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
{
return;
}
calcMan.notifyStart(this);
- long started = System.currentTimeMillis();
+ // long started = System.currentTimeMillis();
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
}
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)
{
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)
{
*/
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);
}
}