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

annotate clustalomega/clustal-omega-0.2.0/src/squid/stockholm.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 /* stockholm.c
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	11 * SRE, Fri May 28 15:46:41 1999
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 * Reading/writing of Stockholm format multiple sequence alignments.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	14 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	15 * example of API:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	16 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	17 * MSA *msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	18 * FILE *fp; -- opened for write with fopen()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	19 * MSAFILE *afp; -- opened for read with MSAFileOpen()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	20 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	21 * while ((msa = ReadStockholm(afp)) != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	22 * {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	23 * WriteStockholm(fp, msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	24 * MSAFree(msa);
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 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	27 * RCS $Id: stockholm.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: stockholm.c,v 1.7 2002/10/12 04:40:36 eddy Exp)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	28 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	29 #include <stdio.h>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	30 #include <string.h>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	31 #include "squid.h"
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	32 #include "msa.h"
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 static int parse_gf(MSA msa, char buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	35 static int parse_gs(MSA msa, char buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	36 static int parse_gc(MSA msa, char buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	37 static int parse_gr(MSA msa, char buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	38 static int parse_comment(MSA msa, char buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	39 static int parse_sequence(MSA msa, char buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	40 static void actually_write_stockholm(FILE fp, MSA msa, int cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	41
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	42 #ifdef TESTDRIVE_STOCKHOLM
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	43 /*****************************************************************
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	44 * stockholm.c test driver:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	45 * cc -DTESTDRIVE_STOCKHOLM -g -O2 -Wall -o test stockholm.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm
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 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	48 int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	49 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	50 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	51 MSAFILE *afp;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	52 MSA *msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	53 char *file;
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 file = argv[1];
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 if ((afp = MSAFileOpen(file, MSAFILE_STOCKHOLM, NULL)) == NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	58 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	59
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	60 while ((msa = ReadStockholm(afp)) != NULL)
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 WriteStockholm(stdout, msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	63 MSAFree(msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	64 }
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 MSAFileClose(afp);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	67 exit(0);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	68 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	69 /******************************************************************/
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	70 #endif /* testdriver */
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
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	73 /* Function: ReadStockholm()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	74 * Date: SRE, Fri May 21 17:33:10 1999 [St. Louis]
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	75 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	76 * Purpose: Parse the next alignment from an open Stockholm
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	77 * format alignment file. Return the alignment, or
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	78 * NULL if there are no more alignments in the file.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	79 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	80 * 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	81 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	82 * 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	83 * 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	84 * 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	85 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	86 * Diagnostics:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	87 * Will Die() here with a (potentially) useful message
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	88 * if a parsing error occurs
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	89 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	90 MSA *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	91 ReadStockholm(MSAFILE *afp)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	92 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	93 MSA *msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	94 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	95 int status;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	96
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	97 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	98
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	99 /* Initialize allocation of the MSA.
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(10, 0);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	102
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	103 /* Check the magic Stockholm header line.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	104 * We have to skip blank lines here, else we perceive
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	105 * trailing blank lines in a file as a format error when
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	106 * reading in multi-record mode.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	107 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	108 do {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	109 if ((s = MSAFileGetLine(afp)) == NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	110 MSAFree(msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	111 return NULL;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	112 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	113 } while (IsBlankline(s));
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	114
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	115 if (strncmp(s, "# STOCKHOLM 1.", 14) != 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	116 Die("\
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	117 File %s doesn't appear to be in Stockholm format.\n\
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	118 Assuming there isn't some other problem with your file (it is an\n\
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	119 alignment file, right?), please either:\n\
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	120 a) use the Babelfish format autotranslator option (-B, usually);\n\
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	121 b) specify the file's format with the --informat option; or\n\
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	122 a) reformat the alignment to Stockholm format.\n",
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	123 afp->fname);
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 /* Read the alignment file one line at a time.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	126 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	127 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	128 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	129 while (s == ' ' \|\| s == '\t') s++; /* skip leading whitespace */
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 if (*s == '#') {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	132 if (strncmp(s, "#=GF", 4) == 0) status = parse_gf(msa, s);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	133 else if (strncmp(s, "#=GS", 4) == 0) status = parse_gs(msa, s);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	134 else if (strncmp(s, "#=GC", 4) == 0) status = parse_gc(msa, s);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	135 else if (strncmp(s, "#=GR", 4) == 0) status = parse_gr(msa, s);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	136 else status = parse_comment(msa, s);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	137 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	138 else if (strncmp(s, "//", 2) == 0) break;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	139 else if (*s == '\n') continue;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	140 else status = parse_sequence(msa, s);
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 if (status == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	143 Die("Stockholm format parse error: line %d of file %s while reading alignment %s",
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	144 afp->linenumber, afp->fname, msa->name == NULL? "" : msa->name);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	145 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	146
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	147 if (s == NULL && msa->nseq != 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	148 Die ("Didn't find // at end of alignment %s", msa->name == NULL ? "" : msa->name);
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 if (s == NULL && msa->nseq == 0) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	151 /* probably just some junk at end of file */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	152 MSAFree(msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	153 return NULL;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	154 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	155
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	156 MSAVerifyParse(msa);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	157 return msa;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	158 }
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
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	161 /* Function: WriteStockholm()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	162 * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis]
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 * Purpose: Write an alignment in standard multi-block
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	165 * Stockholm format to an open file. A wrapper
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	166 * for actually_write_stockholm().
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	167 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	168 * 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	169 * msa - alignment to write
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 * Returns: (void)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	172 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	173 void
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	174 WriteStockholm(FILE fp, MSA msa)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	175 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	176 actually_write_stockholm(fp, msa, 50); /* 50 char per block */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	177 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	178
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	179 /* Function: WriteStockholmOneBlock()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	180 * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis]
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	181 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	182 * Purpose: Write an alignment in Pfam's single-block
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	183 * Stockholm format to an open file. A wrapper
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	184 * for actually_write_stockholm().
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	185 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	186 * 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	187 * msa - alignment to write
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	188 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	189 * Returns: (void)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	190 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	191 void
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	192 WriteStockholmOneBlock(FILE fp, MSA msa)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	193 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	194 actually_write_stockholm(fp, msa, msa->alen); /* one big block */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	195 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	196
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	197
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	198 /* Function: actually_write_stockholm()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	199 * Date: SRE, Fri May 21 17:39:22 1999 [St. Louis]
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	200 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	201 * Purpose: Write an alignment in Stockholm format to
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	202 * an open file. This is the function that actually
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	203 * does the work. The API's WriteStockholm()
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	204 * and WriteStockholmOneBlock() are wrappers.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	205 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	206 * 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	207 * msa - alignment to write
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	208 * cpl - characters to write per line in alignment block
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	209 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	210 * Returns: (void)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	211 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	212 static void
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	213 actually_write_stockholm(FILE fp, MSA msa, int cpl)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	214 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	215 int i, j;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	216 int len = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	217 int namewidth;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	218 int typewidth = 0; /* markup tags are up to 5 chars long */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	219 int markupwidth = 0; /* #=GR, #=GC are four char wide + 1 space */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	220 char *buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	221 int currpos;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	222 char s, tok;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	223
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	224 /* Figure out how much space we need for name + markup
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	225 * to keep the alignment in register. Required by Stockholm
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	226 * spec, even though our Stockholm parser doesn't care (Erik's does).
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	227 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	228 namewidth = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	229 for (i = 0; i < msa->nseq; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	230 if ((len = strlen(msa->sqname[i])) > namewidth)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	231 namewidth = len;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	232
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	233 /* Figure out how much space we need for markup tags
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	234 * markupwidth = always 4 if we're doing markup: strlen("#=GR")
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	235 * typewidth = longest markup tag
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	236 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	237 if (msa->ss != NULL) { markupwidth = 4; typewidth = 2; }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	238 if (msa->sa != NULL) { markupwidth = 4; typewidth = 2; }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	239 for (i = 0; i < msa->ngr; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	240 if ((len = strlen(msa->gr_tag[i])) > typewidth) typewidth = len;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	241
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	242 if (msa->rf != NULL) { markupwidth = 4; if (typewidth < 2) typewidth = 2; }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	243 if (msa->ss_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	244 if (msa->sa_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	245 for (i = 0; i < msa->ngc; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	246 if ((len = strlen(msa->gc_tag[i])) > typewidth) typewidth = len;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	247
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	248 buf = MallocOrDie(sizeof(char) * (cpl+namewidth+typewidth+markupwidth+61));
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	249
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	250 /* Magic Stockholm header
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	251 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	252 fprintf(fp, "# STOCKHOLM 1.0\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	253
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	254 /* Free text comments
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	255 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	256 for (i = 0; i < msa->ncomment; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	257 fprintf(fp, "# %s\n", msa->comment[i]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	258 if (msa->ncomment > 0) fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	259
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	260 /* GF section: per-file annotation
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	261 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	262 if (msa->name != NULL) fprintf(fp, "#=GF ID %s\n", msa->name);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	263 if (msa->acc != NULL) fprintf(fp, "#=GF AC %s\n", msa->acc);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	264 if (msa->desc != NULL) fprintf(fp, "#=GF DE %s\n", msa->desc);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	265 if (msa->au != NULL) fprintf(fp, "#=GF AU %s\n", msa->au);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	266
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	267 /* Thresholds are hacky. Pfam has two. Rfam has one.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	268 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	269 if (msa->cutoff_is_set[MSA_CUTOFF_GA1] && msa->cutoff_is_set[MSA_CUTOFF_GA2])
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	270 fprintf(fp, "#=GF GA %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_GA1], msa->cutoff[MSA_CUTOFF_GA2]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	271 else if (msa->cutoff_is_set[MSA_CUTOFF_GA1])
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	272 fprintf(fp, "#=GF GA %.1f\n", msa->cutoff[MSA_CUTOFF_GA1]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	273 if (msa->cutoff_is_set[MSA_CUTOFF_NC1] && msa->cutoff_is_set[MSA_CUTOFF_NC2])
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	274 fprintf(fp, "#=GF NC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_NC1], msa->cutoff[MSA_CUTOFF_NC2]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	275 else if (msa->cutoff_is_set[MSA_CUTOFF_NC1])
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	276 fprintf(fp, "#=GF NC %.1f\n", msa->cutoff[MSA_CUTOFF_NC1]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	277 if (msa->cutoff_is_set[MSA_CUTOFF_TC1] && msa->cutoff_is_set[MSA_CUTOFF_TC2])
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	278 fprintf(fp, "#=GF TC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_TC1], msa->cutoff[MSA_CUTOFF_TC2]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	279 else if (msa->cutoff_is_set[MSA_CUTOFF_TC1])
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	280 fprintf(fp, "#=GF TC %.1f\n", msa->cutoff[MSA_CUTOFF_TC1]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	281
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	282 for (i = 0; i < msa->ngf; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	283 fprintf(fp, "#=GF %-5s %s\n", msa->gf_tag[i], msa->gf[i]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	284 fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	285
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	286
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	287 /* GS section: per-sequence annotation
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	288 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	289 if (msa->flags & MSA_SET_WGT)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	290 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	291 for (i = 0; i < msa->nseq; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	292 fprintf(fp, "#=GS %-.s WT %.2f\n", namewidth, namewidth, msa->sqname[i], msa->wgt[i]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	293 fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	294 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	295 if (msa->sqacc != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	296 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	297 for (i = 0; i < msa->nseq; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	298 if (msa->sqacc[i] != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	299 fprintf(fp, "#=GS %-.s AC %s\n", namewidth, namewidth, msa->sqname[i], msa->sqacc[i]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	300 fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	301 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	302 if (msa->sqdesc != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	303 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	304 for (i = 0; i < msa->nseq; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	305 if (msa->sqdesc[i] != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	306 fprintf(fp, "#=GS %.s DE %s\n", namewidth, namewidth, msa->sqname[i], msa->sqdesc[i]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	307 fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	308 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	309 for (i = 0; i < msa->ngs; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	310 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	311 /* Multiannotated GS tags are possible; for example,
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	312 * #=GS foo DR PDB; 1xxx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	313 * #=GS foo DR PDB; 2yyy;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	314 * These are stored, for example, as:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	315 * msa->gs[0][0] = "PDB; 1xxx;\nPDB; 2yyy;"
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	316 * and must be decomposed.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	317 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	318 for (j = 0; j < msa->nseq; j++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	319 if (msa->gs[i][j] != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	320 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	321 s = msa->gs[i][j];
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	322 while ((tok = sre_strtok(&s, "\n", NULL)) != NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	323 fprintf(fp, "#=GS %.s %5s %s\n", namewidth, namewidth,
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	324 msa->sqname[j], msa->gs_tag[i], tok);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	325 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	326 fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	327 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	328
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	329 /* Alignment section:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	330 * contains aligned sequence, #=GR annotation, and #=GC annotation
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	331 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	332 for (currpos = 0; currpos < msa->alen; currpos += cpl)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	333 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	334 if (currpos > 0) fprintf(fp, "\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	335 for (i = 0; i < msa->nseq; i++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	336 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	337 strncpy(buf, msa->aseq[i] + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	338 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	339 fprintf(fp, "%-.s %s\n", namewidth+typewidth+markupwidth, namewidth+typewidth+markupwidth,
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	340 msa->sqname[i], buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	341
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	342 if (msa->ss != NULL && msa->ss[i] != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	343 strncpy(buf, msa->ss[i] + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	344 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	345 fprintf(fp, "#=GR %-.s SS %s\n", namewidth, namewidth, msa->sqname[i], buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	346 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	347 if (msa->sa != NULL && msa->sa[i] != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	348 strncpy(buf, msa->sa[i] + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	349 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	350 fprintf(fp, "#=GR %-.s SA %s\n", namewidth, namewidth, msa->sqname[i], buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	351 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	352 for (j = 0; j < msa->ngr; j++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	353 if (msa->gr[j][i] != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	354 strncpy(buf, msa->gr[j][i] + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	355 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	356 fprintf(fp, "#=GR %-.s %5s %s\n",
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	357 namewidth, namewidth, msa->sqname[i], msa->gr_tag[j], buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	358 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	359 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	360 if (msa->ss_cons != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	361 strncpy(buf, msa->ss_cons + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	362 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	363 fprintf(fp, "#=GC %-.s %s\n", namewidth+typewidth, namewidth+typewidth, "SS_cons", buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	364 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	365
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	366 if (msa->sa_cons != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	367 strncpy(buf, msa->sa_cons + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	368 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	369 fprintf(fp, "#=GC %-.s %s\n", namewidth+typewidth, namewidth+typewidth, "SA_cons", buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	370 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	371
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	372 if (msa->rf != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	373 strncpy(buf, msa->rf + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	374 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	375 fprintf(fp, "#=GC %-.s %s\n", namewidth+typewidth, namewidth+typewidth, "RF", buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	376 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	377 for (j = 0; j < msa->ngc; j++) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	378 strncpy(buf, msa->gc[j] + currpos, cpl);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	379 buf[cpl] = '\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	380 fprintf(fp, "#=GC %-.s %s\n", namewidth+typewidth, namewidth+typewidth,
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	381 msa->gc_tag[j], buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	382 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	383 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	384 fprintf(fp, "//\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	385 free(buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	386 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	387
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	388
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	389
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	390
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	391
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	392 /* Format of a GF line:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	393 * #=GF <featurename> <text>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	394 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	395 static int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	396 parse_gf(MSA msa, char buf)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	397 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	398 char *gf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	399 char *featurename;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	400 char *text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	401 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	402
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	403 s = buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	404 if ((gf = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	405 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	406 if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	407 while (text && (text == ' ' \|\| *text == '\t')) text++;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	408
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	409 if (strcmp(featurename, "ID") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	410 msa->name = sre_strdup(text, -1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	411 else if (strcmp(featurename, "AC") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	412 msa->acc = sre_strdup(text, -1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	413 else if (strcmp(featurename, "DE") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	414 msa->desc = sre_strdup(text, -1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	415 else if (strcmp(featurename, "AU") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	416 msa->au = sre_strdup(text, -1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	417 else if (strcmp(featurename, "GA") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	418 { /* Pfam has GA1, GA2. Rfam just has GA1. */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	419 s = text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	420 if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	421 msa->cutoff[MSA_CUTOFF_GA1] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	422 msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	423 if ((text = 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	424 msa->cutoff[MSA_CUTOFF_GA2] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	425 msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	426 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	427 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	428 else if (strcmp(featurename, "NC") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	429 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	430 s = text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	431 if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	432 msa->cutoff[MSA_CUTOFF_NC1] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	433 msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	434 if ((text = 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	435 msa->cutoff[MSA_CUTOFF_NC2] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	436 msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	437 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	438 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	439 else if (strcmp(featurename, "TC") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	440 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	441 s = text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	442 if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	443 msa->cutoff[MSA_CUTOFF_TC1] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	444 msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	445 if ((text = 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	446 msa->cutoff[MSA_CUTOFF_TC2] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	447 msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	448 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	449 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	450 else
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	451 MSAAddGF(msa, featurename, text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	452
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	453 return 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	454 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	455
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	456
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	457 /* Format of a GS line:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	458 * #=GS <seqname> <featurename> <text>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	459 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	460 static int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	461 parse_gs(MSA msa, char buf)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	462 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	463 char *gs;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	464 char *seqname;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	465 char *featurename;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	466 char *text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	467 int seqidx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	468 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	469
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	470 s = buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	471 if ((gs = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	472 if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	473 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	474 if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	475 while (text && (text == ' ' \|\| *text == '\t')) text++;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	476
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	477 /* GS usually follows another GS; guess lastidx+1
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	478 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	479 seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	480 msa->lastidx = seqidx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	481
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	482 if (strcmp(featurename, "WT") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	483 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	484 msa->wgt[seqidx] = atof(text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	485 msa->flags \|= MSA_SET_WGT;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	486 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	487
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	488 else if (strcmp(featurename, "AC") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	489 MSASetSeqAccession(msa, seqidx, text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	490
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	491 else if (strcmp(featurename, "DE") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	492 MSASetSeqDescription(msa, seqidx, text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	493
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	494 else
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	495 MSAAddGS(msa, featurename, seqidx, text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	496
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	497 return 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	498 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	499
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	500 /* Format of a GC line:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	501 * #=GC <featurename> <text>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	502 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	503 static int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	504 parse_gc(MSA msa, char buf)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	505 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	506 char *gc;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	507 char *featurename;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	508 char *text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	509 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	510 int len;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	511
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	512 s = buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	513 if ((gc = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	514 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	515 if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	516
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	517 if (strcmp(featurename, "SS_cons") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	518 sre_strcat(&(msa->ss_cons), -1, text, len);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	519 else if (strcmp(featurename, "SA_cons") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	520 sre_strcat(&(msa->sa_cons), -1, text, len);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	521 else if (strcmp(featurename, "RF") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	522 sre_strcat(&(msa->rf), -1, text, len);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	523 else
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	524 MSAAppendGC(msa, featurename, text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	525
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	526 return 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	527 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	528
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	529 /* Format of a GR line:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	530 * #=GR <seqname> <featurename> <text>
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	531 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	532 static int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	533 parse_gr(MSA msa, char buf)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	534 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	535 char *gr;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	536 char *seqname;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	537 char *featurename;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	538 char *text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	539 int seqidx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	540 int len;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	541 int j;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	542 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	543
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	544 s = buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	545 if ((gr = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	546 if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	547 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	548 if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	549
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	550 /* GR usually follows sequence it refers to; guess msa->lastidx */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	551 seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	552 msa->lastidx = seqidx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	553
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	554 if (strcmp(featurename, "SS") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	555 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	556 if (msa->ss == NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	557 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	558 msa->ss = MallocOrDie(sizeof(char ) msa->nseqalloc);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	559 msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	560 for (j = 0; j < msa->nseqalloc; j++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	561 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	562 msa->ss[j] = NULL;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	563 msa->sslen[j] = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	564 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	565 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	566 msa->sslen[seqidx] = sre_strcat(&(msa->ss[seqidx]), msa->sslen[seqidx], text, len);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	567 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	568 else if (strcmp(featurename, "SA") == 0)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	569 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	570 if (msa->sa == NULL)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	571 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	572 msa->sa = MallocOrDie(sizeof(char ) msa->nseqalloc);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	573 msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	574 for (j = 0; j < msa->nseqalloc; j++)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	575 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	576 msa->sa[j] = NULL;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	577 msa->salen[j] = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	578 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	579 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	580 msa->salen[seqidx] = sre_strcat(&(msa->sa[seqidx]), msa->salen[seqidx], text, len);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	581 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	582 else
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	583 MSAAppendGR(msa, featurename, seqidx, text);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	584
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	585 return 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	586 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	587
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	588
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	589 /* comments are simply stored verbatim, not parsed
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	590 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	591 static int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	592 parse_comment(MSA msa, char buf)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	593 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	594 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	595 char *comment;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	596
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	597 s = buf + 1; /* skip leading '#' */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	598 if (s == '\n') { s = '\0'; comment = s; } /* deal with blank comment */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	599 else if ((comment = sre_strtok(&s, "\n", NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	600
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	601 MSAAddComment(msa, comment);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	602 return 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	603 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	604
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	605 static int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	606 parse_sequence(MSA msa, char buf)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	607 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	608 char *s;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	609 char *seqname;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	610 char *text;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	611 int seqidx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	612 int len;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	613
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	614 s = buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	615 if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	616 if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	617
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	618 /* seq usually follows another seq; guess msa->lastidx +1 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	619 seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	620 msa->lastidx = seqidx;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	621
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	622 msa->sqlen[seqidx] = sre_strcat(&(msa->aseq[seqidx]), msa->sqlen[seqidx], text, len);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	623 return 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	624 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	625
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	626
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository clustalomega parents: diff changeset	627

Mercurial > repos > clustalomega > clustalomega

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