/*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
- * 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 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
{
- 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 String getCalcName()
+ {
+ return "Conservation";
+ }
+
@Override
public void run()
{
- try
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
{
- calcMan.notifyStart(this); // updatingConservation = true;
-
- while (!calcMan.notifyWorking(this))
- {
- try
- {
- if (ap != null)
- {
- // ap.paintAlignment(false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed()) {
- abortAndDestroy();
- }
- List<AlignmentAnnotation>ourAnnot = new ArrayList<AlignmentAnnotation>();
- AlignmentI alignment=alignViewport.getAlignment();
- conservation=alignViewport.getAlignmentConservationAnnotation();
- quality=alignViewport.getAlignmentQualityAnnot();
- ourAnnot.add(conservation);
- ourAnnot.add(quality);
- ourAnnots = ourAnnot;
-
- // AlignViewport.UPDATING_CONSERVATION = true;
-
- if (alignment==null || (alWidth=alignment.getWidth())< 0)
- {
- calcMan.workerComplete(this);
- //.updatingConservation = false;
- //AlignViewport.UPDATING_CONSERVATION = false;
-
- return;
- }
+ abortAndDestroy();
+ return;
+ }
+ List<AlignmentAnnotation> 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)
+ {
+ // .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);
- updateResultAnnotation(true);
- } catch (OutOfMemoryError error)
+ alignment.getSequences(), 0, alWidth - 1, false,
+ ConsPercGaps, quality != null);
+ } catch (IndexOutOfBoundsException x)
{
- ap.raiseOOMWarning("calculating conservation", error);
- calcMan.workerCannotRun(this);
- // alignViewport.conservation = null;
- // this.alignViewport.quality = null;
-
+ // probable race condition. just finish and return without any fuss.
+ return;
}
- calcMan.workerComplete(this);
+ updateResultAnnotation(true);
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
+ {
+ abortAndDestroy();
+ return;
+ }
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
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()
{