/* 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;
}
/*****************************************************************
* msf.c test driver:
* cc -DTESTDRIVE_CLUSTAL -g -O2 -Wall -o test clustal.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm
*
*/
int
main(int argc, char **argv)
{
MSAFILE *afp;
MSA *msa;
char *file;
file = argv[1];
if ((afp = MSAFileOpen(file, MSAFILE_CLUSTAL, NULL)) == NULL)
Die("Couldn't open %s\n", file);
while ((msa = ReadClustal(afp)) != NULL)
{
WriteClustal(stdout, msa);
MSAFree(msa);
}
MSAFileClose(afp);
exit(0);
}
