clustalomega: clustalomega/clustal-omega-0.2.0/src/squid/phylip.c annotate

annotate clustalomega/clustal-omega-0.2.0/src/squid/phylip.c @ 0:ff1768533a07

Migrated tool version 0.2 from old tool shed archive to new tool shed repository

author	clustalomega
date	Tue, 07 Jun 2011 17:04:25 -0400
parents
children

rev	line source
0 ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	1 /*****************************************************************
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	2 * SQUID - a library of functions for biological sequence analysis
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	3 * Copyright (C) 1992-2002 Washington University School of Medicine
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	4 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	5 * This source code is freely distributed under the terms of the
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	6 * GNU General Public License. See the files COPYRIGHT and LICENSE
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	7 * for details.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	8 *****************************************************************/
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	9
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	10 /* phylip.c
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	11 * SRE, Mon Jun 14 14:08:33 1999 [St. Louis]
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	12 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	13 * Import/export of PHYLIP interleaved multiple sequence alignment
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	14 * format files.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	15 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	16 * RCS $Id: phylip.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: phylip.c,v 1.1 1999/07/15 22:29:20 eddy Exp)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	17 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	18
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	19 #include <stdio.h>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	20 #include <stdlib.h>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	21 #include <string.h>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	22 #include <ctype.h>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	23 #include "squid.h"
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	24 #include "msa.h"
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	25
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	26 #ifdef TESTDRIVE_PHYLIP
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	27 /*****************************************************************
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	28 * phylip.c test driver:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	29 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	30 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	31 int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	32 main(int argc, char **argv)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	33 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	34 MSAFILE *afp;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	35 MSA *msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	36 char *file;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	37
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	38 file = argv[1];
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	39
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	40 if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	41 Die("Couldn't open %s\n", file);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	42
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	43 printf("format %d\n", afp->format);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	44
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	45 while ((msa = ReadPhylip(afp)) != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	46 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	47 WritePhylip(stdout, msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	48 MSAFree(msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	49 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	50
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	51 MSAFileClose(afp);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	52 exit(0);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	53 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	54 /******************************************************************/
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	55 #endif /* testdrive_phylip */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	56
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	57
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	58
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	59 /* Function: ReadPhylip()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	60 * Date: SRE, Fri Jun 18 12:59:37 1999 [Sanger Centre]
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	61 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	62 * Purpose: Parse an alignment from an open Phylip format
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	63 * alignment file. Phylip is a single-alignment format.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	64 * Return the alignment, or NULL if we have no data.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	65 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	66 * Args: afp - open alignment file
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	67 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	68 * Returns: MSA * - an alignment object
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	69 * Caller responsible for an MSAFree()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	70 * NULL if no more alignments
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	71 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	72 MSA *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	73 ReadPhylip(MSAFILE *afp)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	74 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	75 MSA *msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	76 char s, s1, *s2;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	77 char name[11]; /* seq name max len = 10 char */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	78 int nseq, alen;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	79 int idx; /* index of current sequence */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	80 int slen;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	81 int nblock;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	82
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	83 if (feof(afp->f)) return NULL;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	84
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	85 /* Skip until we see a nonblank line; it's the header,
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	86 * containing nseq/alen
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	87 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	88 nseq = 0; alen = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	89 while ((s = MSAFileGetLine(afp)) != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	90 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	91 if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	92 if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	93 Die("Failed to parse nseq/alen from first line of PHYLIP file %s\n", afp->fname);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	94 if (! IsInt(s1) \|\| ! IsInt(s2))
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	95 Die("nseq and/or alen not an integer in first line of PHYLIP file %s\n", afp->fname);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	96 nseq = atoi(s1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	97 alen = atoi(s2);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	98 break;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	99 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	100
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	101 msa = MSAAlloc(nseq, 0);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	102 idx = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	103 nblock = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	104 while ((s = MSAFileGetLine(afp)) != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	105 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	106 /* ignore blank lines. nonblank lines start w/ nonblank char */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	107 if (isspace(*s)) continue;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	108 /* First block has seq names */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	109 if (nblock == 0) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	110 strncpy(name, s, 10);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	111 name[10] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	112 GKIStoreKey(msa->index, name);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	113 msa->sqname[idx] = sre_strdup(name, -1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	114 s += 10;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	115 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	116 /* be careful of trailing whitespace on lines */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	117 if ((s1 = sre_strtok(&s, WHITESPACE, &slen)) == NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	118 Die("Failed to parse sequence at line %d of PHYLIP file %s\n",
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	119 afp->linenumber, afp->fname);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	120 msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], s1, slen);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	121
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	122 idx++;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	123 if (idx == nseq) { idx = 0; nblock++; }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	124 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	125 msa->nseq = nseq;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	126 MSAVerifyParse(msa); /* verifies; sets alen, wgt; frees sqlen[] */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	127 return msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	128 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	129
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	130
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	131
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	132 /* Function: WritePhylip()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	133 * Date: SRE, Fri Jun 18 12:07:41 1999 [Sanger Centre]
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	134 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	135 * Purpose: Write an alignment in Phylip format to an open file.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	136 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	137 * Args: fp - file that's open for writing.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	138 * msa - alignment to write.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	139 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	140 * Returns: (void)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	141 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	142 void
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	143 WritePhylip(FILE fp, MSA msa)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	144 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	145 int idx; /* counter for sequences */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	146 int cpl = 50; /* 50 seq char per line */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	147 char buf[51]; /* buffer for writing seq */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	148 int pos;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	149
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	150 /* First line has nseq, alen
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	151 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	152 fprintf(fp, " %d %d\n", msa->nseq, msa->alen);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	153
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	154 /* Alignment section.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	155 * PHYLIP is a multiblock format, blocks (optionally) separated
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	156 * by blanks; names only attached to first block. Names are
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	157 * restricted to ten char; we achieve this by simple truncation (!).
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	158 * (Do we need to convert gap characters from our ./- convention?)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	159 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	160 for (pos = 0; pos < msa->alen; pos += cpl)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	161 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	162 if (pos > 0) fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	163
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	164 for (idx = 0; idx < msa->nseq; idx++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	165 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	166 strncpy(buf, msa->aseq[idx] + pos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	167 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	168 if (pos > 0) fprintf(fp, "%s\n", buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	169 else fprintf(fp, "%-10.10s%s\n", msa->sqname[idx], buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	170 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	171 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	172 return;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	173 }

Mercurial > repos > clustalomega > clustalomega

annotate clustalomega/clustal-omega-0.2.0/src/squid/phylip.c @ 0:ff1768533a07