/* Function: ReadAlignment()
*
* Purpose: Given a seqfile name and format, hand it off to appropriate
* parser.
*
* Currently, squid can parse alignments from the following
* interleaved multiple sequence alignment formats:
* MSF (U. of Wisconsin GCG package MSF format)
* SELEX (NeXagen/CU Boulder SELEX format)
* CLUSTAL (Des Higgins' CLUSTALV and CLUSTALW programs)
* and can sequentially read:
* FASTA (aka UCSC's "a2m")
*
* Return: 1 on success; 0 on failure.
* Returned data should be freed by caller with FreeAlignment()
*/
int
ReadAlignment(char *seqfile,
int format,
char ***ret_aseqs,
struct aliinfo_s *ret_ainfo)
{
switch (format) {
case kMSF:
if (! ReadInterleaved(seqfile, skip_MSF, parse_MSF, dataline_MSF, ret_aseqs, ret_ainfo))
return 0;
break;
case kSelex:
if (! ReadSELEX(seqfile, ret_aseqs, ret_ainfo))
return 0;
break;
case kClustal:
if (! ReadInterleaved(seqfile, skip_clustal, parse_clustal, dataline_clustal,
ret_aseqs, ret_ainfo))
return 0;
break;
case kPearson:
ReadAlignedFASTA(seqfile, NULL, ret_aseqs, ret_ainfo);
break;
default: squid_errno = SQERR_FORMAT; return 0;
}
return 1;
}
/* Function: MSAFileRead()
* Date: SRE, Fri May 28 16:01:43 1999 [St. Louis]
*
* Purpose: Read the next msa from an open alignment file.
* This is a wrapper around format-specific calls.
*
* Args: afp - open alignment file
*
* Returns: next alignment, or NULL if out of alignments
*/
MSA *
MSAFileRead(MSAFILE *afp)
{
MSA *msa = NULL;
switch (afp->format) {
case MSAFILE_STOCKHOLM: msa = ReadStockholm(afp); break;
case MSAFILE_MSF: msa = ReadMSF(afp); break;
case MSAFILE_A2M: msa = ReadA2M(afp); break;
case MSAFILE_CLUSTAL: msa = ReadClustal(afp); break;
case MSAFILE_SELEX: msa = ReadSELEX(afp); break;
case MSAFILE_PHYLIP: msa = ReadPhylip(afp); break;
default:
Die("MSAFILE corrupted: bad format index");
}
return msa;
}
