try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- AlignmentAnnotation gap = getGapAnnotation();
+ AlignmentAnnotation gap = getOccupancyAnnotation();
if ((consensus == null && gap == null) || calcMan.isPending(this))
{
calcMan.workerComplete(this);
{
AlignmentAnnotation consensus = getConsensusAnnotation();
consensus.annotations = new Annotation[aWidth];
- AlignmentAnnotation gap = getGapAnnotation();
+ AlignmentAnnotation gap = getOccupancyAnnotation();
if (gap != null)
{
gap.annotations = new Annotation[aWidth];
ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
true);
- alignViewport.setSequenceConsensusHash(hconsensus);
+ alignViewport.setConsensusProfiles(hconsensus);
setColourSchemeConsensus(hconsensus);
}
*
* @return
*/
- protected AlignmentAnnotation getGapAnnotation()
+ protected AlignmentAnnotation getOccupancyAnnotation()
{
- return alignViewport.getAlignmentGapAnnotation();
+ return alignViewport.getOccupancyAnnotation();
}
/**
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
- AlignmentAnnotation gap = getGapAnnotation();
- if (gap != null)
+ AlignmentAnnotation occupancy = getOccupancyAnnotation();
+ if (occupancy != null)
{
- deriveGap(gap, hconsensus);
+ deriveOccupancy(occupancy, hconsensus);
}
}
}
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
ProfilesI hconsensus)
{
-
long nseq = getSequences().length;
AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
* @param hconsensus
* the computed consensus data
*/
- protected void deriveGap(AlignmentAnnotation gapAnnotation,
+ protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
ProfilesI hconsensus)
{
long nseq = getSequences().length;
- AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+ AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
nseq);
}
protected Object getViewportConsensus()
{
// TODO convert ComplementConsensusThread to use Profile
- return alignViewport.getSequenceConsensusHash();
+ return alignViewport.getConsensusProfiles();
}
}