import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
groupConsensus = null;
groupConservation = null;
hconsensus = null;
- hcomplementConsensus = null;
hconservation = null;
+ hcomplementConsensus = null;
gapcounts = null;
calculator = null;
- // colour scheme may hold reference to consensus
- residueShading = null;
- // TODO remove listeners from changeSupport?
+ residueShading = null; // may hold a reference to Consensus
changeSupport = null;
ranges = null;
+ currentTree = null;
+ selectionGroup = null;
setAlignment(null);
}
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ if (changeSupport != null)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
}
/**
}
@Override
- public CigarArray getViewAsCigars(boolean selectedRegionOnly)
- {
- return new CigarArray(alignment, alignment.getHiddenColumns(),
- (selectedRegionOnly ? selectionGroup : null));
- }
-
- @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
{
*/
private SearchResultsI searchResults = null;
+ protected TreeModel currentTree = null;
+
@Override
public boolean hasSearchResults()
{
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
+
+ @Override
+ public void setCurrentTree(TreeModel tree)
+ {
+ currentTree = tree;
+ }
+
+ @Override
+ public TreeModel getCurrentTree()
+ {
+ return currentTree;
+ }
}