/**
* consensus calculation property
*/
- private boolean showConsensusProfile=false;
+ private boolean showSequenceLogo=false;
/**
* @return the includeAllConsSymbols
*/
- public boolean isIncludeAllConsSymbols()
+ public boolean isShowSequenceLogo()
{
- return showConsensusProfile;
+ return showSequenceLogo;
}
try
{
- Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, showConsensusProfile);
+ Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo);
if (consensus != null)
{
_updateConsensusRow(cnsns);
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth]; // should be alignment width
- AAFrequency.completeConsensus(consensus,cnsns,startRes,endRes+1,ignoreGapsInConsensus, showConsensusProfile); // TODO: setting container for ignoreGapsInConsensusCalculation);
+ AAFrequency.completeConsensus(consensus,cnsns,startRes,endRes+1,ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container for ignoreGapsInConsensusCalculation);
}
/**
*/
public void setIncludeAllConsSymbols(boolean includeAllConsSymbols)
{
- if (this.showConsensusProfile!=includeAllConsSymbols && consensus!=null) {
- this.showConsensusProfile = includeAllConsSymbols;
+ if (this.showSequenceLogo!=includeAllConsSymbols && consensus!=null) {
+ this.showSequenceLogo = includeAllConsSymbols;
recalcConservation();
}
- this.showConsensusProfile = includeAllConsSymbols;
+ this.showSequenceLogo = includeAllConsSymbols;
}