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JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...
[jalview.git]
/
src
/
jalview
/
workers
/
ConservationThread.java
diff --git
a/src/jalview/workers/ConservationThread.java
b/src/jalview/workers/ConservationThread.java
index
c0b901e
..
54b0191
100644
(file)
--- a/
src/jalview/workers/ConservationThread.java
+++ b/
src/jalview/workers/ConservationThread.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*
* This file is part of Jalview.
*
@@
-21,7
+21,6
@@
package jalview.workers;
import jalview.analysis.Conservation;
package jalview.workers;
import jalview.analysis.Conservation;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-30,8
+29,7
@@
import jalview.datamodel.AlignmentI;
import java.util.ArrayList;
import java.util.List;
import java.util.ArrayList;
import java.util.List;
-public class ConservationThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class ConservationThread extends AlignCalcWorker
{
private int ConsPercGaps = 25; // JBPNote : This should be a configurable
{
private int ConsPercGaps = 25; // JBPNote : This should be a configurable
@@
-57,7
+55,7
@@
public class ConservationThread extends AlignCalcWorker implements
{
calcMan.notifyStart(this); // updatingConservation = true;
{
calcMan.notifyStart(this); // updatingConservation = true;
- while (!calcMan.notifyWorking(this))
+ while ((calcMan != null) && (!calcMan.notifyWorking(this)))
{
try
{
{
try
{
@@
-71,12
+69,13
@@
public class ConservationThread extends AlignCalcWorker implements
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
- if (alignViewport.isClosed())
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
{
abortAndDestroy();
return;
}
{
abortAndDestroy();
return;
}
- List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
AlignmentI alignment = alignViewport.getAlignment();
conservation = alignViewport.getAlignmentConservationAnnotation();
quality = alignViewport.getAlignmentQualityAnnot();
AlignmentI alignment = alignViewport.getAlignment();
conservation = alignViewport.getAlignmentConservationAnnotation();
quality = alignViewport.getAlignmentQualityAnnot();
@@
-97,7
+96,6
@@
public class ConservationThread extends AlignCalcWorker implements
try
{
cons = Conservation.calculateConservation("All",
try
{
cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
@@
-110,16
+108,22
@@
public class ConservationThread extends AlignCalcWorker implements
} catch (OutOfMemoryError error)
{
ap.raiseOOMWarning("calculating conservation", error);
} catch (OutOfMemoryError error)
{
ap.raiseOOMWarning("calculating conservation", error);
- calcMan.workerCannotRun(this);
+ calcMan.disableWorker(this);
// alignViewport.conservation = null;
// this.alignViewport.quality = null;
}
calcMan.workerComplete(this);
// alignViewport.conservation = null;
// this.alignViewport.quality = null;
}
calcMan.workerComplete(this);
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
+ {
+ abortAndDestroy();
+ return;
+ }
if (ap != null)
{
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
}
}