import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.ProfileI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
/**
* results of alignment consensus analysis for visible portion of view
*/
- protected Profile[] hconsensus = null;
+ protected ProfileI[] hconsensus = null;
/**
* results of cDNA complement consensus visible portion of view
}
@Override
- public void setSequenceConsensusHash(Profile[] hconsensus)
+ public void setSequenceConsensusHash(ProfileI[] hconsensus)
{
this.hconsensus = hconsensus;
}
}
@Override
- public Profile[] getSequenceConsensusHash()
+ public ProfileI[] getSequenceConsensusHash()
{
return hconsensus;
}
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
- cs.setConservation(Conservation.calculateConservation("All", 3,
+ cs.setConservation(Conservation.calculateConservation("All",
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}