*/
package jalview.workers;
+import java.util.Hashtable;
+
import jalview.analysis.AAFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
-import java.util.Hashtable;
-
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
- private long nseq = -1;
-
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
long started = System.currentTimeMillis();
try
{
- AlignmentAnnotation consensus = alignViewport
- .getAlignmentConsensusAnnotation();
+ AlignmentAnnotation consensus = getConsensusAnnotation();
if (consensus == null || calcMan.isPending(this))
{
calcMan.workerComplete(this);
if (alignment == null || (aWidth = alignment.getWidth()) < 0)
{
calcMan.workerComplete(this);
- // .updatingConservation = false;
- // AlignViewport.UPDATING_CONSERVATION = false;
-
return;
}
- consensus = alignViewport.getAlignmentConsensusAnnotation();
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
- hconsensus = new Hashtable[aWidth];
- try
- {
- SequenceI aseqs[] = alignment.getSequencesArray();
- nseq = aseqs.length;
- AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
- true);
- } catch (ArrayIndexOutOfBoundsException x)
- {
- // this happens due to a race condition -
- // alignment was edited at same time as calculation was running
- //
- // calcMan.workerCannotRun(this);
- calcMan.workerComplete(this);
- return;
- }
- alignViewport.setSequenceConsensusHash(hconsensus);
+ eraseConsensus(aWidth);
+ computeConsensus(alignment);
updateResultAnnotation(true);
- ColourSchemeI globalColourScheme = alignViewport
- .getGlobalColourScheme();
- if (globalColourScheme != null)
+
+ if (ap != null)
{
- globalColourScheme.setConsensus(hconsensus);
+ ap.paintAlignment(true);
}
-
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
ap.raiseOOMWarning("calculating consensus", error);
+ } finally
+ {
+ /*
+ * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
+ * - alignment was edited at same time as calculation was running
+ */
+ calcMan.workerComplete(this);
}
+ }
+
+ /**
+ * Clear out any existing consensus annotations
+ *
+ * @param aWidth
+ * the width (number of columns) of the annotated alignment
+ */
+ protected void eraseConsensus(int aWidth)
+ {
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ consensus.annotations = new Annotation[aWidth];
+ }
+
+ /**
+ * @param alignment
+ */
+ protected void computeConsensus(AlignmentI alignment)
+ {
+ Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+
+ SequenceI[] aseqs = getSequences();
+ AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
+ true);
- calcMan.workerComplete(this);
- if (ap != null)
+ alignViewport.setSequenceConsensusHash(hconsensus);
+ setColourSchemeConsensus(hconsensus);
+ }
+
+ /**
+ * @return
+ */
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
+
+ /**
+ * @param hconsensus
+ */
+ protected void setColourSchemeConsensus(Hashtable[] hconsensus)
+ {
+ ColourSchemeI globalColourScheme = alignViewport
+ .getGlobalColourScheme();
+ if (globalColourScheme != null)
{
- ap.paintAlignment(true);
+ globalColourScheme.setConsensus(hconsensus);
}
}
/**
+ * Get the Consensus annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getConsensusAnnotation()
+ {
+ return alignViewport.getAlignmentConsensusAnnotation();
+ }
+
+ /**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
public void updateResultAnnotation(boolean immediate)
{
- AlignmentAnnotation consensus = alignViewport
- .getAlignmentConsensusAnnotation();
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ Hashtable[] hconsensus = getViewportConsensus();
if (immediate || !calcMan.isWorking(this) && consensus != null
&& hconsensus != null)
{
- AAFrequency.completeConsensus(consensus, hconsensus, 0,
- hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo(), nseq);
+ deriveConsensus(consensus, hconsensus);
}
}
+
+ /**
+ * Convert the computed consensus data into the desired annotation for
+ * display.
+ *
+ * @param consensusAnnotation
+ * the annotation to be populated
+ * @param consensusData
+ * the computed consensus data
+ */
+ protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
+ Hashtable[] consensusData)
+ {
+ long nseq = getSequences().length;
+ AAFrequency.completeConsensus(consensusAnnotation, consensusData, 0,
+ consensusData.length, alignViewport.isIgnoreGapsConsensus(),
+ alignViewport.isShowSequenceLogo(), nseq);
+ }
+
+ /**
+ * Get the consensus data stored on the viewport.
+ *
+ * @return
+ */
+ protected Hashtable[] getViewportConsensus()
+ {
+ return alignViewport.getSequenceConsensusHash();
+ }
}