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JAL-2230 JAL-2049 added sequence feature transfer to
[jalview.git]
/
src
/
jalview
/
workers
/
ConservationThread.java
diff --git
a/src/jalview/workers/ConservationThread.java
b/src/jalview/workers/ConservationThread.java
index
236bccf
..
11ec521
100644
(file)
--- a/
src/jalview/workers/ConservationThread.java
+++ b/
src/jalview/workers/ConservationThread.java
@@
-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
@@
-96,8
+94,7
@@
public class ConservationThread extends AlignCalcWorker implements
}
try
{
}
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)
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
@@
-110,7
+107,7
@@
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;
// alignViewport.conservation = null;
// this.alignViewport.quality = null;