formatting changes

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 99d0328..d6ee70e 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,158 +1,158 @@
-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import jalview.io.NewickFile;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
-import java.awt.event.*;
-import java.util.*;
-import jalview.io.NewickFile;
-
-
-public class TreePanel extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  AlignViewport av;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
-
-  public NJTree getTree()
-  {
-    return tree;
-  }
-
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
-  {
-    super();
-
-    this.type = type;
-    this.pwtype = pwtype;
-
-    start = s;
-    end = e;
-
-    String longestName = "";
-    seq = new Sequence [seqVector.size()];
-    for (int i=0;i < seqVector.size();i++)
-    {
-      seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
-        longestName = seq[i].getName();
-    }
-
-    tree = new NJTree(seq, type, pwtype, start, end);
-
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.add(treeCanvas);
-
-  }
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
-    {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
-      this.type = type;
-      this.pwtype = pwtype;
-
-      start = 0;
-      end = seqVector.size();
-
-      String longestName = "";
-      seq = new Sequence [seqVector.size()];
-      for (int i=0;i < seqVector.size();i++)
-      {
-        seq[i] = (Sequence) seqVector.elementAt(i);
-      }
-      // This constructor matches sequence names to treenodes and sets up the tree layouts.
-      tree = new NJTree(seq, newtree);
-      // Now have to calculate longest name based on the leaves
-      Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
-
-      for (int i=0;i < leaves.size();i++)
-        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
-          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
-
-      tree.reCount(tree.getTopNode());
-      tree.findHeight(tree.getTopNode());
-
-      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-      treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-      treeCanvas.setShowDistances(newtree.HasDistances());
-      distanceMenu.setState(newtree.HasDistances());
-      bootstrapMenu.setState(newtree.HasBootstrap());
-      if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
-        placeholdersMenu.setState(treeCanvas.markPlaceholders);
-      scrollPane.add(treeCanvas);
-
-    }
-
-public String getText(String format) {
-  return null;
-}
-
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.getState();
-    repaint();
-  }
-
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)
-  {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-    String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-    cap.setText(output);
-    java.awt.Frame frame = new java.awt.Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
-  }
-
-
-
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
- /*   if( treeCanvas==null )
-     return;
-
-   String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
-
-   Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                               "Select font size",
-                               "Font size",
-                               JOptionPane.QUESTION_MESSAGE,
-                               null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                               ,"Font Size - "+size);
-   if(selection!=null)
-   {
-     fontSize.setText("Font Size - " + selection);
-
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
-*/
-  }
-
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.getState());
-  }
-
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.getState());
-  }
-
-  protected void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
-  }
-
-}
+package jalview.appletgui;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.io.NewickFile;\r
+import jalview.analysis.*;\r
+import jalview.jbappletgui.GTreePanel;\r
+import java.awt.event.*;\r
+import java.util.*;\r
+import jalview.io.NewickFile;\r
+\r
+\r
+public class TreePanel extends GTreePanel\r
+{\r
+  SequenceI[] seq;\r
+  String type;\r
+  String pwtype;\r
+  AlignViewport av;\r
+  int start;\r
+  int end;\r
+  TreeCanvas treeCanvas;\r
+  NJTree tree;\r
+\r
+  public NJTree getTree()\r
+  {\r
+    return tree;\r
+  }\r
+\r
+  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
+  {\r
+    super();\r
+\r
+    this.type = type;\r
+    this.pwtype = pwtype;\r
+\r
+    start = s;\r
+    end = e;\r
+\r
+    String longestName = "";\r
+    seq = new Sequence [seqVector.size()];\r
+    for (int i=0;i < seqVector.size();i++)\r
+    {\r
+      seq[i] = (Sequence) seqVector.elementAt(i);\r
+      if(seq[i].getName().length()>longestName.length())\r
+        longestName = seq[i].getName();\r
+    }\r
+\r
+    tree = new NJTree(seq, type, pwtype, start, end);\r
+\r
+    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+\r
+    tree.reCount(tree.getTopNode());\r
+    tree.findHeight(tree.getTopNode());\r
+    scrollPane.add(treeCanvas);\r
+\r
+  }\r
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
+                   String type, String pwtype)\r
+    {\r
+      super();\r
+      // These are probably only  arbitrary strings reflecting source of tree\r
+      this.type = type;\r
+      this.pwtype = pwtype;\r
+\r
+      start = 0;\r
+      end = seqVector.size();\r
+\r
+      String longestName = "";\r
+      seq = new Sequence [seqVector.size()];\r
+      for (int i=0;i < seqVector.size();i++)\r
+      {\r
+        seq[i] = (Sequence) seqVector.elementAt(i);\r
+      }\r
+      // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
+      tree = new NJTree(seq, newtree);\r
+      // Now have to calculate longest name based on the leaves\r
+      Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
+\r
+      for (int i=0;i < leaves.size();i++)\r
+        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())\r
+          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();\r
+\r
+      tree.reCount(tree.getTopNode());\r
+      tree.findHeight(tree.getTopNode());\r
+\r
+      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+      treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+      treeCanvas.setShowDistances(newtree.HasDistances());\r
+      distanceMenu.setState(newtree.HasDistances());\r
+      bootstrapMenu.setState(newtree.HasBootstrap());\r
+      if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
+        placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
+      scrollPane.add(treeCanvas);\r
+\r
+    }\r
+\r
+public String getText(String format) {\r
+  return null;\r
+}\r
+\r
+  protected void fitToWindow_actionPerformed(ActionEvent e)\r
+  {\r
+    treeCanvas.fitToWindow = fitToWindow.getState();\r
+    repaint();\r
+  }\r
+\r
+  public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
+  {\r
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+    String output = fout.print(false, true);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+    cap.setText(output);\r
+    java.awt.Frame frame = new java.awt.Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);\r
+  }\r
+\r
+\r
+\r
+  protected void fontSize_actionPerformed(ActionEvent e)\r
+  {\r
+ /*   if( treeCanvas==null )\r
+     return;\r
+\r
+   String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
+\r
+   Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+                               "Select font size",\r
+                               "Font size",\r
+                               JOptionPane.QUESTION_MESSAGE,\r
+                               null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
+                               ,"Font Size - "+size);\r
+   if(selection!=null)\r
+   {\r
+     fontSize.setText("Font Size - " + selection);\r
+\r
+     int i = Integer.parseInt(selection.toString());\r
+     treeCanvas.setFontSize(i);\r
+   }\r
+    scrollPane.setViewportView(treeCanvas);\r
+*/\r
+  }\r
+\r
+  protected void distanceMenu_actionPerformed(ActionEvent e)\r
+  {\r
+    treeCanvas.setShowDistances(distanceMenu.getState());\r
+  }\r
+\r
+  protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
+  {\r
+    treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
+  }\r
+\r
+  protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
+  {\r
+      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+  }\r
+\r
+}\r