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JAL-4366 JAL-728 simple hack to use 3di matrix when gecos-3di is enabled
[jalview.git]
/
src
/
jalview
/
workers
/
ConservationThread.java
diff --git
a/src/jalview/workers/ConservationThread.java
b/src/jalview/workers/ConservationThread.java
index
e71c4f5
..
0afa711
100644
(file)
--- a/
src/jalview/workers/ConservationThread.java
+++ b/
src/jalview/workers/ConservationThread.java
@@
-21,6
+21,7
@@
package jalview.workers;
import jalview.analysis.Conservation;
package jalview.workers;
import jalview.analysis.Conservation;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-55,7
+56,7
@@
public class ConservationThread extends AlignCalcWorker
{
calcMan.notifyStart(this); // updatingConservation = true;
{
calcMan.notifyStart(this); // updatingConservation = true;
- while (!calcMan.notifyWorking(this))
+ while ((calcMan != null) && (!calcMan.notifyWorking(this)))
{
try
{
{
try
{
@@
-69,12
+70,13
@@
public class ConservationThread extends AlignCalcWorker
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();
@@
-94,9
+96,10
@@
public class ConservationThread extends AlignCalcWorker
}
try
{
}
try
{
+ // TODO - TDI is there a conservation measure ?
cons = Conservation.calculateConservation("All",
alignment.getSequences(), 0, alWidth - 1, false,
cons = Conservation.calculateConservation("All",
alignment.getSequences(), 0, alWidth - 1, false,
- ConsPercGaps, quality != null);
+ ConsPercGaps, quality != null, alignViewport.is3di() ? ScoreModels.getInstance().getFOLDSEEK3DI():ScoreModels.getInstance().getDefaultModel(true));
} catch (IndexOutOfBoundsException x)
{
// probable race condition. just finish and return without any fuss.
} catch (IndexOutOfBoundsException x)
{
// probable race condition. just finish and return without any fuss.
@@
-114,9
+117,15
@@
public class ConservationThread extends AlignCalcWorker
}
calcMan.workerComplete(this);
}
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);
}
}
}
}