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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
gui
/
TreePanel.java
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
fea4704
..
9c1e42e
100755
(executable)
--- a/
src/jalview/gui/TreePanel.java
+++ b/
src/jalview/gui/TreePanel.java
@@
-38,7
+38,6
@@
import java.util.*;
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import javax.imageio.*;
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\r
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import javax.imageio.*;
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\r
-import javax.swing.*;
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import java.beans.PropertyChangeEvent;
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\r
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import java.beans.PropertyChangeEvent;
\r
\r
\r
@@
-94,6
+93,11
@@
public class TreePanel extends GTreePanel
initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
\r
}
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\r
initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
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}
\r
\r
+ public AlignmentI getAlignment()
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+ {
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+ return treeCanvas.av.getAlignment();
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+ }
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+
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\r
void initTreePanel(AlignViewport av, Vector seqVector, String type,
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String pwtype, int s, int e, NewickFile newTree)
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\r
void initTreePanel(AlignViewport av, Vector seqVector, String type,
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String pwtype, int s, int e, NewickFile newTree)
\r
@@
-232,7
+236,7
@@
public class TreePanel extends GTreePanel
Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
\r
\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
\r
\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
\r
- cap.setText(fout.print(false, true));
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+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
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}
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/**
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}
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/**
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@@
-259,7
+263,7
@@
public class TreePanel extends GTreePanel
try
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{
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jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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try
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{
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jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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- String output = fout.print(false, true); // distances only
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+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
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java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
\r
choice));
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out.println(output);
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java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
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choice));
\r
out.println(output);
\r