X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=4471b6e8905be30fee016dcd7e8aa0f61bd24ae3;hb=91c77a3db54eb4a270b03bcf9a6d97255c1fce35;hp=25e5cde1c50152d718ff739248272ffc7362a1dd;hpb=abeb1ce92e146611f2e7b57ff3e0f8169a216991;p=jalview.git
diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 25e5cde..4471b6e 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,24 +1,25 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
@@ -28,6 +29,8 @@ import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
+import java.util.Hashtable;
+
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
@@ -41,7 +44,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
Hashtable[] hStrucConsensus;
- private long nseq=-1;
+ private long nseq = -1;
@Override
public void run()
@@ -71,6 +74,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
@@ -110,11 +114,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements
try
{
- final SequenceI[] arr=
- alignment.getSequencesArray();
+ final SequenceI[] arr = alignment.getSequencesArray();
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);
@@ -163,7 +166,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
}