import java.util.Hashtable;
-import jalview.analysis.AAFrequency;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker implements
+ AlignCalcWorkerI
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
super(alignViewport, alignPanel);
}
+
AlignmentAnnotation strucConsensus;
+
Hashtable[] hStrucConsensus;
+ @Override
public void run()
{
try
{
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
calcMan.notifyStart(this);
while (!calcMan.notifyWorking(this))
{
{
if (ap != null)
{
- ap.paintAlignment(false);
+ // ap.paintAlignment(false);
}
Thread.sleep(200);
calcMan.workerComplete(this);
return;
}
- strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
- hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+ strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
+ hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
strucConsensus.annotations = null;
strucConsensus.annotations = new Annotation[aWidth];
}
}
// check to see if its valid
-
- if (rnaStruc==null || !rnaStruc.isValidStruc())
+
+ if (rnaStruc == null || !rnaStruc.isValidStruc())
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ try
+ {
+ jalview.analysis.StructureFrequency.calculate(
+ alignment.getSequencesArray(), 0, alignment.getWidth(),
+ hStrucConsensus, true, rnaStruc);
+ } catch (ArrayIndexOutOfBoundsException x)
{
calcMan.workerComplete(this);
return;
}
-
- jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hStrucConsensus, true, rnaStruc);
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
- if (alignViewport.getGlobalColourScheme()!= null)
+ if (alignViewport.getGlobalColourScheme() != null)
{
alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
}
// consensus = null;
// hconsensus = null;
ap.raiseOOMWarning("calculating RNA structure consensus", error);
- }
-
- calcMan.workerComplete(this);
- if (ap != null)
+ } finally
{
- ap.paintAlignment(true);
+ calcMan.workerComplete(this);
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
}
}
+
/**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
+ @Override
public void updateAnnotation()
{
updateResultAnnotation(false);
public void updateResultAnnotation(boolean immediate)
{
- if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
+ if (immediate || !calcMan.isWorking(this) && strucConsensus != null
+ && hStrucConsensus != null)
{
- StructureFrequency.completeConsensus(strucConsensus,
- hStrucConsensus, 0, hStrucConsensus.length,
+ StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
+ 0, hStrucConsensus.length,
alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isShowSequenceLogo());
}
}