/* Function: MSAFileFormat()
* Date: SRE, Fri Jun 18 14:26:49 1999 [Sanger Centre]
*
* Purpose: (Attempt to) determine the format of an alignment file.
* Since it rewinds the file pointer when it's done,
* cannot be used on a pipe or gzip'ed file. Works by
* calling SeqfileFormat() from sqio.c, then making sure
* that the format is indeed an alignment. If the format
* comes back as FASTA, it assumes that the format as A2M
* (e.g. aligned FASTA).
*
* Args: fname - file to evaluate
*
* Returns: format code; e.g. MSAFILE_STOCKHOLM
*/
int
MSAFileFormat(MSAFILE *afp)
{
int fmt;
fmt = SeqfileFormat(afp->f);
if (fmt == SQFILE_FASTA) fmt = MSAFILE_A2M;
if (fmt != MSAFILE_UNKNOWN && ! IsAlignmentFormat(fmt))
Die("File %s does not appear to be an alignment file;\n\
rather, it appears to be an unaligned file in %s format.\n\
I'm expecting an alignment file in this context.\n",
afp->fname,
SeqfileFormat2String(fmt));
return fmt;
}
/* Function: include_alignment()
* Date: SRE, Sun Jul 5 15:25:13 1998 [St. Louis]
*
* Purpose: Given the name of a multiple alignment file,
* align that alignment to the HMM, and add traces
* to an existing array of traces. If do_mapped
* is TRUE, we use the HMM's map file. If not,
* we use P7ViterbiAlignAlignment().
*
* Args: seqfile - name of alignment file
* hmm - model to align to
* do_mapped- TRUE if we're to use the HMM's alignment map
* rsq - RETURN: array of rseqs to add to
* dsq - RETURN: array of dsq to add to
* sqinfo - RETURN: array of SQINFO to add to
* tr - RETURN: array of traces to add to
* nseq - RETURN: number of seqs
*
* Returns: new, realloc'ed arrays for rsq, dsq, sqinfo, tr; nseq is
* increased to nseq+ainfo.nseq.
*/
void
include_alignment(char *seqfile, struct plan7_s *hmm, int do_mapped,
char ***rsq, char ***dsq, SQINFO **sqinfo,
struct p7trace_s ***tr, int *nseq)
{
int format; /* format of alignment file */
char **aseq; /* aligned seqs */
char **newdsq;
char **newrseq;
AINFO ainfo; /* info that goes with aseq */
int idx; /* counter over aseqs */
struct p7trace_s *master; /* master trace */
struct p7trace_s **addtr; /* individual traces for aseq */
if (! SeqfileFormat(seqfile, &format, NULL))
switch (squid_errno) {
case SQERR_NOFILE:
ajFatal("Alignment file %s could not be opened for reading", seqfile);
/*FALLTHRU*/ /* a white lie to shut lint up */
case SQERR_FORMAT:
default:
ajFatal("Failed to determine format of alignment file %s", seqfile);
}
/* read the alignment from file */
if (! ReadAlignment(seqfile, format, &aseq, &ainfo))
ajFatal("Failed to read aligned sequence file %s", seqfile);
for (idx = 0; idx < ainfo.nseq; idx++)
s2upper(aseq[idx]);
/* Verify checksums before mapping */
if (do_mapped && GCGMultchecksum(aseq, ainfo.nseq) != hmm->checksum)
ajFatal("The checksums for alignment file %s and the HMM alignment map don't match.",
seqfile);
/* Get a master trace */
if (do_mapped) master = MasterTraceFromMap(hmm->map, hmm->M, ainfo.alen);
else master = P7ViterbiAlignAlignment(aseq, &ainfo, hmm);
/* convert to individual traces */
ImposeMasterTrace(aseq, ainfo.nseq, master, &addtr);
/* add those traces to existing ones */
*tr = MergeTraceArrays(*tr, *nseq, addtr, ainfo.nseq);
/* additional bookkeeping: add to dsq, sqinfo */
*rsq = ReallocOrDie((*rsq), sizeof(char *) * (*nseq + ainfo.nseq));
DealignAseqs(aseq, ainfo.nseq, &newrseq);
for (idx = *nseq; idx < *nseq + ainfo.nseq; idx++)
(*rsq)[idx] = newrseq[idx - (*nseq)];
free(newrseq);
*dsq = ReallocOrDie((*dsq), sizeof(char *) * (*nseq + ainfo.nseq));
DigitizeAlignment(aseq, &ainfo, &newdsq);
for (idx = *nseq; idx < *nseq + ainfo.nseq; idx++)
(*dsq)[idx] = newdsq[idx - (*nseq)];
free(newdsq);
/* unnecessarily complex, but I can't be bothered... */
*sqinfo = ReallocOrDie((*sqinfo), sizeof(SQINFO) * (*nseq + ainfo.nseq));
for (idx = *nseq; idx < *nseq + ainfo.nseq; idx++)
SeqinfoCopy(&((*sqinfo)[idx]), &(ainfo.sqinfo[idx - (*nseq)]));
*nseq = *nseq + ainfo.nseq;
/* Cleanup */
P7FreeTrace(master);
FreeAlignment(aseq, &ainfo);
/* Return */
return;
}
