import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+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)
{
hconsensus = new Hashtable[aWidth];
try
{
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ SequenceI aseqs[] = alignment.getSequencesArray();
+ nseq = aseqs.length;
+ AAFrequency.calculate(aseqs, 0,
alignment.getWidth(), hconsensus, true);
} catch (ArrayIndexOutOfBoundsException x)
{
{
AAFrequency.completeConsensus(consensus, hconsensus, 0,
hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isShowSequenceLogo(), nseq);
}
}
}