if (aa.groupRef!=null)
{
renderHistogram = aa.groupRef.isShowConsensusHistogram();
- renderProfile = aa.groupRef.isIncludeAllConsSymbols();
+ renderProfile = aa.groupRef.isShowSequenceLogo();
} else {
renderHistogram = av.isShowConsensusHistogram();
- renderProfile = av.isShowConsensusProfile();
+ renderProfile = av.isShowSequenceLogo();
}
}
while (x < eRes - sRes)
private int[] getProfileFor(AlignmentAnnotation aa, int column)
{
if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
- if (aa.groupRef!=null && aa.groupRef.consensusData!=null && aa.groupRef.isIncludeAllConsSymbols()) {
+ if (aa.groupRef!=null && aa.groupRef.consensusData!=null && aa.groupRef.isShowSequenceLogo()) {
return AAFrequency.extractProfile(aa.groupRef.consensusData[column],aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to be stored
- if (aa.groupRef==null && aa.sequenceRef==null && av.isShowConsensusProfile())
+ if (aa.groupRef==null && aa.sequenceRef==null && av.isShowSequenceLogo())
{
return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
}