X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=194c389cef1d8df1f043a2c13bc5a2a3b4a81f4a;hb=6c87693cd4f9dcf81b01983a3dbebc5dec6fde06;hp=bd025a54cb7529d1a7a283c36422a4ac04bc7e93;hpb=d401de55954416f6f76237715199097a64cc99bd;p=jalview.git
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index bd025a5..194c389 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,22 +1,25 @@
/*
* 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
- *
+ *
* 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
+ * 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.
- *
- * 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
+ *
+ * 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 .
*/
package jalview.workers;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignmentViewPanel;
@@ -28,26 +31,30 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
{
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;
+ 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)
@@ -58,28 +65,35 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
if (alignViewport.isClosed()) {
abortAndDestroy();
}
-
+ ListourAnnot = new ArrayList();
AlignmentI alignment=alignViewport.getAlignment();
- AlignmentAnnotation conservation=alignViewport.getAlignmentConservationAnnotation();
- AlignmentAnnotation quality=alignViewport.getAlignmentQualityAnnot();
+ conservation=alignViewport.getAlignmentConservationAnnotation();
+ quality=alignViewport.getAlignmentQualityAnnot();
+ ourAnnot.add(conservation);
+ ourAnnot.add(quality);
+ ourAnnots = ourAnnot;
+
// AlignViewport.UPDATING_CONSERVATION = true;
- int alWidth;
-
if (alignment==null || (alWidth=alignment.getWidth())< 0)
{
calcMan.workerComplete(this);
//.updatingConservation = false;
//AlignViewport.UPDATING_CONSERVATION = false;
-
+
return;
}
-
- Conservation cons = Conservation.calculateConservation("All",
+ try {
+ cons = Conservation.calculateConservation("All",
jalview.schemes.ResidueProperties.propHash, 3,
alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
- cons.completeAnnotations(conservation,
- quality, 0, alWidth);
+ } catch (IndexOutOfBoundsException x)
+ {
+ // probable race condition. just finish and return without any fuss.
+ calcMan.workerComplete(this);
+ return;
+ }
+ updateResultAnnotation(true);
} catch (OutOfMemoryError error)
{
ap.raiseOOMWarning("calculating conservation", error);
@@ -96,4 +110,17 @@ 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);
+ }
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+
+ }
}