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Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
SeqSearchWSThread.java
diff --git
a/src/jalview/ws/jws1/SeqSearchWSThread.java
b/src/jalview/ws/jws1/SeqSearchWSThread.java
index
a6e3731
..
66fddd1
100644
(file)
--- a/
src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/
src/jalview/ws/jws1/SeqSearchWSThread.java
@@
-21,6
+21,7
@@
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
@@
-34,7
+35,9
@@
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
import vamsas.objects.simple.MsaResult;
import java.util.Vector;
import vamsas.objects.simple.MsaResult;
@@
-150,6
+153,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
*
* @return true if getAlignment will return a valid alignment result.
*/
*
* @return true if getAlignment will return a valid alignment result.
*/
+ @Override
public boolean hasResults()
{
if (subjobComplete
public boolean hasResults()
{
if (subjobComplete
@@
-168,7
+172,8
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ public Object[] getAlignment(Alignment dataset,
+ Map<String, FeatureColourI> featureColours)
{
if (result != null && result.isFinished())
{
if (result != null && result.isFinished())
@@
-285,6
+290,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
*
* @return boolean true if job can be submitted.
*/
*
* @return boolean true if job can be submitted.
*/
+ @Override
public boolean hasValidInput()
{
if (seqs.getSeqs() != null)
public boolean hasValidInput()
{
if (seqs.getSeqs() != null)
@@
-371,11
+377,13
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
}
}
}
+ @Override
public boolean isCancellable()
{
return true;
}
public boolean isCancellable()
{
return true;
}
+ @Override
public void cancelJob()
{
if (!jobComplete && jobs != null)
public void cancelJob()
{
if (!jobComplete && jobs != null)
@@
-442,12
+450,14
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
}
}
}
+ @Override
public void pollJob(AWsJob job) throws Exception
{
((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
.getJobId());
}
public void pollJob(AWsJob job) throws Exception
{
((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
.getJobId());
}
+ @Override
public void StartJob(AWsJob job)
{
if (!(job instanceof SeqSearchWSJob))
public void StartJob(AWsJob job)
{
if (!(job instanceof SeqSearchWSJob))
@@
-534,6
+544,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
return msa;
}
return msa;
}
+ @Override
public void parseResult()
{
int results = 0; // number of result sets received
public void parseResult()
{
int results = 0; // number of result sets received
@@
-577,6
+588,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
@@
-585,6
+597,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
@@
-610,7
+623,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Hashtable featureColours = new Hashtable();
+ Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
@@
-662,6
+675,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
}
}
}
+ @Override
public boolean canMergeResults()
{
return false;
public boolean canMergeResults()
{
return false;