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JAL-2629 hmmer searches now read domain rather than full scores
[jalview.git]
/
src
/
jalview
/
hmmer
/
JackHMMER.java
diff --git
a/src/jalview/hmmer/JackHMMER.java
b/src/jalview/hmmer/JackHMMER.java
index
d822439
..
12c0492
100644
(file)
--- a/
src/jalview/hmmer/JackHMMER.java
+++ b/
src/jalview/hmmer/JackHMMER.java
@@
-26,6
+26,8
@@
import javax.swing.JOptionPane;
public class JackHMMER extends Search
{
public class JackHMMER extends Search
{
+ SequenceI seq = null;
+
/**
* Constructor for the JackhmmerThread
*
/**
* Constructor for the JackhmmerThread
*
@@
-45,7
+47,7
@@
public class JackHMMER extends Search
@Override
public void run()
{
@Override
public void run()
{
- SequenceI seq = getSequence();
+ seq = getSequence();
if (seq == null)
{
// shouldn't happen if we got this far
if (seq == null)
{
// shouldn't happen if we got this far
@@
-138,15
+140,18
@@
public class JackHMMER extends Search
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
+ readDomainTable(searchOutputFile, true);
+
if (searchAlignment)
{
recoverSequences(sequencesHash, seqs);
}
if (searchAlignment)
{
recoverSequences(sequencesHash, seqs);
}
- readTable(searchOutputFile);
+
int seqCount = seqs.length;
int seqCount = seqs.length;
+
AlignmentI al = new Alignment(seqs);
AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignmentI al = new Alignment(seqs);
AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,