import jalview.datamodel.Annotation;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
public class ConsensusThread extends AlignCalcWorker
{
}
while (!calcMan.notifyWorking(this))
{
- // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
+ // System.err.println("Thread
+ // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
try
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
Thread.sleep(200);
} catch (Exception ex)
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
} catch (OutOfMemoryError error)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
consensus.annotations = new Annotation[aWidth];
AlignmentAnnotation gap = getGapAnnotation();
- if (gap!=null) {
+ if (gap != null)
+ {
gap.annotations = new Annotation[aWidth];
}
}
SequenceI[] aseqs = getSequences();
int width = alignment.getWidth();
- ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0,
- width, true);
+ ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+ true);
alignViewport.setSequenceConsensusHash(hconsensus);
setColourSchemeConsensus(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);
}
}
long nseq = getSequences().length;
AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
- hconsensus.getStartColumn(),
- hconsensus.getEndColumn() + 1,
+ 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,
+ /**
+ * 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);
-
}
/**