X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=11ec5212593d67803a905de96e98e479f5c34c23;hb=73fd64da56448bcb2a7771cc174d9d9c62da87ad;hp=681007e1bc473bda00f8df1f05132e81ff59359a;hpb=8f1b417b654a575bf7a368b4edeffee813042a5c;p=jalview.git
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 681007e..11ec521 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,35 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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
@@ -72,6 +72,7 @@ public class ConservationThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
List ourAnnot = new ArrayList();
AlignmentI alignment = alignViewport.getAlignment();
@@ -80,7 +81,7 @@ public class ConservationThread extends AlignCalcWorker implements
ourAnnot.add(conservation);
ourAnnot.add(quality);
ourAnnots = ourAnnot;
-
+ ConsPercGaps = alignViewport.getConsPercGaps();
// AlignViewport.UPDATING_CONSERVATION = true;
if (alignment == null || (alWidth = alignment.getWidth()) < 0)
@@ -93,8 +94,7 @@ public class ConservationThread extends AlignCalcWorker implements
}
try
{
- cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
+ cons = Conservation.calculateConservation("All", 3,
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
@@ -107,7 +107,7 @@ 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;