the:
Free Software Foundation, Inc.,
59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA
-/_|:|_|_\-
*/
#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);
}
|
