private boolean shownpfeats;
/**
+ * consensus annotation includes all percentage for all symbols in column
+ */
+ private boolean includeAllConsensusSymbols=true;
+
+ /**
* trigger update of conservation annotation
*/
public void updateConservation(final AlignmentPanel ap)
hconsensus = new Hashtable[aWidth];
AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
- .getWidth(), hconsensus);
- AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation);
+ .getWidth(), hconsensus, includeAllConsensusSymbols);
+ AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols);
if (globalColourScheme != null)
{
* should consensus rows be shown for groups
*/
boolean showGroupConsensus = false;
-
+
/**
* @return the showGroupConservation
*/
{
this.showGroupConsensus = showGroupConsensus;
}
+ /**
+ * @return the includeAllConsensusSymbols
+ */
+ public boolean isIncludeAllConsensusSymbols()
+ {
+ return includeAllConsensusSymbols;
+ }
+ /**
+ * @param includeAllConsensusSymbols the includeAllConsensusSymbols to set
+ */
+ public void setIncludeAllConsensusSymbols(boolean includeAllConsensusSymbols)
+ {
+ this.includeAllConsensusSymbols = includeAllConsensusSymbols;
+ }
}