/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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)
{
int start, end;
SequenceI[] seqs;
- boolean selview = (av.getSelectionGroup() != null)
- && (av.getSelectionGroup().getSize() > 1);
+ boolean selview = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 1;
AlignmentView seqStrings = av.getAlignmentView(selview);
if (!selview)
{
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)