--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* File: sqio.c
+ * From: ureadseq.c in Don Gilbert's sequence i/o package
+ *
+ * Reads and writes nucleic/protein sequence in various
+ * formats. Data files may have multiple sequences.
+ *
+ * Heavily modified from READSEQ package
+ * Copyright (C) 1990 by D.G. Gilbert
+ * Biology Dept., Indiana University, Bloomington, IN 47405
+ * email: gilbertd@bio.indiana.edu
+ * Thanks Don!
+ *
+ * SRE: Modifications as noted. Fri Jul 3 09:44:54 1992
+ * Packaged for squid, Thu Oct 1 10:07:11 1992
+ * ANSI conversion in full swing, Mon Jul 12 12:22:21 1993
+ *
+ * CVS $Id: sqio.c,v 1.29 2002/08/26 23:10:52 eddy Exp)
+ *
+ *****************************************************************
+ * Basic API for single sequence reading:
+ *
+ * SQFILE *sqfp;
+ * char *seqfile;
+ * int format; - see squid.h for formats; example: SQFILE_FASTA
+ * char *seq;
+ * SQINFO sqinfo;
+ *
+ * if ((sqfp = SeqfileOpen(seqfile, format, "BLASTDB")) == NULL)
+ * Die("Failed to open sequence database file %s\n%s\n", seqfile, usage);
+ * while (ReadSeq(sqfp, sqfp->format, &seq, &sqinfo)) {
+ * do_stuff;
+ * FreeSequence(seq, &sqinfo);
+ * }
+ * SeqfileClose(sqfp);
+ *
+ *****************************************************************
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+
+#ifndef SEEK_SET
+#include <unistd.h>
+#endif
+
+#include "squid.h"
+#include "msa.h"
+#include "ssi.h"
+
+static void SeqfileGetLine(SQFILE *V);
+
+#define kStartLength 500
+
+static char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
+static char *primenuc = "ACGTUN";
+static char *protonly = "EFIPQZ";
+
+static SQFILE *seqfile_open(char *filename, int format, char *env, int ssimode);
+
+/* Function: SeqfileOpen()
+ *
+ * Purpose : Open a sequence database file and prepare for reading
+ * sequentially.
+ *
+ * Args: filename - name of file to open
+ * format - format of file
+ * env - environment variable for path (e.g. BLASTDB)
+ * ssimode - -1, SSI_OFFSET_I32, or SSI_OFFSET_I64
+ *
+ * Returns opened SQFILE ptr, or NULL on failure.
+ */
+SQFILE *
+SeqfileOpen(char *filename, int format, char *env)
+{
+ return seqfile_open(filename, format, env, -1);
+}
+SQFILE *
+SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode)
+{
+ return seqfile_open(filename, format, env, ssimode);
+}
+static SQFILE *
+seqfile_open(char *filename, int format, char *env, int ssimode)
+{
+ SQFILE *dbfp;
+
+ dbfp = (SQFILE *) MallocOrDie (sizeof(SQFILE));
+
+ dbfp->ssimode = ssimode;
+ dbfp->rpl = -1; /* flag meaning "unset" */
+ dbfp->lastrpl = 0;
+ dbfp->maxrpl = 0;
+ dbfp->bpl = -1; /* flag meaning "unset" */
+ dbfp->lastbpl = 0;
+ dbfp->maxbpl = 0;
+
+ /* Open our file handle.
+ * Three possibilities:
+ * 1. normal file open
+ * 2. filename = "-"; read from stdin
+ * 3. filename = "*.gz"; read thru pipe from gzip
+ * If we're reading from stdin or a pipe, we can't reliably
+ * back up, so we can't do two-pass parsers like the interleaved alignment
+ * formats.
+ */
+ if (strcmp(filename, "-") == 0)
+ {
+ dbfp->f = stdin;
+ dbfp->do_stdin = TRUE;
+ dbfp->do_gzip = FALSE;
+ dbfp->fname = sre_strdup("[STDIN]", -1);
+ }
+#ifndef SRE_STRICT_ANSI
+ /* popen(), pclose() aren't portable to non-POSIX systems; disable */
+ else if (Strparse("^.*\\.gz$", filename, 0))
+ {
+ char cmd[256];
+
+ /* Note that popen() will return "successfully"
+ * if file doesn't exist, because gzip works fine
+ * and prints an error! So we have to check for
+ * existence of file ourself.
+ */
+ if (! FileExists(filename))
+ Die("%s: file does not exist", filename);
+
+ if (strlen(filename) + strlen("gzip -dc ") >= 256)
+ Die("filename > 255 char in SeqfileOpen()");
+ sprintf(cmd, "gzip -dc %s", filename);
+ if ((dbfp->f = popen(cmd, "r")) == NULL)
+ return NULL;
+
+ dbfp->do_stdin = FALSE;
+ dbfp->do_gzip = TRUE;
+ dbfp->fname = sre_strdup(filename, -1);
+ }
+#endif /*SRE_STRICT_ANSI*/
+ else
+ {
+ if ((dbfp->f = fopen(filename, "r")) == NULL &&
+ (dbfp->f = EnvFileOpen(filename, env, NULL)) == NULL)
+ return NULL;
+
+ dbfp->do_stdin = FALSE;
+ dbfp->do_gzip = FALSE;
+ dbfp->fname = sre_strdup(filename, -1);
+ }
+
+
+ /* Invoke autodetection if we haven't already been told what
+ * to expect.
+ */
+ if (format == SQFILE_UNKNOWN)
+ {
+ if (dbfp->do_stdin == TRUE || dbfp->do_gzip)
+ Die("Can't autodetect sequence file format from a stdin or gzip pipe");
+ format = SeqfileFormat(dbfp->f);
+ if (format == SQFILE_UNKNOWN)
+ Die("Can't determine format of sequence file %s", dbfp->fname);
+ }
+
+ /* The hack for sequential access of an interleaved alignment file:
+ * read the alignment in, we'll copy sequences out one at a time.
+ */
+ dbfp->msa = NULL;
+ dbfp->afp = NULL;
+ dbfp->format = format;
+ dbfp->linenumber = 0;
+ dbfp->buf = NULL;
+ dbfp->buflen = 0;
+ if (IsAlignmentFormat(format))
+ {
+ /* We'll be reading from the MSA interface. Copy our data
+ * to the MSA afp's structure.
+ */
+ dbfp->afp = MallocOrDie(sizeof(MSAFILE));
+ dbfp->afp->f = dbfp->f; /* just a ptr, don't close */
+ dbfp->afp->do_stdin = dbfp->do_stdin;
+ dbfp->afp->do_gzip = dbfp->do_gzip;
+ dbfp->afp->fname = dbfp->fname; /* just a ptr, don't free */
+ dbfp->afp->format = dbfp->format; /* e.g. format */
+ dbfp->afp->linenumber = dbfp->linenumber; /* e.g. 0 */
+ dbfp->afp->buf = NULL;
+ dbfp->afp->buflen = 0;
+
+ if ((dbfp->msa = MSAFileRead(dbfp->afp)) == NULL)
+ Die("Failed to read any alignment data from file %s", dbfp->fname);
+ /* hack: overload/reuse msa->lastidx; indicates
+ next seq to return upon a ReadSeq() call */
+ dbfp->msa->lastidx = 0;
+
+ return dbfp;
+ }
+
+ /* Load the first line.
+ */
+ SeqfileGetLine(dbfp);
+ return dbfp;
+}
+
+/* Function: SeqfilePosition()
+ *
+ * Purpose: Move to a particular offset in a seqfile.
+ * Will not work on alignment files.
+ */
+void
+SeqfilePosition(SQFILE *sqfp, SSIOFFSET *offset)
+{
+ if (sqfp->do_stdin || sqfp->do_gzip || IsAlignmentFormat(sqfp->format))
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ if (SSISetFilePosition(sqfp->f, offset) != 0)
+ Die("SSISetFilePosition failed, but that shouldn't happen.");
+ SeqfileGetLine(sqfp);
+}
+
+
+/* Function: SeqfileRewind()
+ *
+ * Purpose: Set a sequence file back to the first sequence.
+ *
+ * Won't work on alignment files. Although it would
+ * seem that it could (just set msa->lastidx back to 0),
+ * that'll fail on "multiple multiple" alignment file formats
+ * (e.g. Stockholm).
+ */
+void
+SeqfileRewind(SQFILE *sqfp)
+{
+ if (sqfp->do_stdin || sqfp->do_gzip)
+ Die("SeqfileRewind() failed: in a nonrewindable data file or stream");
+
+ rewind(sqfp->f);
+ SeqfileGetLine(sqfp);
+}
+
+/* Function: SeqfileLineParameters()
+ * Date: SRE, Thu Feb 15 17:00:41 2001 [St. Louis]
+ *
+ * Purpose: After all the sequences have been read from the file,
+ * but before closing it, retrieve overall bytes-per-line and
+ * residues-per-line info. If non-zero, these mean that
+ * the file contains homogeneous sequence line lengths (except
+ * the last line in each record).
+ *
+ * If either of bpl or rpl is determined to be inhomogeneous,
+ * both are returned as 0.
+ *
+ * Args: *sqfp - an open but fully read sequence file
+ * ret_bpl - RETURN: bytes per line, or 0 if inhomogeneous
+ * ret_rpl - RETURN: residues per line, or 0 if inhomogenous.
+ *
+ * Returns: void
+ */
+void
+SeqfileLineParameters(SQFILE *V, int *ret_bpl, int *ret_rpl)
+{
+ if (V->rpl > 0 && V->maxrpl == V->rpl &&
+ V->bpl > 0 && V->maxbpl == V->bpl) {
+ *ret_bpl = V->bpl;
+ *ret_rpl = V->rpl;
+ } else {
+ *ret_bpl = 0;
+ *ret_rpl = 0;
+ }
+}
+
+
+void
+SeqfileClose(SQFILE *sqfp)
+{
+ /* note: don't test for sqfp->msa being NULL. Now that
+ * we're holding afp open and allowing access to multi-MSA
+ * databases (e.g. Stockholm format, Pfam), msa ends
+ * up being NULL when we run out of alignments.
+ */
+ if (sqfp->afp != NULL) {
+ if (sqfp->msa != NULL) MSAFree(sqfp->msa);
+ if (sqfp->afp->buf != NULL) free(sqfp->afp->buf);
+ free(sqfp->afp);
+ }
+#ifndef SRE_STRICT_ANSI /* gunzip functionality only on POSIX systems */
+ if (sqfp->do_gzip) pclose(sqfp->f);
+#endif
+ else if (! sqfp->do_stdin) fclose(sqfp->f);
+ if (sqfp->buf != NULL) free(sqfp->buf);
+ if (sqfp->fname != NULL) free(sqfp->fname);
+ free(sqfp);
+}
+
+
+/* Function: SeqfileGetLine()
+ * Date: SRE, Tue Jun 22 09:15:49 1999 [Sanger Centre]
+ *
+ * Purpose: read a line from a sequence file into V->buf
+ * If the fgets() is NULL, sets V->buf[0] to '\0'.
+ *
+ * Args: V
+ *
+ * Returns: void
+ */
+static void
+SeqfileGetLine(SQFILE *V)
+{
+ if (V->ssimode >= 0)
+ if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->ssioffset)))
+ Die("SSIGetFilePosition() failed");
+ if (sre_fgets(&(V->buf), &(V->buflen), V->f) == NULL)
+ *(V->buf) = '\0';
+ V->linenumber++;
+}
+
+
+void
+FreeSequence(char *seq, SQINFO *sqinfo)
+{
+ if (seq != NULL) free(seq); /* FS, r244, here is potential problem in profile/profile */
+ if (sqinfo->flags & SQINFO_SS){
+ if (NULL != sqinfo->ss){ /* FS, r244 -> r245 */
+ free(sqinfo->ss);
+ }
+ }
+ if (sqinfo->flags & SQINFO_SA){
+ if (NULL != sqinfo->sa){ /* FS, r244 -> r245 */
+ free(sqinfo->sa);
+ }
+ }
+}
+
+int
+SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag)
+{
+ int len;
+ int pos;
+
+ /* silently ignore NULL. */
+ if (sptr == NULL) return 1;
+
+ while (*sptr == ' ') sptr++; /* ignore leading whitespace */
+ for (pos = strlen(sptr)-1; pos >= 0; pos--)
+ if (! isspace((int) sptr[pos])) break;
+ sptr[pos+1] = '\0'; /* ignore trailing whitespace */
+
+ switch (flag) {
+ case SQINFO_NAME:
+ if (*sptr != '-')
+ {
+ strncpy(sqinfo->name, sptr, SQINFO_NAMELEN-1);
+ sqinfo->name[SQINFO_NAMELEN-1] = '\0';
+ sqinfo->flags |= SQINFO_NAME;
+ }
+ break;
+
+ case SQINFO_ID:
+ if (*sptr != '-')
+ {
+ strncpy(sqinfo->id, sptr, SQINFO_NAMELEN-1);
+ sqinfo->id[SQINFO_NAMELEN-1] = '\0';
+ sqinfo->flags |= SQINFO_ID;
+ }
+ break;
+
+ case SQINFO_ACC:
+ if (*sptr != '-')
+ {
+ strncpy(sqinfo->acc, sptr, SQINFO_NAMELEN-1);
+ sqinfo->acc[SQINFO_NAMELEN-1] = '\0';
+ sqinfo->flags |= SQINFO_ACC;
+ }
+ break;
+
+ case SQINFO_DESC:
+ if (*sptr != '-')
+ {
+ if (sqinfo->flags & SQINFO_DESC) /* append? */
+ {
+ len = strlen(sqinfo->desc);
+ if (len < SQINFO_DESCLEN-2) /* is there room? */
+ {
+ strncat(sqinfo->desc, " ", SQINFO_DESCLEN-1-len); len++;
+ strncat(sqinfo->desc, sptr, SQINFO_DESCLEN-1-len);
+ }
+ }
+ else /* else copy */
+ strncpy(sqinfo->desc, sptr, SQINFO_DESCLEN-1);
+ sqinfo->desc[SQINFO_DESCLEN-1] = '\0';
+ sqinfo->flags |= SQINFO_DESC;
+ }
+ break;
+
+ case SQINFO_START:
+ if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
+ sqinfo->start = atoi(sptr);
+ if (sqinfo->start != 0) sqinfo->flags |= SQINFO_START;
+ break;
+
+ case SQINFO_STOP:
+ if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
+ sqinfo->stop = atoi(sptr);
+ if (sqinfo->stop != 0) sqinfo->flags |= SQINFO_STOP;
+ break;
+
+ case SQINFO_OLEN:
+ if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
+ sqinfo->olen = atoi(sptr);
+ if (sqinfo->olen != 0) sqinfo->flags |= SQINFO_OLEN;
+ break;
+
+ default:
+ Die("Invalid flag %d to SetSeqinfoString()", flag);
+ }
+ return 1;
+}
+
+void
+SeqinfoCopy(SQINFO *sq1, SQINFO *sq2)
+{
+ sq1->flags = sq2->flags;
+ if (sq2->flags & SQINFO_NAME) strcpy(sq1->name, sq2->name);
+ if (sq2->flags & SQINFO_ID) strcpy(sq1->id, sq2->id);
+ if (sq2->flags & SQINFO_ACC) strcpy(sq1->acc, sq2->acc);
+ if (sq2->flags & SQINFO_DESC) strcpy(sq1->desc, sq2->desc);
+ if (sq2->flags & SQINFO_LEN) sq1->len = sq2->len;
+ if (sq2->flags & SQINFO_START) sq1->start = sq2->start;
+ if (sq2->flags & SQINFO_STOP) sq1->stop = sq2->stop;
+ if (sq2->flags & SQINFO_OLEN) sq1->olen = sq2->olen;
+ if (sq2->flags & SQINFO_TYPE) sq1->type = sq2->type;
+ if (sq2->flags & SQINFO_SS) sq1->ss = Strdup(sq2->ss);
+ if (sq2->flags & SQINFO_SA) sq1->sa = Strdup(sq2->sa);
+}
+
+/* Function: ToDNA()
+ *
+ * Purpose: Convert a sequence to DNA.
+ * U --> T
+ */
+void
+ToDNA(char *seq)
+{
+ for (; *seq != '\0'; seq++)
+ {
+ if (*seq == 'U') *seq = 'T';
+ else if (*seq == 'u') *seq = 't';
+ }
+}
+
+/* Function: ToRNA()
+ *
+ * Purpose: Convert a sequence to RNA.
+ * T --> U
+ */
+void
+ToRNA(char *seq)
+{
+ for (; *seq != '\0'; seq++)
+ {
+ if (*seq == 'T') *seq = 'U';
+ else if (*seq == 't') *seq = 'u';
+ }
+}
+
+
+/* Function: ToIUPAC()
+ *
+ * Purpose: Convert X's, o's, other junk in a nucleic acid sequence to N's,
+ * to comply with IUPAC code. If is_aseq is TRUE, will allow gap
+ * characters though, so we can call ToIUPAC() on aligned seqs.
+ *
+ * NUCLEOTIDES is defined in squid.h as:
+ * "ACGTUNRYMKSWHBVDacgtunrymkswhbvd"
+ * gap chars allowed by isgap() are defined in squid.h as:
+ * " ._-~"
+ *
+ * WU-BLAST's pressdb will
+ * choke on X's, for instance, necessitating conversion
+ * of certain genome centers' data.
+ */
+void
+ToIUPAC(char *seq, int is_aseq)
+{
+ if (is_aseq) {
+ for (; *seq != '\0'; seq++)
+ if (strchr(NUCLEOTIDES, *seq) == NULL && ! isgap(*seq)) *seq = 'N';
+ } else {
+ for (; *seq != '\0'; seq++)
+ if (strchr(NUCLEOTIDES, *seq) == NULL) *seq = 'N';
+ }
+}
+
+
+/* Function: addseq()
+ *
+ * Purpose: Add a line of sequence to the growing string in V.
+ *
+ * In the seven supported unaligned formats, all sequence
+ * lines may contain whitespace that must be filtered out;
+ * four formats (PIR, EMBL, Genbank, GCG) include coordinates
+ * that must be filtered out. Thus an (!isdigit && !isspace)
+ * test on each character before we accept it.
+ */
+static void
+addseq(char *s, struct ReadSeqVars *V)
+{
+ char *s0;
+ char *sq;
+ int rpl; /* valid residues per line */
+ int bpl; /* characters per line */
+
+ if (V->ssimode == -1)
+ { /* Normal mode: keeping the seq */
+ /* Make sure we have enough room. We know that s is <= buflen,
+ * so just make sure we've got room for a whole new buflen worth
+ * of sequence.
+ */
+ if (V->seqlen + V->buflen > V->maxseq) {
+ V->maxseq += MAX(V->buflen, kStartLength);
+ V->seq = ReallocOrDie (V->seq, V->maxseq+1);
+ }
+
+ sq = V->seq + V->seqlen;
+ while (*s != 0) {
+#ifdef CLUSTALO
+ if (! isdigit((int) *s) && ! isspace((int) *s) && isprint((int) *s)) {
+#else
+ if (! isdigit((int) *s) && ! isspace((int) *s)) {
+#endif
+ *sq = *s;
+ sq++;
+ }
+ s++;
+ }
+ V->seqlen = sq - V->seq;
+ }
+ else /* else: indexing mode, discard the seq */
+ {
+ s0 = s;
+ rpl = 0;
+ while (*s != 0) {
+ if (! isdigit((int) *s) && ! isspace((int) *s)) {
+ rpl++;
+ }
+ s++;
+ }
+ V->seqlen += rpl;
+ bpl = s - s0;
+
+ /* Keep track of the global rpl, bpl for the file.
+ * This is overly complicated because we have to
+ * allow the last line of each record (e.g. the last addseq() call
+ * on each sequence) to have a different length - and sometimes
+ * we'll have one-line sequence records, too. Thus we only
+ * do something with the global V->rpl when we have *passed over*
+ * a line - we keep the last line's rpl in last_rpl. And because
+ * a file might consist entirely of single-line records, we keep
+ * a third guy, maxrpl, that tells us the maximum rpl of any line
+ * in the file. If we reach the end of file and rpl is still unset,
+ * we'll set it to maxrpl. If we reach eof and rpl is set, but is
+ * less than maxrpl, that's a weird case where a last line in some
+ * record is longer than every other line.
+ */
+ if (V->rpl != 0) { /* 0 means we already know rpl is invalid */
+ if (V->lastrpl > 0) { /* we're on something that's not the first line */
+ if (V->rpl > 0 && V->lastrpl != V->rpl) V->rpl = 0;
+ else if (V->rpl == -1) V->rpl = V->lastrpl;
+ }
+ V->lastrpl = rpl;
+ if (rpl > V->maxrpl) V->maxrpl = rpl; /* make sure we check max length of final lines */
+ }
+ if (V->bpl != 0) { /* 0 means we already know bpl is invalid */
+ if (V->lastbpl > 0) { /* we're on something that's not the first line */
+ if (V->bpl > 0 && V->lastbpl != V->bpl) V->bpl = 0;
+ else if (V->bpl == -1) V->bpl = V->lastbpl;
+ }
+ V->lastbpl = bpl;
+ if (bpl > V->maxbpl) V->maxbpl = bpl; /* make sure we check max length of final lines */
+ }
+ } /* end of indexing mode of addseq(). */
+
+}
+
+static void
+readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
+{
+ int addend = 0;
+ int done = 0;
+
+ V->seqlen = 0;
+ V->lastrpl = V->lastbpl = 0;
+ if (addfirst) {
+ if (V->ssimode >= 0) V->d_off = V->ssioffset;
+ addseq(V->buf, V);
+ } else if (V->ssimode >= 0)
+ if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->d_off)))
+ Die("SSIGetFilePosition() failed");
+
+ do {
+ SeqfileGetLine(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->buf) == '\0' && feof(V->f))
+ done = TRUE;
+ done |= (*endTest)(V->buf, &addend);
+ if (addend || !done)
+ addseq(V->buf, V);
+ } while (!done);
+}
+
+
+static int
+endPIR(char *s, int *addend)
+{
+ *addend = 0;
+ if ((strncmp(s, "///", 3) == 0) ||
+ (strncmp(s, "ENTRY", 5) == 0))
+ return 1;
+ else
+ return 0;
+}
+
+static void
+readPIR(struct ReadSeqVars *V)
+{
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) {
+ SeqfileGetLine(V);
+ }
+ if (feof(V->f)) return;
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if ((sptr = strtok(V->buf + 15, "\n\t ")) != NULL)
+ {
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+ SeqfileGetLine(V);
+ if (!feof(V->f) && strncmp(V->buf, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->buf+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->buf, "ACCESSION", 9) == 0)
+ {
+ if ((sptr = strtok(V->buf+15, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->buf,"SEQUENCE", 8) != 0));
+ SeqfileGetLine(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+ /* reading a real PIR-CODATA database file, we keep the source coords
+ */
+ V->sqinfo->start = 1;
+ V->sqinfo->stop = V->seqlen;
+ V->sqinfo->olen = V->seqlen;
+ V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
+
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) {
+ SeqfileGetLine(V);
+ }
+}
+
+
+
+static int
+endIG(char *s, int *addend)
+{
+ *addend = 1; /* 1 or 2 occur in line w/ bases */
+ return((strchr(s,'1')!=NULL) || (strchr(s,'2')!=NULL));
+}
+
+static void
+readIG(struct ReadSeqVars *V)
+{
+ char *nm;
+ /* position past ';' comments */
+ do {
+ SeqfileGetLine(V);
+ } while (! (feof(V->f) || ((*V->buf != 0) && (*V->buf != ';')) ));
+
+ if (!feof(V->f))
+ {
+ if ((nm = strtok(V->buf, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+
+ readLoop(0, endIG, V);
+ }
+
+ while (!(feof(V->f) || ((*V->buf != '\0') && (*V->buf == ';'))))
+ SeqfileGetLine(V);
+}
+
+static int
+endStrider(char *s, int *addend)
+{
+ *addend = 0;
+ return (strstr( s, "//") != NULL);
+}
+
+static void
+readStrider(struct ReadSeqVars *V)
+{
+ char *nm;
+
+ while ((!feof(V->f)) && (*V->buf == ';'))
+ {
+ if (strncmp(V->buf,"; DNA sequence", 14) == 0)
+ {
+ if ((nm = strtok(V->buf+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+ SeqfileGetLine(V);
+ }
+
+ if (! feof(V->f))
+ readLoop(1, endStrider, V);
+
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->buf != ';'))
+ SeqfileGetLine(V);
+}
+
+
+static int
+endGB(char *s, int *addend)
+{
+ *addend = 0;
+ return ((strstr(s,"//") != NULL) || (strstr(s,"LOCUS") == s));
+}
+
+static void
+readGenBank(struct ReadSeqVars *V)
+{
+ char *sptr;
+ int in_definition;
+
+ /* We'll map three genbank identifiers onto names:
+ * LOCUS -> sqinfo.name
+ * ACCESSION -> sqinfo.acc [primary accession only]
+ * VERSION -> sqinfo.id
+ * We don't currently store the GI number, or secondary accessions.
+ */
+ while (strncmp(V->buf, "LOCUS", 5) != 0) {
+ SeqfileGetLine(V);
+ }
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+ SeqfileGetLine(V);
+ if (! feof(V->f) && strstr(V->buf, "DEFINITION") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+12, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ in_definition = TRUE;
+ }
+ else if (! feof(V->f) && strstr(V->buf, "ACCESSION") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ in_definition = FALSE;
+ }
+ else if (! feof(V->f) && strstr(V->buf, "VERSION") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ in_definition = FALSE;
+ }
+ else if (strncmp(V->buf,"ORIGIN", 6) != 0)
+ {
+ if (in_definition)
+ SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC);
+ }
+ else
+ break;
+ }
+
+ readLoop(0, endGB, V);
+
+ /* reading a real GenBank database file, we keep the source coords
+ */
+ V->sqinfo->start = 1;
+ V->sqinfo->stop = V->seqlen;
+ V->sqinfo->olen = V->seqlen;
+ V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
+
+
+ while (!(feof(V->f) || ((*V->buf!=0) && (strstr(V->buf,"LOCUS") == V->buf))))
+ SeqfileGetLine(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->buf, "LOCUS ") != V->buf)
+ SeqfileGetLine(V);
+}
+
+static int
+endGCGdata(char *s, int *addend)
+{
+ *addend = 0;
+ return (*s == '>');
+}
+
+static void
+readGCGdata(struct ReadSeqVars *V)
+{
+ int binary = FALSE; /* whether data are binary or not */
+ int blen = 0; /* length of binary sequence */
+
+ /* first line contains ">>>>" followed by name */
+ if (Strparse(">>>>([^ ]+) .+2BIT +Len: ([0-9]+)", V->buf, 2))
+ {
+ binary = TRUE;
+ SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME);
+ blen = atoi(sqd_parse[2]);
+ }
+ else if (Strparse(">>>>([^ ]+) .+ASCII +Len: [0-9]+", V->buf, 1))
+ SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME);
+ else
+ Die("bogus GCGdata format? %s", V->buf);
+
+ /* second line contains free text description */
+ SeqfileGetLine(V);
+ SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC);
+
+ if (binary) {
+ /* allocate for blen characters +3... (allow for 3 bytes of slop) */
+ if (blen >= V->maxseq) {
+ V->maxseq = blen;
+ if ((V->seq = (char *) realloc (V->seq, sizeof(char)*(V->maxseq+4)))==NULL)
+ Die("malloc failed");
+ }
+ /* read (blen+3)/4 bytes from file */
+ if (fread(V->seq, sizeof(char), (blen+3)/4, V->f) < (size_t) ((blen+3)/4))
+ Die("fread failed");
+ V->seqlen = blen;
+ /* convert binary code to seq */
+ GCGBinaryToSequence(V->seq, blen);
+ }
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>'))))
+ SeqfileGetLine(V);
+}
+
+static int
+endPearson(char *s, int *addend)
+{
+ *addend = 0;
+ return(*s == '>');
+}
+
+static void
+readPearson(struct ReadSeqVars *V)
+{
+ char *sptr;
+
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if (*V->buf != '>')
+ Die("\
+File %s does not appear to be in FASTA format at line %d.\n\
+You may want to specify the file format on the command line.\n\
+Usually this is done with an option --informat <fmt>.\n",
+ V->fname, V->linenumber);
+
+ if ((sptr = strtok(V->buf+1, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>')))) {
+ SeqfileGetLine(V);
+ }
+}
+
+
+static int
+endEMBL(char *s, int *addend)
+{
+ *addend = 0;
+ /* Some people (Berlin 5S rRNA database, f'r instance) use
+ * an extended EMBL format that attaches extra data after
+ * the sequence -- watch out for that. We use the fact that
+ * real EMBL sequence lines begin with five spaces.
+ *
+ * We can use this as the sole end test because readEMBL() will
+ * advance to the next ID line before starting to read again.
+ */
+ return (strncmp(s," ",5) != 0);
+/* return ((strstr(s,"//") != NULL) || (strstr(s,"ID ") == s)); */
+}
+
+static void
+readEMBL(struct ReadSeqVars *V)
+{
+ char *sptr;
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) {
+ SeqfileGetLine(V);
+ }
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if ((sptr = strtok(V->buf+5, "\n\t ")) != NULL)
+ {
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+
+ do {
+ SeqfileGetLine(V);
+ if (!feof(V->f) && strstr(V->buf, "AC ") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+5, "; \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ else if (!feof(V->f) && strstr(V->buf, "DE ") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+5, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ }
+ } while (! feof(V->f) && strncmp(V->buf,"SQ",2) != 0);
+
+ readLoop(0, endEMBL, V);
+
+ /* Hack for Staden experiment files: convert - to N
+ */
+ if (V->ssimode == -1) /* if we're in ssi mode, we're not keeping the seq */
+ for (sptr = V->seq; *sptr != '\0'; sptr++)
+ if (*sptr == '-') *sptr = 'N';
+
+ /* reading a real EMBL database file, we keep the source coords
+ */
+ V->sqinfo->start = 1;
+ V->sqinfo->stop = V->seqlen;
+ V->sqinfo->olen = V->seqlen;
+ V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) {
+ SeqfileGetLine(V);
+ }
+
+}
+
+
+static int
+endZuker(char *s, int *addend)
+{
+ *addend = 0;
+ return( *s == '(' );
+}
+
+static void
+readZuker(struct ReadSeqVars *V)
+{
+ char *sptr;
+
+ SeqfileGetLine(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->buf+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->buf != '\0') & (*V->buf == '('))))
+ SeqfileGetLine(V);
+}
+
+static void
+readUWGCG(struct ReadSeqVars *V)
+{
+ char *si;
+ char *sptr;
+ int done;
+
+ V->seqlen = 0;
+
+ /*writeseq: " %s Length: %d (today) Check: %d ..\n" */
+ /*drop above or ".." from id*/
+ if ((si = strstr(V->buf," Length: ")) != NULL) *si = 0;
+ else if ((si = strstr(V->buf,"..")) != NULL) *si = 0;
+
+ if ((sptr = strtok(V->buf, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+ do {
+ done = feof(V->f);
+ SeqfileGetLine(V);
+ if (! done) addseq(V->buf, V);
+ } while (!done);
+}
+
+
+/* Function: ReadSeq()
+ *
+ * Purpose: Read next sequence from an open database file.
+ * Return the sequence and associated info.
+ *
+ * Args: fp - open sequence database file pointer
+ * format - format of the file (previously determined
+ * by call to SeqfileFormat()).
+ * Currently unused, since we carry it in V.
+ * ret_seq - RETURN: sequence
+ * sqinfo - RETURN: filled in w/ other information
+ *
+ * Limitations: uses squid_errno, so it's not threadsafe.
+ *
+ * Return: 1 on success, 0 on failure.
+ * ret_seq and some field of sqinfo are allocated here,
+ * The preferred call mechanism to properly free the memory is:
+ *
+ * SQINFO sqinfo;
+ * char *seq;
+ *
+ * ReadSeq(fp, format, &seq, &sqinfo);
+ * ... do something...
+ * FreeSequence(seq, &sqinfo);
+ */
+int
+ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
+{
+ int gotuw;
+
+ squid_errno = SQERR_OK;
+
+ /* Here's the hack for sequential access of sequences from
+ * the multiple sequence alignment formats
+ */
+ if (IsAlignmentFormat(V->format))
+ {
+ if (V->msa->lastidx >= V->msa->nseq)
+ { /* out of data. try to read another alignment */
+ MSAFree(V->msa);
+ if ((V->msa = MSAFileRead(V->afp)) == NULL)
+ return 0;
+ V->msa->lastidx = 0;
+ }
+ /* copy and dealign the appropriate aligned seq */
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ V->seq = sre_strdup(V->msa->aseq[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->aseq[V->msa->lastidx], &(V->seq));
+#endif
+ V->seqlen = strlen(V->seq);
+
+ /* Extract sqinfo stuff for this sequence from the msa.
+ * Tedious; code that should be cleaned.
+ */
+ sqinfo->flags = 0;
+ if (V->msa->sqname[V->msa->lastidx] != NULL)
+ SetSeqinfoString(sqinfo, V->msa->sqname[V->msa->lastidx], SQINFO_NAME);
+ if (V->msa->sqacc != NULL && V->msa->sqacc[V->msa->lastidx] != NULL)
+ SetSeqinfoString(sqinfo, V->msa->sqacc[V->msa->lastidx], SQINFO_ACC);
+ if (V->msa->sqdesc != NULL && V->msa->sqdesc[V->msa->lastidx] != NULL)
+ SetSeqinfoString(sqinfo, V->msa->sqdesc[V->msa->lastidx], SQINFO_DESC);
+ if (V->msa->ss != NULL && V->msa->ss[V->msa->lastidx] != NULL) {
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ sqinfo->ss = sre_strdup(V->msa->ss[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->ss[V->msa->lastidx], &(sqinfo->ss));
+#endif
+ sqinfo->flags |= SQINFO_SS;
+ }
+ if (V->msa->sa != NULL && V->msa->sa[V->msa->lastidx] != NULL) {
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ sqinfo->sa = sre_strdup(V->msa->sa[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->sa[V->msa->lastidx], &(sqinfo->sa));
+#endif
+ sqinfo->flags |= SQINFO_SA;
+ }
+ V->msa->lastidx++;
+ }
+ else {
+ if (feof(V->f)) return 0;
+
+ if (V->ssimode == -1) { /* normal mode */
+ V->seq = (char*) calloc (kStartLength+1, sizeof(char));
+ V->maxseq = kStartLength;
+ } else { /* index mode: discarding seq */
+ V->seq = NULL;
+ V->maxseq = 0;
+ }
+ V->seqlen = 0;
+ V->sqinfo = sqinfo;
+ V->sqinfo->flags = 0;
+
+ switch (V->format) {
+ case SQFILE_IG : readIG(V); break;
+ case SQFILE_STRIDER : readStrider(V); break;
+ case SQFILE_GENBANK : readGenBank(V); break;
+ case SQFILE_FASTA : readPearson(V); break;
+ case SQFILE_EMBL : readEMBL(V); break;
+ case SQFILE_ZUKER : readZuker(V); break;
+ case SQFILE_PIR : readPIR(V); break;
+ case SQFILE_GCGDATA : readGCGdata(V); break;
+
+ case SQFILE_GCG :
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->buf,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+ SeqfileGetLine(V);
+ } while (! feof(V->f));
+ break;
+
+ case SQFILE_IDRAW: /* SRE: no attempt to read idraw postscript */
+ default:
+ squid_errno = SQERR_FORMAT;
+ free(V->seq);
+ return 0;
+ }
+ if (V->seq != NULL) /* (it can be NULL in indexing mode) */
+ V->seq[V->seqlen] = 0; /* stick a string terminator on it */
+ }
+
+ /* Cleanup
+ */
+ sqinfo->len = V->seqlen;
+ sqinfo->flags |= SQINFO_LEN;
+ *ret_seq = V->seq;
+ if (squid_errno == SQERR_OK) return 1; else return 0;
+}
+
+/* Function: SeqfileFormat()
+ * Date: SRE, Tue Jun 22 10:58:58 1999 [Sanger Centre]
+ *
+ * Purpose: Determine format of an open file.
+ * Returns format code.
+ * Rewinds the file.
+ *
+ * Autodetects the following unaligned formats:
+ * SQFILE_FASTA
+ * SQFILE_GENBANK
+ * SQFILE_EMBL
+ * SQFILE_GCG
+ * SQFILE_GCGDATA
+ * SQFILE_PIR
+ * Also autodetects the following alignment formats:
+ * MSAFILE_STOCKHOLM
+ * MSAFILE_MSF
+ * MSAFILE_CLUSTAL
+ * MSAFILE_SELEX
+ * MSAFILE_PHYLIP
+ *
+ * Can't autodetect MSAFILE_A2M, calls it SQFILE_FASTA.
+ * MSAFileFormat() does the opposite.
+ *
+ * Args: sfp - open SQFILE
+ *
+ * Return: format code, or SQFILE_UNKNOWN if unrecognized
+ */
+int
+SeqfileFormat(FILE *fp)
+{
+ char *buf;
+ int len;
+ int fmt = SQFILE_UNKNOWN;
+ int ndataline;
+ char *bufcpy, *s, *s1, *s2;
+ int has_junk;
+
+ buf = NULL;
+ len = 0;
+ ndataline = 0;
+ has_junk = FALSE;
+ while (sre_fgets(&buf, &len, fp) != NULL)
+ {
+ if (IsBlankline(buf)) continue;
+
+ /* Well-behaved formats identify themselves in first nonblank line.
+ */
+ if (ndataline == 0)
+ {
+ if (strncmp(buf, ">>>>", 4) == 0 && strstr(buf, "Len: "))
+ { fmt = SQFILE_GCGDATA; goto DONE; }
+
+ if (buf[0] == '>')
+ { fmt = SQFILE_FASTA; goto DONE; }
+
+ if (strncmp(buf, "!!AA_SEQUENCE", 13) == 0 ||
+ strncmp(buf, "!!NA_SEQUENCE", 13) == 0)
+ { fmt = SQFILE_GCG; goto DONE; }
+
+ if (strncmp(buf, "# STOCKHOLM 1.", 14) == 0)
+ { fmt = MSAFILE_STOCKHOLM; goto DONE; }
+
+ if (strncmp(buf, "CLUSTAL", 7) == 0 &&
+ strstr(buf, "multiple sequence alignment") != NULL)
+ { fmt = MSAFILE_CLUSTAL; goto DONE; }
+
+ if (strncmp(buf, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0 ||
+ strncmp(buf, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0)
+ { fmt = MSAFILE_MSF; goto DONE; }
+
+ /* PHYLIP id: also just a good bet */
+ bufcpy = sre_strdup(buf, -1);
+ s = bufcpy;
+ if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) != NULL &&
+ (s2 = sre_strtok(&s, WHITESPACE, NULL)) != NULL &&
+ IsInt(s1) &&
+ IsInt(s2))
+ { free(bufcpy); fmt = MSAFILE_PHYLIP; goto DONE; }
+ free(bufcpy);
+ }
+
+ /* We trust that other formats identify themselves soon.
+ */
+ /* dead giveaways for extended SELEX */
+ if (strncmp(buf, "#=AU", 4) == 0 ||
+ strncmp(buf, "#=ID", 4) == 0 ||
+ strncmp(buf, "#=AC", 4) == 0 ||
+ strncmp(buf, "#=DE", 4) == 0 ||
+ strncmp(buf, "#=GA", 4) == 0 ||
+ strncmp(buf, "#=TC", 4) == 0 ||
+ strncmp(buf, "#=NC", 4) == 0 ||
+ strncmp(buf, "#=SQ", 4) == 0 ||
+ strncmp(buf, "#=SS", 4) == 0 ||
+ strncmp(buf, "#=CS", 4) == 0 ||
+ strncmp(buf, "#=RF", 4) == 0)
+ { fmt = MSAFILE_SELEX; goto DONE; }
+
+ if (strncmp(buf, "///", 3) == 0 || strncmp(buf, "ENTRY ", 6) == 0)
+ { fmt = SQFILE_PIR; goto DONE; }
+
+ /* a ha, diagnostic of an (old) MSF file */
+ if ((strstr(buf, "..") != NULL) &&
+ (strstr(buf, "MSF:") != NULL) &&
+ (strstr(buf, "Check:")!= NULL))
+ { fmt = MSAFILE_MSF; goto DONE; }
+
+ /* unaligned GCG (must follow MSF test!) */
+ if (strstr(buf, " Check: ") != NULL && strstr(buf, "..") != NULL)
+ { fmt = SQFILE_GCG; goto DONE; }
+
+ if (strncmp(buf,"LOCUS ",6) == 0 || strncmp(buf,"ORIGIN ",6) == 0)
+ { fmt = SQFILE_GENBANK; goto DONE; }
+
+ if (strncmp(buf,"ID ",5) == 0 || strncmp(buf,"SQ ",5) == 0)
+ { fmt = SQFILE_EMBL; goto DONE; }
+
+ /* But past here, we're being desperate. A simple SELEX file is
+ * very difficult to detect; we can only try to disprove it.
+ */
+ s = buf;
+ if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; /* skip blank lines */
+ if (strchr("#%", *s1) != NULL) continue; /* skip comment lines */
+
+ /* Disproof 1. Noncomment, nonblank lines in a SELEX file
+ * must have at least two space-delimited fields (name/seq)
+ */
+ if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL)
+ has_junk = TRUE;
+
+ /* Disproof 2.
+ * The sequence field should look like a sequence.
+ */
+ if (s2 != NULL && Seqtype(s2) == kOtherSeq)
+ has_junk = TRUE;
+
+ ndataline++;
+ if (ndataline == 300) break; /* only look at first 300 lines */
+ }
+
+ if (ndataline == 0)
+ Die("Sequence file contains no data");
+
+ /* If we've made it this far, we've run out of data, but there
+ * was at least one line of it; check if we've
+ * disproven SELEX. If not, cross our fingers, pray, and guess SELEX.
+ */
+ if (has_junk == TRUE) fmt = SQFILE_UNKNOWN;
+ else fmt = MSAFILE_SELEX;
+
+ DONE:
+ if (buf != NULL) free(buf);
+ rewind(fp);
+ return fmt;
+}
+
+/* Function: GCGBinaryToSequence()
+ *
+ * Purpose: Convert a GCG 2BIT binary string to DNA sequence.
+ * 0 = C 1 = T 2 = A 3 = G
+ * 4 nts/byte
+ *
+ * Args: seq - binary sequence. Converted in place to DNA.
+ * len - length of DNA. binary is (len+3)/4 bytes
+ */
+int
+GCGBinaryToSequence(char *seq, int len)
+{
+ int bpos; /* position in binary */
+ int spos; /* position in sequence */
+ char twobit;
+ int i;
+
+ for (bpos = (len-1)/4; bpos >= 0; bpos--)
+ {
+ twobit = seq[bpos];
+ spos = bpos*4;
+
+ for (i = 3; i >= 0; i--)
+ {
+ switch (twobit & 0x3) {
+ case 0: seq[spos+i] = 'C'; break;
+ case 1: seq[spos+i] = 'T'; break;
+ case 2: seq[spos+i] = 'A'; break;
+ case 3: seq[spos+i] = 'G'; break;
+ }
+ twobit = twobit >> 2;
+ }
+ }
+ seq[len] = '\0';
+ return 1;
+}
+
+
+/* Function: GCGchecksum()
+ * Date: SRE, Mon May 31 11:13:21 1999 [St. Louis]
+ *
+ * Purpose: Calculate a GCG checksum for a sequence.
+ * Code provided by Steve Smith of Genetics
+ * Computer Group.
+ *
+ * Args: seq - sequence to calculate checksum for.
+ * may contain gap symbols.
+ * len - length of sequence (usually known,
+ * so save a strlen() call)
+ *
+ * Returns: GCG checksum.
+ */
+int
+GCGchecksum(char *seq, int len)
+{
+ int i; /* position in sequence */
+ int chk = 0; /* calculated checksum */
+
+ for (i = 0; i < len; i++)
+ chk = (chk + (i % 57 + 1) * (sre_toupper((int) seq[i]))) % 10000;
+ return chk;
+}
+
+
+/* Function: GCGMultchecksum()
+ *
+ * Purpose: GCG checksum for a multiple alignment: sum of
+ * individual sequence checksums (including their
+ * gap characters) modulo 10000.
+ *
+ * Implemented using spec provided by Steve Smith of
+ * Genetics Computer Group.
+ *
+ * Args: seqs - sequences to be checksummed; aligned or not
+ * nseq - number of sequences
+ *
+ * Return: the checksum, a number between 0 and 9999
+ */
+int
+GCGMultchecksum(char **seqs, int nseq)
+{
+ int chk = 0;
+ int idx;
+
+ for (idx = 0; idx < nseq; idx++)
+ chk = (chk + GCGchecksum(seqs[idx], strlen(seqs[idx]))) % 10000;
+ return chk;
+}
+
+
+
+
+/* Function: Seqtype()
+ *
+ * Purpose: Returns a (very good) guess about type of sequence:
+ * kDNA, kRNA, kAmino, or kOtherSeq.
+ *
+ * Modified from, and replaces, Gilbert getseqtype().
+ */
+int
+Seqtype(char *seq)
+{
+ int saw; /* how many non-gap characters I saw */
+ char c;
+ int po = 0; /* count of protein-only */
+ int nt = 0; /* count of t's */
+ int nu = 0; /* count of u's */
+ int na = 0; /* count of nucleotides */
+ int aa = 0; /* count of amino acids */
+ int no = 0; /* count of others */
+
+ /* Look at the first 300 non-gap characters
+ */
+
+#ifdef CLUSTALO
+ /* VGGNGDDYLSGGTGNDTL is recognized as unknown using squid's default
+ * approach.
+ * We change it to the following:
+
+ * 1. counting: ignore gaps and not alpha characters. if protein-only then
+ * count as such (po). otherwise decide if amino-acid (aa) or nucleic-acid
+ * (na) or unknown (no)
+ *
+ * 2. determine type: if we saw more unknown than aa or na, return unknown.
+ * if encountered protein-only return protein-only. otherwise decide based
+ * on majority. (if aa==na return na)
+ */
+ for (saw = 0; *seq != '\0' && saw < 300; seq++) {
+ c = sre_toupper((int) *seq);
+ int unknown = 1;
+
+ if (isgap(c) || ! isalpha((int) c)) {
+ continue;
+ }
+
+ if (strchr(protonly, c)) {
+ po++;
+ unknown = 0;
+ }
+
+ if (strchr(aminos,c)) {
+ aa++;
+ unknown = 0;
+ }
+
+ if (strchr(primenuc,c)) {
+ na++;
+ unknown = 0;
+
+ if (c == 'T')
+ nt++;
+ else if (c == 'U')
+ nu++;
+ }
+
+ if (unknown) {
+ no ++;
+ }
+
+ saw++;
+ }
+
+ if (no > aa && no > na)
+ return kOtherSeq;
+
+ if (po > 0 || aa>na)
+ return kAmino;
+
+ if (na >= aa) {
+ if (nu > nt)
+ return kRNA;
+ else
+ return kDNA;
+ }
+
+ return kOtherSeq;
+
+
+#else
+ for (saw = 0; *seq != '\0' && saw < 300; seq++)
+ {
+ c = sre_toupper((int) *seq);
+ if (! isgap(c))
+ {
+ if (strchr(protonly, c)) po++;
+ else if (strchr(primenuc,c)) {
+ na++;
+ if (c == 'T') nt++;
+ else if (c == 'U') nu++;
+ }
+ else if (strchr(aminos,c)) aa++;
+ else if (isalpha((int) c)) no++;
+ saw++;
+ }
+ }
+
+ if (no > 0) return kOtherSeq;
+ else if (po > 0) return kAmino;
+ else if (na > aa) {
+ if (nu > nt) return kRNA;
+ else return kDNA;
+ }
+ else return kAmino; /* ooooh. risky. */
+#endif
+
+}
+
+
+/* Function: GuessAlignmentSeqtype()
+ * Date: SRE, Wed Jul 7 09:42:34 1999 [St. Louis]
+ *
+ * Purpose: Try to guess whether an alignment is protein
+ * or nucleic acid; return a code for the
+ * type (kRNA, kDNA, or kAmino).
+ *
+ * Args: aseq - array of aligned sequences. (Could also
+ * be an rseq unaligned sequence array)
+ * nseq - number of aseqs
+ *
+ * Returns: kRNA, kDNA, kAmino;
+ * kOtherSeq if inconsistency is detected.
+ */
+int
+GuessAlignmentSeqtype(char **aseq, int nseq)
+{
+ int idx;
+ int nrna = 0;
+ int ndna = 0;
+ int namino = 0;
+ int nother = 0;
+
+ for (idx = 0; idx < nseq; idx++)
+ switch (Seqtype(aseq[idx])) {
+ case kRNA: nrna++; break;
+ case kDNA: ndna++; break;
+ case kAmino: namino++; break;
+ default: nother++;
+ }
+
+ /* Unambiguous decisions:
+ */
+ if (nother) return kOtherSeq;
+ if (namino == nseq) return kAmino;
+ if (ndna == nseq) return kDNA;
+ if (nrna == nseq) return kRNA;
+
+ /* Ambiguous decisions:
+ */
+ if (namino == 0) return kRNA; /* it's nucleic acid, but seems mixed RNA/DNA */
+ return kAmino; /* some amino acid seen; others probably short seqs, some
+ of which may be entirely ACGT (ala,cys,gly,thr). We
+ could be a little more sophisticated: U would be a giveaway
+ that we're not in protein seqs */
+}
+
+/* Function: WriteSimpleFASTA()
+ * Date: SRE, Tue Nov 16 18:06:00 1999 [St. Louis]
+ *
+ * Purpose: Just write a FASTA format sequence to a file;
+ * minimal interface, mostly for quick and dirty programs.
+ *
+ * Args: fp - open file handle (stdout, possibly)
+ * seq - sequence to output
+ * name - name for the sequence
+ * desc - optional description line, or NULL.
+ *
+ * Returns: void
+ */
+void
+WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc)
+{
+ char buf[61];
+ int len;
+ int pos;
+
+ len = strlen(seq);
+ buf[60] = '\0';
+ fprintf(fp, ">%s %s\n", name, desc != NULL ? desc : "");
+ for (pos = 0; pos < len; pos += 60)
+ {
+ strncpy(buf, seq+pos, 60);
+ fprintf(fp, "%s\n", buf);
+ }
+}
+
+int
+WriteSeq(FILE *outf, int outform, char *seq, SQINFO *sqinfo)
+{
+ int numline = 0;
+ int lines = 0, spacer = 0, width = 50, tab = 0;
+ int i, j, l, l1, ibase;
+ char endstr[10];
+ char s[100]; /* buffer for sequence */
+ char ss[100]; /* buffer for structure */
+ int checksum = 0;
+ int seqlen;
+ int which_case; /* 0 = do nothing. 1 = upper case. 2 = lower case */
+ int dostruc; /* TRUE to print structure lines*/
+
+ which_case = 0;
+ dostruc = FALSE;
+ seqlen = (sqinfo->flags & SQINFO_LEN) ? sqinfo->len : strlen(seq);
+
+ if (IsAlignmentFormat(outform))
+ Die("Tried to write an aligned format with WriteSeq() -- bad, bad.");
+
+
+ strcpy( endstr,"");
+ l1 = 0;
+ checksum = GCGchecksum(seq, seqlen);
+
+ switch (outform) {
+ case SQFILE_UNKNOWN: /* no header, just sequence */
+ strcpy(endstr,"\n"); /* end w/ extra blank line */
+ break;
+
+ case SQFILE_GENBANK:
+ fprintf(outf,"LOCUS %s %d bp\n",
+ sqinfo->name, seqlen);
+ fprintf(outf,"ACCESSION %s\n",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : ".");
+ fprintf(outf,"DEFINITION %s\n",
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : ".");
+ fprintf(outf,"VERSION %s\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : ".");
+ fprintf(outf,"ORIGIN \n");
+ spacer = 11;
+ numline = 1;
+ strcpy(endstr, "\n//");
+ break;
+
+ case SQFILE_GCGDATA:
+ fprintf(outf, ">>>>%s 9/95 ASCII Len: %d\n", sqinfo->name, seqlen);
+ fprintf(outf, "%s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-");
+ break;
+
+ case SQFILE_PIR:
+ fprintf(outf, "ENTRY %s\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name);
+ fprintf(outf, "TITLE %s\n",
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-");
+ fprintf(outf, "ACCESSION %s\n",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-");
+ fprintf(outf, "SUMMARY #Length %d #Checksum %d\n",
+ sqinfo->len, checksum);
+ fprintf(outf, "SEQUENCE\n");
+ fprintf(outf, " 5 10 15 20 25 30\n");
+ spacer = 2; /* spaces after every residue */
+ numline = 1; /* number lines w/ coords */
+ width = 30; /* 30 aa per line */
+ strcpy(endstr, "\n///");
+ break;
+
+ case SQFILE_SQUID:
+ fprintf(outf, "NAM %s\n", sqinfo->name);
+ if (sqinfo->flags & (SQINFO_ID | SQINFO_ACC | SQINFO_START | SQINFO_STOP | SQINFO_OLEN))
+ fprintf(outf, "SRC %s %s %d..%d::%d\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : "-",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-",
+ (sqinfo->flags & SQINFO_START) ? sqinfo->start : 0,
+ (sqinfo->flags & SQINFO_STOP) ? sqinfo->stop : 0,
+ (sqinfo->flags & SQINFO_OLEN) ? sqinfo->olen : 0);
+ if (sqinfo->flags & SQINFO_DESC)
+ fprintf(outf, "DES %s\n", sqinfo->desc);
+ if (sqinfo->flags & SQINFO_SS)
+ {
+ fprintf(outf, "SEQ +SS\n");
+ dostruc = TRUE; /* print structure lines too */
+ }
+ else
+ fprintf(outf, "SEQ\n");
+ numline = 1; /* number seq lines w/ coords */
+ strcpy(endstr, "\n++");
+ break;
+
+ case SQFILE_EMBL:
+ fprintf(outf,"ID %s\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name);
+ fprintf(outf,"AC %s\n",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-");
+ fprintf(outf,"DE %s\n",
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-");
+ fprintf(outf,"SQ %d BP\n", seqlen);
+ strcpy(endstr, "\n//"); /* 11Oct90: bug fix*/
+ tab = 5; /** added 31jan91 */
+ spacer = 11; /** added 31jan91 */
+ break;
+
+ case SQFILE_GCG:
+ fprintf(outf,"%s\n", sqinfo->name);
+ if (sqinfo->flags & SQINFO_ACC)
+ fprintf(outf,"ACCESSION %s\n", sqinfo->acc);
+ if (sqinfo->flags & SQINFO_DESC)
+ fprintf(outf,"DEFINITION %s\n", sqinfo->desc);
+ fprintf(outf," %s Length: %d (today) Check: %d ..\n",
+ sqinfo->name, seqlen, checksum);
+ spacer = 11;
+ numline = 1;
+ strcpy(endstr, "\n"); /* this is insurance to help prevent misreads at eof */
+ break;
+
+ case SQFILE_STRIDER: /* ?? map ?*/
+ fprintf(outf,"; ### from DNA Strider ;-)\n");
+ fprintf(outf,"; DNA sequence %s, %d bases, %d checksum.\n;\n",
+ sqinfo->name, seqlen, checksum);
+ strcpy(endstr, "\n//");
+ break;
+
+ /* SRE: Don had Zuker default to Pearson, which is not
+ intuitive or helpful, since Zuker's MFOLD can't read
+ Pearson format. More useful to use kIG */
+ case SQFILE_ZUKER:
+ which_case = 1; /* MFOLD requires upper case. */
+ /*FALLTHRU*/
+ case SQFILE_IG:
+ fprintf(outf,";%s %s\n",
+ sqinfo->name,
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "");
+ fprintf(outf,"%s\n", sqinfo->name);
+ strcpy(endstr,"1"); /* == linear dna */
+ break;
+
+ case SQFILE_RAW: /* Raw: no header at all. */
+ break;
+
+ default :
+ case SQFILE_FASTA:
+ fprintf(outf,">%s %s\n", sqinfo->name,
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "");
+ break;
+ }
+
+ if (which_case == 1) s2upper(seq);
+ if (which_case == 2) s2lower(seq);
+
+
+ width = MIN(width,100);
+ for (i=0, l=0, ibase = 1, lines = 0; i < seqlen; ) {
+ if (l1 < 0) l1 = 0;
+ else if (l1 == 0) {
+ if (numline) fprintf(outf,"%8d ",ibase);
+ for (j=0; j<tab; j++) fputc(' ',outf);
+ }
+ if ((spacer != 0) && ((l+1) % spacer == 1))
+ { s[l] = ' '; ss[l] = ' '; l++; }
+ s[l] = seq[i];
+ ss[l] = (sqinfo->flags & SQINFO_SS) ? sqinfo->ss[i] : '.';
+ l++; i++;
+ l1++; /* don't count spaces for width*/
+ if (l1 == width || i == seqlen) {
+ s[l] = ss[l] = '\0';
+ l = 0; l1 = 0;
+ if (dostruc)
+ {
+ fprintf(outf, "%s\n", s);
+ if (numline) fprintf(outf," ");
+ for (j=0; j<tab; j++) fputc(' ',outf);
+ if (i == seqlen) fprintf(outf,"%s%s\n",ss,endstr);
+ else fprintf(outf,"%s\n",ss);
+ }
+ else
+ {
+ if (i == seqlen) fprintf(outf,"%s%s\n",s,endstr);
+ else fprintf(outf,"%s\n",s);
+ }
+ lines++;
+ ibase = i+1;
+ }
+ }
+ return lines;
+}
+
+
+/* Function: ReadMultipleRseqs()
+ *
+ * Purpose: Open a data file and
+ * parse it into an array of rseqs (raw, unaligned
+ * sequences).
+ *
+ * Caller is responsible for free'ing memory allocated
+ * to ret_rseqs, ret_weights, and ret_names.
+ *
+ * Weights are currently only supported for MSF format.
+ * Sequences read from all other formats will be assigned
+ * weights of 1.0. If the caller isn't interested in
+ * weights, it passes NULL as ret_weights.
+ *
+ * Returns 1 on success. Returns 0 on failure and sets
+ * squid_errno to indicate the cause.
+ */
+int
+ReadMultipleRseqs(char *seqfile,
+ int fformat,
+ char ***ret_rseqs,
+ SQINFO **ret_sqinfo,
+ int *ret_num)
+{
+ SQINFO *sqinfo; /* array of sequence optional info */
+ SQFILE *dbfp; /* open ptr for sequential access of file */
+ char **rseqs; /* sequence array */
+ int numalloced; /* num of seqs currently alloced for */
+ int num;
+
+
+ num = 0;
+ numalloced = 16;
+ rseqs = (char **) MallocOrDie (numalloced * sizeof(char *));
+ sqinfo = (SQINFO *) MallocOrDie (numalloced * sizeof(SQINFO));
+ if ((dbfp = SeqfileOpen(seqfile, fformat, NULL)) == NULL) return 0;
+
+ while (ReadSeq(dbfp, dbfp->format, &rseqs[num], &(sqinfo[num])))
+ {
+ num++;
+ if (num == numalloced) /* more seqs coming, alloc more room */
+ {
+ numalloced += 16;
+ rseqs = (char **) ReallocOrDie (rseqs, numalloced*sizeof(char *));
+ sqinfo = (SQINFO *) ReallocOrDie (sqinfo, numalloced * sizeof(SQINFO));
+ }
+ }
+ SeqfileClose(dbfp);
+
+ *ret_rseqs = rseqs;
+ *ret_sqinfo = sqinfo;
+ *ret_num = num;
+ return 1;
+}
+
+
+/* Function: String2SeqfileFormat()
+ * Date: SRE, Sun Jun 27 15:25:54 1999 [TW 723 over Canadian Shield]
+ *
+ * Purpose: Convert a string (e.g. from command line option arg)
+ * to a format code. Case insensitive. Return
+ * MSAFILE_UNKNOWN/SQFILE_UNKNOWN if string is bad.
+ * Uses codes defined in squid.h (unaligned formats) and
+ * msa.h (aligned formats).
+ *
+ * Args: s - string to convert; e.g. "stockholm"
+ *
+ * Returns: format code; e.g. MSAFILE_STOCKHOLM
+ */
+int
+String2SeqfileFormat(char *s)
+{
+ char *s2;
+ int code = SQFILE_UNKNOWN;
+
+ if (s == NULL) return SQFILE_UNKNOWN;
+ s2 = sre_strdup(s, -1);
+ s2upper(s2);
+
+ if (strcmp(s2, "FASTA") == 0) code = SQFILE_FASTA;
+#ifdef CLUSTALO
+ if (strcmp(s2, "FA") == 0) code = SQFILE_FASTA;
+ else if (strcmp(s2, "VIENNA") == 0) code = SQFILE_VIENNA;
+ else if (strcmp(s2, "VIE") == 0) code = SQFILE_VIENNA;
+#endif
+ else if (strcmp(s2, "GENBANK") == 0) code = SQFILE_GENBANK;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "GB") == 0) code = SQFILE_GENBANK;
+#endif
+ else if (strcmp(s2, "EMBL") == 0) code = SQFILE_EMBL;
+ else if (strcmp(s2, "GCG") == 0) code = SQFILE_GCG;
+ else if (strcmp(s2, "GCGDATA") == 0) code = SQFILE_GCGDATA;
+ else if (strcmp(s2, "RAW") == 0) code = SQFILE_RAW;
+ else if (strcmp(s2, "IG") == 0) code = SQFILE_IG;
+ else if (strcmp(s2, "STRIDER") == 0) code = SQFILE_STRIDER;
+ else if (strcmp(s2, "IDRAW") == 0) code = SQFILE_IDRAW;
+ else if (strcmp(s2, "ZUKER") == 0) code = SQFILE_ZUKER;
+ else if (strcmp(s2, "PIR") == 0) code = SQFILE_PIR;
+ else if (strcmp(s2, "SQUID") == 0) code = SQFILE_SQUID;
+ else if (strcmp(s2, "STOCKHOLM") == 0) code = MSAFILE_STOCKHOLM;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "ST") == 0) code = MSAFILE_STOCKHOLM;
+ else if (strcmp(s2, "STK") == 0) code = MSAFILE_STOCKHOLM;
+#endif
+ else if (strcmp(s2, "SELEX") == 0) code = MSAFILE_SELEX;
+ else if (strcmp(s2, "MSF") == 0) code = MSAFILE_MSF;
+ else if (strcmp(s2, "CLUSTAL") == 0) code = MSAFILE_CLUSTAL;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "CLU") == 0) code = MSAFILE_CLUSTAL;
+#endif
+ else if (strcmp(s2, "A2M") == 0) code = MSAFILE_A2M;
+ else if (strcmp(s2, "PHYLIP") == 0) code = MSAFILE_PHYLIP;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "PHY") == 0) code = MSAFILE_PHYLIP;
+#endif
+ else if (strcmp(s2, "EPS") == 0) code = MSAFILE_EPS;
+#ifdef CLUSTALO
+ else code = SQFILE_UNKNOWN;
+#endif
+ free(s2);
+ return code;
+}
+char *
+SeqfileFormat2String(int code)
+{
+ switch (code) {
+ case SQFILE_UNKNOWN: return "unknown";
+ case SQFILE_FASTA: return "FASTA";
+#ifdef CLUSTALO
+ case SQFILE_VIENNA: return "Vienna";
+#endif
+ case SQFILE_GENBANK: return "Genbank";
+ case SQFILE_EMBL: return "EMBL";
+ case SQFILE_GCG: return "GCG";
+ case SQFILE_GCGDATA: return "GCG data library";
+ case SQFILE_RAW: return "raw";
+ case SQFILE_IG: return "Intelligenetics";
+ case SQFILE_STRIDER: return "MacStrider";
+ case SQFILE_IDRAW: return "Idraw Postscript";
+ case SQFILE_ZUKER: return "Zuker";
+ case SQFILE_PIR: return "PIR";
+ case SQFILE_SQUID: return "SQUID";
+ case MSAFILE_STOCKHOLM: return "Stockholm";
+ case MSAFILE_SELEX: return "SELEX";
+ case MSAFILE_MSF: return "MSF";
+ case MSAFILE_CLUSTAL: return "Clustal";
+ case MSAFILE_A2M: return "a2m";
+ case MSAFILE_PHYLIP: return "Phylip";
+ case MSAFILE_EPS: return "EPS";
+ default:
+ Die("Bad code passed to MSAFormat2String()");
+ }
+ /*NOTREACHED*/
+ return NULL;
+}
+
+
+/* Function: MSAToSqinfo()
+ * Date: SRE, Tue Jul 20 14:36:56 1999 [St. Louis]
+ *
+ * Purpose: Take an MSA and generate a SQINFO array suitable
+ * for use in annotating the unaligned sequences.
+ * Return the array.
+ *
+ * Permanent temporary code. sqinfo was poorly designed.
+ * it must eventually be replaced, but the odds
+ * of this happening soon are nil, so I have to deal.
+ *
+ * Args: msa - the alignment
+ *
+ * Returns: ptr to allocated sqinfo array.
+ * Freeing is ghastly: free in each individual sqinfo[i]
+ * with FreeSequence(NULL, &(sqinfo[i])), then
+ * free(sqinfo).
+ */
+SQINFO *
+MSAToSqinfo(MSA *msa)
+{
+ int idx;
+ SQINFO *sqinfo;
+
+ sqinfo = MallocOrDie(sizeof(SQINFO) * msa->nseq);
+
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ sqinfo[idx].flags = 0;
+ SetSeqinfoString(&(sqinfo[idx]),
+ msa->sqname[idx], SQINFO_NAME);
+ SetSeqinfoString(&(sqinfo[idx]),
+ MSAGetSeqAccession(msa, idx), SQINFO_ACC);
+ SetSeqinfoString(&(sqinfo[idx]),
+ MSAGetSeqDescription(msa, idx), SQINFO_DESC);
+
+ if (msa->ss != NULL && msa->ss[idx] != NULL) {
+ MakeDealignedString(msa->aseq[idx], msa->alen,
+ msa->ss[idx], &(sqinfo[idx].ss));
+ sqinfo[idx].flags |= SQINFO_SS;
+ }
+
+ if (msa->sa != NULL && msa->sa[idx] != NULL) {
+ MakeDealignedString(msa->aseq[idx], msa->alen,
+ msa->sa[idx], &(sqinfo[idx].sa));
+ sqinfo[idx].flags |= SQINFO_SA;
+ }
+
+ sqinfo[idx].len = DealignedLength(msa->aseq[idx]);
+ sqinfo[idx].flags |= SQINFO_LEN;
+ }
+ return sqinfo;
+}
+
+
+
+/* cc -o sqio_test -DA_QUIET_DAY -L. sqio.c -lsquid */
+#ifdef A_QUIET_DAY
+#include "ssi.h"
+int
+main(int argc, char **argv)
+{
+ FILE *fp;
+ char *filename;
+ char *buf;
+ int len;
+ int mode = 3;
+ SSIOFFSET off;
+
+ filename = argv[1];
+
+ if (mode == 1) {
+ buf = malloc(sizeof(char) * 256);
+ if ((fp = fopen(filename, "r")) == NULL)
+ Die("open of %s failed", filename);
+ while (fgets(buf, 255, fp) != NULL)
+ ;
+ fclose(fp);
+ free(buf);
+ } else if (mode == 2) {
+ if ((fp = fopen(filename, "r")) == NULL)
+ Die("open of %s failed", filename);
+ buf = NULL; len = 0;
+ while (sre_fgets(&buf, &len, fp) != NULL)
+ SSIGetFilePosition(fp, SSI_OFFSET_I32, &off);
+ fclose(fp);
+ free(buf);
+ } else if (mode == 3) {
+ SQFILE *dbfp;
+ SQINFO info;
+
+ if ((dbfp = SeqfileOpen(filename, SQFILE_FASTA, NULL)) == NULL)
+ Die("open of %s failed", filename);
+ while (ReadSeq(dbfp, dbfp->format, &buf, &info)) {
+ SSIGetFilePosition(dbfp->f, SSI_OFFSET_I32, &off);
+ FreeSequence(buf, &info);
+ }
+ SeqfileClose(dbfp);
+ }
+
+}
+
+
+#endif
git://source.jalview.org / jabaws.git / blobdiff