/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * 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.
*
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
-
-import java.util.Hashtable;
+import jalview.renderer.ResidueShaderI;
public class ConsensusThread extends AlignCalcWorker
{
@Override
public void run()
{
- if (calcMan.isPending(this))
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ AlignmentAnnotation gap = getGapAnnotation();
+ if ((consensus == null && gap == null))
{
return;
}
- calcMan.notifyStart(this);
- long started = System.currentTimeMillis();
- try
+ if (alignViewport.isClosed())
{
- AlignmentAnnotation consensus = getConsensusAnnotation();
- if (consensus == null || calcMan.isPending(this))
- {
- calcMan.workerComplete(this);
- return;
- }
- while (!calcMan.notifyWorking(this))
- {
- // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return;
- }
- AlignmentI alignment = alignViewport.getAlignment();
+ 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)
+ {
+ return;
+ }
- eraseConsensus(aWidth);
- computeConsensus(alignment);
- updateResultAnnotation(true);
+ eraseConsensus(aWidth);
+ computeConsensus(alignment);
+ updateResultAnnotation(true);
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- } catch (OutOfMemoryError error)
- {
- calcMan.disableWorker(this);
- ap.raiseOOMWarning("calculating consensus", error);
- } finally
+ if (ap != null)
{
- /*
- * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
- * - alignment was edited at same time as calculation was running
- */
- calcMan.workerComplete(this);
+ ap.paintAlignment(true, true);
}
}
protected void eraseConsensus(int aWidth)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- consensus.annotations = new Annotation[aWidth];
+ if (consensus != null)
+ {
+ consensus.annotations = new Annotation[aWidth];
+ }
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ gap.annotations = new Annotation[aWidth];
+ }
}
/**
*/
protected void computeConsensus(AlignmentI alignment)
{
- Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
SequenceI[] aseqs = getSequences();
- AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
+ int width = alignment.getWidth();
+ ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+ true);
alignViewport.setSequenceConsensusHash(hconsensus);
setColourSchemeConsensus(hconsensus);
/**
* @param hconsensus
*/
- protected void setColourSchemeConsensus(Hashtable[] hconsensus)
+ protected void setColourSchemeConsensus(ProfilesI hconsensus)
{
- ColourSchemeI globalColourScheme = alignViewport
- .getGlobalColourScheme();
- if (globalColourScheme != null)
+ ResidueShaderI cs = alignViewport.getResidueShading();
+ if (cs != null)
{
- globalColourScheme.setConsensus(hconsensus);
+ cs.setConsensus(hconsensus);
}
}
}
/**
+ * Get the Gap annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getGapAnnotation()
+ {
+ return alignViewport.getAlignmentGapAnnotation();
+ }
+
+ /**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
public void updateResultAnnotation(boolean immediate)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- Hashtable[] hconsensus = getViewportConsensus();
+ ProfilesI hconsensus = (ProfilesI) getViewportConsensus();
if (immediate || !calcMan.isWorking(this) && consensus != null
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ deriveGap(gap, hconsensus);
+ }
}
}
*
* @param consensusAnnotation
* the annotation to be populated
- * @param consensusData
+ * @param hconsensus
* the computed consensus data
*/
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
- Hashtable[] consensusData)
+ ProfilesI hconsensus)
{
long nseq = getSequences().length;
- AAFrequency.completeConsensus(consensusAnnotation, consensusData, 0,
- consensusData.length, alignViewport.isIgnoreGapsConsensus(),
+ AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
+ hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
/**
+ * Convert the computed consensus data into a gap annotation row for display.
+ *
+ * @param gapAnnotation
+ * the annotation to be populated
+ * @param hconsensus
+ * the computed consensus data
+ */
+ protected void deriveGap(AlignmentAnnotation gapAnnotation,
+ ProfilesI hconsensus)
+ {
+ long nseq = getSequences().length;
+ AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+ hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+ nseq);
+ }
+
+ /**
* Get the consensus data stored on the viewport.
*
* @return
*/
- protected Hashtable[] getViewportConsensus()
+ protected Object getViewportConsensus()
{
+ // TODO convert ComplementConsensusThread to use Profile
return alignViewport.getSequenceConsensusHash();
}
}