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JAL-2629 hmmer searches now read domain rather than full scores
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMSearch.java
diff --git
a/src/jalview/hmmer/HMMSearch.java
b/src/jalview/hmmer/HMMSearch.java
index
f670633
..
f05823e
100644
(file)
--- a/
src/jalview/hmmer/HMMSearch.java
+++ b/
src/jalview/hmmer/HMMSearch.java
@@
-157,6
+157,8
@@
public class HMMSearch extends Search
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
+ readDomainTable(searchOutputFile, false);
+
if (searchAlignment)
{
recoverSequences(sequencesHash, seqs);
if (searchAlignment)
{
recoverSequences(sequencesHash, seqs);
@@
-179,7
+181,7
@@
public class HMMSearch extends Search
}
}
}
}
}
}
- readTable(searchOutputFile);
+
int seqCount = Math.min(seqs.length, seqsToReturn);
SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
int seqCount = Math.min(seqs.length, seqsToReturn);
SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];