X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=20568bf76d4149142b6d854757c4bc22883cd72a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=7d5c661253bc713024a5e434fc23915690004201;hpb=ebec7bf5754da64c85a0b1f26511a503247f158f;p=jalview.git
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 7d5c661..20568bf 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,59 +1,69 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.ArrayList;
-import java.util.List;
-
import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignmentViewPanel;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-public class ConservationThread extends AlignCalcWorker implements AlignCalcWorkerI
+import java.util.ArrayList;
+import java.util.List;
+
+public class ConservationThread extends AlignCalcWorker implements
+ AlignCalcWorkerI
{
- private int ConsPercGaps = 25; // JBPNote : This should be a configurable property!
-
- public ConservationThread(AlignViewportI alignViewport, AlignmentViewPanel alignPanel)
+ private int ConsPercGaps = 25; // JBPNote : This should be a configurable
+ // property!
+
+ public ConservationThread(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
{
super(alignViewport, alignPanel);
ConsPercGaps = alignViewport.getConsPercGaps();
}
-
+
private Conservation cons;
- AlignmentAnnotation conservation,quality;
+
+ AlignmentAnnotation conservation, quality;
+
int alWidth;
+
+ @Override
public void run()
{
try
{
calcMan.notifyStart(this); // updatingConservation = true;
- while (!calcMan.notifyWorking(this))
+ while (!calcMan.notifyWorking(this))
{
try
{
if (ap != null)
{
- ap.paintAlignment(false);
+ // ap.paintAlignment(false);
}
Thread.sleep(200);
} catch (Exception ex)
@@ -61,31 +71,41 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
ex.printStackTrace();
}
}
- if (alignViewport.isClosed()) {
+ if (alignViewport.isClosed())
+ {
abortAndDestroy();
+ return;
}
- ListourAnnot = new ArrayList();
- AlignmentI alignment=alignViewport.getAlignment();
- conservation=alignViewport.getAlignmentConservationAnnotation();
- quality=alignViewport.getAlignmentQualityAnnot();
+ List ourAnnot = new ArrayList();
+ AlignmentI alignment = alignViewport.getAlignment();
+ conservation = alignViewport.getAlignmentConservationAnnotation();
+ quality = alignViewport.getAlignmentQualityAnnot();
ourAnnot.add(conservation);
ourAnnot.add(quality);
ourAnnots = ourAnnot;
-
+ ConsPercGaps = alignViewport.getConsPercGaps();
// AlignViewport.UPDATING_CONSERVATION = true;
-
- if (alignment==null || (alWidth=alignment.getWidth())< 0)
+
+ if (alignment == null || (alWidth = alignment.getWidth()) < 0)
{
calcMan.workerComplete(this);
- //.updatingConservation = false;
- //AlignViewport.UPDATING_CONSERVATION = false;
-
+ // .updatingConservation = false;
+ // AlignViewport.UPDATING_CONSERVATION = false;
+
+ return;
+ }
+ try
+ {
+ cons = Conservation.calculateConservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1, false,
+ ConsPercGaps, quality != null);
+ } catch (IndexOutOfBoundsException x)
+ {
+ // probable race condition. just finish and return without any fuss.
+ calcMan.workerComplete(this);
return;
}
-
- cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
updateResultAnnotation(true);
} catch (OutOfMemoryError error)
{
@@ -106,14 +126,18 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
private void updateResultAnnotation(boolean b)
{
- if (b || !calcMan.isWorking(this) && cons!=null && conservation!=null && quality!=null)
- cons.completeAnnotations(conservation,
- quality, 0, alWidth);
+ if (b || !calcMan.isWorking(this) && cons != null
+ && conservation != null && quality != null)
+ {
+ alignViewport.setConservation(cons);
+ cons.completeAnnotations(conservation, quality, 0, alWidth);
+ }
}
+
@Override
public void updateAnnotation()
{
updateResultAnnotation(false);
-
+
}
}