import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ SequenceI aseqs[] = alignment.getSequencesArray();
+ nseq = aseqs.length;
+ AAFrequency.calculate(aseqs, 0,
alignment.getWidth(), hconsensus, true);
} catch (ArrayIndexOutOfBoundsException x)
{
alignment.getWidth(), hconsensus, true);
} catch (ArrayIndexOutOfBoundsException x)
{
{
AAFrequency.completeConsensus(consensus, hconsensus, 0,
hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
{
AAFrequency.completeConsensus(consensus, hconsensus, 0,
hconsensus.length, alignViewport.getIgnoreGapsConsensus(),