X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=e71c4f58a60d1ca927d0829db7a7a5f9e6f286c5;hb=ce50fa39f4fb3617b344d77f230caa6486acd0a4;hp=021e6e2cfb63d928755823bb3759a15230b2c92c;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 021e6e2..e71c4f5 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
@@ -71,6 +72,7 @@ public class ConservationThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
List ourAnnot = new ArrayList();
AlignmentI alignment = alignViewport.getAlignment();
@@ -79,7 +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)
@@ -93,7 +95,6 @@ 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)
@@ -106,7 +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;
@@ -124,7 +125,10 @@ 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