inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
+ readDomainTable(searchOutputFile, false);
+
if (searchAlignment)
{
recoverSequences(sequencesHash, seqs);
}
}
}
- readTable(searchOutputFile);
+
int seqCount = Math.min(seqs.length, seqsToReturn);
SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];