X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=3e26a4b0e31c939b2f2c6f01218b2cad83ecf803;hb=39ef69a1e99aac47b3737f57605f68029ec4d897;hp=1785961f78dbb2f2adc138721d8162b555b323b4;hpb=d7c94f1d531ef43bbabb7d1951c8e34c1366eeb2;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 1785961..3e26a4b 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -45,87 +45,95 @@ public class TreePanel
     return tree;
   }
 
-  public TreePanel(AlignmentPanel ap, Vector seqVector, String type,
+  /**
+   * Creates a new TreePanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param seqVector DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param pwtype DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   * @param e DOCUMENT ME!
+   */
+  public TreePanel(AlignViewport av, Vector seqVector, String type,
                    String pwtype, int s, int e)
   {
     super();
+    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+  }
+
+  /**
+   * Creates a new TreePanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param seqVector DOCUMENT ME!
+   * @param newtree DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param pwtype DOCUMENT ME!
+   */
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
+                   String type, String pwtype)
+  {
+    super();
+    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+  }
+
+
+  void initTreePanel(AlignViewport av, Vector seqVector, String type,
+                     String pwtype, int s, int e, NewickFile newTree)
+  {
 
-    this.ap = ap;
     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);
+    for(int i=0; i<seqVector.size(); i++)
+      seq[i] = (SequenceI)seqVector.elementAt(i);
 
-    treeCanvas = new TreeCanvas(ap.av, tree, scrollPane, longestName);
 
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
+    treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
+
+    TreeLoader tl = new TreeLoader(newTree);
+    tl.start();
+
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+  class TreeLoader extends Thread
   {
-    super();
-    // These are probably only  arbitrary strings reflecting source of tree
-    this.type = type;
-    this.pwtype = pwtype;
-
-    start = 0;
-    end = seqVector.size();
+    NewickFile newtree;
 
-    String longestName = "";
-    seq = new Sequence[seqVector.size()];
-    for (int i = 0; i < seqVector.size(); i++)
+    public TreeLoader(NewickFile newtree)
     {
-      seq[i] = (Sequence) seqVector.elementAt(i);
+      this.newtree = newtree;
     }
-    // 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++)
+    public void run()
     {
-      if (longestName.length() <
-          ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().
-          length())
+      if(newtree!=null)
+        tree = new NJTree(seq, newtree);
+      else
+        tree = new NJTree(seq, type, pwtype, start, end);
+
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
+      treeCanvas.setTree(tree);
+      if(newtree!=null)
       {
-        longestName = TreeCanvas.PLACEHOLDER +
-            ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).
-            getName();
+        distanceMenu.setState(newtree.HasDistances());
+        bootstrapMenu.setState(newtree.HasBootstrap());
+        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+        treeCanvas.setShowDistances(newtree.HasDistances());
       }
-    }
 
-    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);
+      treeCanvas.repaint();
 
+    }
   }
 
   public String getText(String format)
@@ -136,7 +144,7 @@ public class TreePanel
   protected void fitToWindow_actionPerformed(ActionEvent e)
   {
     treeCanvas.fitToWindow = fitToWindow.getState();
-    repaint();
+    treeCanvas.repaint();
   }
 
   public void newickOutput_actionPerformed(ActionEvent actionEvent)
@@ -150,28 +158,23 @@ public class TreePanel
     jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
   }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
+  public java.awt.Font getTreeFont()
   {
-    /*   if( treeCanvas==null )
-        return;
+    return treeCanvas.font;
+  }
 
-      String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
+  public void setTreeFont(java.awt.Font font)
+  {
+    treeCanvas.font = font;
+    treeCanvas.repaint();
+  }
 
-      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);
+  protected void fontSize_actionPerformed(ActionEvent e)
+  {
+     if( treeCanvas==null )
+        return;
 
-        int i = Integer.parseInt(selection.toString());
-        treeCanvas.setFontSize(i);
-      }
-       scrollPane.setViewportView(treeCanvas);
-     */
+    new FontChooser(this);
   }
 
   protected void distanceMenu_actionPerformed(ActionEvent e)