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JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to
[jalview.git]
/
src
/
jalview
/
appletgui
/
TreePanel.java
diff --git
a/src/jalview/appletgui/TreePanel.java
b/src/jalview/appletgui/TreePanel.java
index
2e0edfd
..
5b12fa6
100644
(file)
--- a/
src/jalview/appletgui/TreePanel.java
+++ b/
src/jalview/appletgui/TreePanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*
* This file is part of Jalview.
*
@@
-21,6
+21,7
@@
package jalview.appletgui;
import jalview.analysis.NJTree;
package jalview.appletgui;
import jalview.analysis.NJTree;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.datamodel.Alignment;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.datamodel.Alignment;
@@
-28,7
+29,6
@@
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
-import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
@@
-69,6
+69,7
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
return tree;
}
return tree;
}
+ @Override
public void finalize() throws Throwable
{
ap = null;
public void finalize() throws Throwable
{
ap = null;
@@
-200,6
+201,7
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
this.newtree = newtree;
}
this.newtree = newtree;
}
+ @Override
public void run()
{
if (newtree != null)
public void run()
{
if (newtree != null)
@@
-235,7
+237,7
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
seqs = av.getSelectionGroup().getSequencesInOrder(
av.getAlignment());
}
seqs = av.getSelectionGroup().getSequencesInOrder(
av.getAlignment());
}
- ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
if (sm instanceof ViewBasedAnalysisI)
{
try
if (sm instanceof ViewBasedAnalysisI)
{
try
@@
-249,13
+251,8
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
+ sm.getName());
q.printStackTrace();
}
+ sm.getName());
q.printStackTrace();
}
- tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
- }
- else
- {
- tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
- end);
}
}
+ tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
}
tree.reCount(tree.getTopNode());
}
tree.reCount(tree.getTopNode());
@@
-286,6
+283,7
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
}
}
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == newickOutput)
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == newickOutput)
@@
-302,6
+300,7
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
}
}
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == fitToWindow)
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == fitToWindow)