import jalview.datamodel.Annotation;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.schemes.CollectionColourSchemeI;
public class ConsensusThread extends AlignCalcWorker
{
*/
protected void setColourSchemeConsensus(ProfilesI hconsensus)
{
- ColourSchemeI globalColourScheme = alignViewport
- .getGlobalColourScheme();
- if (globalColourScheme != null)
+ CollectionColourSchemeI cs = alignViewport.getViewportColourScheme();
+ if (cs != null)
{
- globalColourScheme.setConsensus(hconsensus);
+ cs.setConsensus(hconsensus);
}
}
{
long nseq = getSequences().length;
- AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,
+ AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
+ hconsensus.getStartColumn(),
hconsensus.getEndColumn() + 1,
alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);