/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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.
- *
- * 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
+ * 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
* 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 <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-public class ConservationThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class ConservationThread extends AlignCalcWorker implements
+ AlignCalcWorkerI
{
- private int ConsPercGaps = 25; // JBPNote : This should be a configurable property!
+ private int ConsPercGaps = 25; // JBPNote : This should be a configurable
+ // property!
- public ConservationThread(AlignViewportI alignViewport, AlignmentViewPanel alignPanel)
+ 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()
{
ex.printStackTrace();
}
}
- if (alignViewport.isClosed()) {
+ if (alignViewport.isClosed())
+ {
abortAndDestroy();
}
- List<AlignmentAnnotation>ourAnnot = new ArrayList<AlignmentAnnotation>();
- AlignmentI alignment=alignViewport.getAlignment();
- conservation=alignViewport.getAlignmentConservationAnnotation();
- quality=alignViewport.getAlignmentQualityAnnot();
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+ 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;
}
-
- cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
+ 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;
+ }
updateResultAnnotation(true);
} catch (OutOfMemoryError error)
{
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()
{