public class InformationThread extends AlignCalcWorker
{
-
+
Float max = 0f;
-
+
/**
* Constructor for information thread.
*
* @param alignPanel
*/
public InformationThread(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ @Override
+ public void run()
+ {
+ if (calcMan.isPending(this))
{
- super(alignViewport, alignPanel);
+ return;
}
+ calcMan.notifyStart(this);
+ long started = System.currentTimeMillis();
- @Override
- public void run()
+ List<AlignmentAnnotation> information = getInformationAnnotations();
+ try
{
- if (calcMan.isPending(this))
+ if ((information == null) || calcMan.isPending(this))
{
+ calcMan.workerComplete(this);
return;
}
- calcMan.notifyStart(this);
- long started = System.currentTimeMillis();
-
- List<AlignmentAnnotation> information = getInformationAnnotations();
- try
+ while (!calcMan.notifyWorking(this))
{
- if ((information == null) || calcMan.isPending(this))
- {
- calcMan.workerComplete(this);
- return;
- }
- while (!calcMan.notifyWorking(this))
- {
- // System.err.println("Thread
+ // System.err.println("Thread
// (Information"+Thread.currentThread().getName()+") Waiting around.");
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
+ try
+ {
+ if (ap != null)
{
- ex.printStackTrace();
+ ap.paintAlignment(false, false);
}
- }
- if (alignViewport.isClosed())
+ Thread.sleep(200);
+ } catch (Exception ex)
{
- abortAndDestroy();
- return;
+ ex.printStackTrace();
}
- AlignmentI alignment = alignViewport.getAlignment();
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return;
+ }
+ AlignmentI alignment = alignViewport.getAlignment();
- int aWidth = -1;
+ int aWidth = -1;
- if (alignment == null || (aWidth = alignment.getWidth()) < 0)
- {
- calcMan.workerComplete(this);
- return;
- }
+ if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
eraseInformation(aWidth);
computeInformation(alignment);
- updateResultAnnotation(true);
+ updateResultAnnotation(true);
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- } catch (OutOfMemoryError error)
+ if (ap != null)
{
- calcMan.disableWorker(this);
+ ap.paintAlignment(true, true);
+ }
+ } catch (OutOfMemoryError error)
+ {
+ calcMan.disableWorker(this);
ap.raiseOOMWarning("calculating information", error);
} finally
{
calcMan.workerComplete(this);
- }
-
-
-
}
+ }
- /**
+ /**
* Clear out any existing information annotations
*
* @param aWidth
* the width (number of columns) of the annotated alignment
*/
protected void eraseInformation(int aWidth)
- {
+ {
List<AlignmentAnnotation> information = getInformationAnnotations();
for (AlignmentAnnotation info : information)
{
info.annotations = new Annotation[aWidth];
}
- }
-
+ }
- /**
+ /**
* Computes the profiles from a HMM for an alignment.
*
* @param alignment
*/
protected void computeInformation(AlignmentI alignment)
- {
-
- int width = alignment.getWidth();
+ {
+ int width = alignment.getWidth();
List<SequenceI> hmmSeqs = alignment.getHMMConsensusSequences(false);
int index = 0;
// setColourSchemeInformation(hinformation);
index++;
}
- }
+ }
- /**
+ /**
* gets the sequences on the alignment on the viewport.
*
* @return
*/
- protected SequenceI[] getSequences()
- {
- return alignViewport.getAlignment().getSequencesArray();
- }
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
protected void setColourSchemeInformation(ProfilesI information)
+ {
+ ResidueShaderI cs = alignViewport.getResidueShading();
+ if (cs != null)
{
- ResidueShaderI cs = alignViewport.getResidueShading();
- if (cs != null)
- {
cs.setInformation(information);
- }
}
+ }
- /**
+ /**
* Get the Information annotation for the alignment
*
* @return
*/
protected List<AlignmentAnnotation> getInformationAnnotations()
- {
+ {
return alignViewport.getInformationAnnotations();
- }
+ }
- /**
- * Get the Gap annotation for the alignment
- *
- * @return
- */
- protected AlignmentAnnotation getGapAnnotation()
- {
- return alignViewport.getAlignmentGapAnnotation();
- }
+ /**
+ * Get the Gap annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getGapAnnotation()
+ {
+ return alignViewport.getAlignmentGapAnnotation();
+ }
- /**
+ /**
* update the information annotation from the sequence profile data using
* current visualization settings.
*/
- @Override
- public void updateAnnotation()
- {
-
- updateResultAnnotation(false);
- }
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+ }
/**
* Derives the information content for an information annotation.
*
* @param immediate
*/
- public void updateResultAnnotation(boolean immediate)
- {
+ public void updateResultAnnotation(boolean immediate)
+ {
List<AlignmentAnnotation> annots = getInformationAnnotations();
int index = 0;
for (AlignmentAnnotation information : annots)
{
ProfilesI hinformation = (ProfilesI) getSequenceInformation(index);
if (immediate || !calcMan.isWorking(this) && information != null
- && hinformation != null)
+ && hinformation != null)
{
deriveInformation(information, hinformation);
}
index++;
- }
}
+ }
- /**
+ /**
* Convert the computed information data into the desired annotation for
* display.
*
*/
protected void deriveInformation(
AlignmentAnnotation informationAnnotation, ProfilesI hinformation)
- {
- long nseq = getSequences().length;
+ {
+ long nseq = getSequences().length;
max = AAFrequency.completeInformation(informationAnnotation,
hinformation, hinformation.getStartColumn(),
hinformation.getEndColumn() + 1, nseq, max);
- }
-
-
+ }
- /**
+ /**
* Get the information data stored on the viewport.
*
* @return
*/
protected Object getSequenceInformation(int index)
- {
- // TODO convert ComplementInformationThread to use Profile
+ {
return alignViewport.getSequenceInformationHash(index);
- }
}
-
-
-
-
-
+}
git://source.jalview.org / jalview.git / blobdiff