package jalview.appletgui;
import jalview.analysis.NJTree;
-import jalview.api.analysis.ScoreModelI;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.DistanceModelI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
-import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
return tree;
}
+ @Override
public void finalize() throws Throwable
{
ap = null;
this.newtree = newtree;
}
+ @Override
public void run()
{
if (newtree != null)
seqs = av.getSelectionGroup().getSequencesInOrder(
av.getAlignment());
}
- ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ DistanceModelI sm = ScoreModels.getInstance().forName(pwtype);
if (sm instanceof ViewBasedAnalysisI)
{
try
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == newickOutput)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == fitToWindow)