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Merge branch 'features/JAL-1641_JSON-tests-and-docs' into develop
[jalview.git]
/
src
/
jalview
/
workers
/
StrucConsensusThread.java
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
1122663
..
4471b6e
100644
(file)
--- a/
src/jalview/workers/StrucConsensusThread.java
+++ b/
src/jalview/workers/StrucConsensusThread.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,8
+20,6
@@
*/
package jalview.workers;
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
@@
-31,6
+29,8
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
+import java.util.Hashtable;
+
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
@@
-44,7
+44,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
Hashtable[] hStrucConsensus;
Hashtable[] hStrucConsensus;
- private long nseq=-1;
+ private long nseq = -1;
@Override
public void run()
@Override
public void run()
@@
-74,6
+74,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
}
AlignmentI alignment = alignViewport.getAlignment();
@@
-113,11
+114,10
@@
public class StrucConsensusThread extends AlignCalcWorker implements
try
{
try
{
- final SequenceI[] arr=
- alignment.getSequencesArray();
+ final SequenceI[] arr = alignment.getSequencesArray();
nseq = arr.length;
nseq = arr.length;
- jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
- hStrucConsensus, true, rnaStruc);
+ jalview.analysis.StructureFrequency.calculate(arr, 0,
+ alignment.getWidth(), hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
calcMan.workerComplete(this);
} catch (ArrayIndexOutOfBoundsException x)
{
calcMan.workerComplete(this);
@@
-166,7
+166,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
}
alignViewport.isShowSequenceLogo(), nseq);
}
}