X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=54b0191169f79e21eebc431d55d75c3dbf5efc9c;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=021e6e2cfb63d928755823bb3759a15230b2c92c;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 021e6e2..54b0191 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,34 +1,35 @@
/*
- * 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 .
+ *
+ * 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
{
private int ConsPercGaps = 25; // JBPNote : This should be a configurable
@@ -54,7 +55,7 @@ public class ConservationThread extends AlignCalcWorker implements
{
calcMan.notifyStart(this); // updatingConservation = true;
- while (!calcMan.notifyWorking(this))
+ while ((calcMan != null) && (!calcMan.notifyWorking(this)))
{
try
{
@@ -68,18 +69,20 @@ public class ConservationThread extends AlignCalcWorker implements
ex.printStackTrace();
}
}
- if (alignViewport.isClosed())
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
{
abortAndDestroy();
+ return;
}
- List ourAnnot = new ArrayList();
+ 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)
@@ -93,7 +96,6 @@ public class ConservationThread extends AlignCalcWorker implements
try
{
cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
@@ -106,16 +108,22 @@ public class ConservationThread extends AlignCalcWorker implements
} catch (OutOfMemoryError error)
{
ap.raiseOOMWarning("calculating conservation", error);
- calcMan.workerCannotRun(this);
+ calcMan.disableWorker(this);
// alignViewport.conservation = null;
// this.alignViewport.quality = null;
}
calcMan.workerComplete(this);
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
+ {
+ abortAndDestroy();
+ return;
+ }
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
@@ -124,7 +132,10 @@ public class ConservationThread extends AlignCalcWorker implements
{
if (b || !calcMan.isWorking(this) && cons != null
&& conservation != null && quality != null)
+ {
+ alignViewport.setConservation(cons);
cons.completeAnnotations(conservation, quality, 0, alWidth);
+ }
}
@Override