X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=e3f6c3cd0911a241b955545d8d6d968df4ac1e28;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=075d8cb9c8121975ae5329158cc4731c31d81489;hpb=6495cefecdc75353b5fb9e8af9e45cc7069b4cc2;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 075d8cb..e3f6c3c 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -37,15 +37,13 @@ public class TreeCanvas
   AlignViewport av;
   public static final String PLACEHOLDER = " * ";
   Font font;
-  int fontSize = 12;
-
   boolean fitToWindow = true;
   boolean showDistances = false;
   boolean showBootstrap = false;
   boolean markPlaceholders = false;
 
   int offx = 20;
-  int offy = 20;
+  int offy;
 
   float threshold;
 
@@ -59,15 +57,12 @@ public class TreeCanvas
   Hashtable nameHash = new Hashtable();
   Hashtable nodeHash = new Hashtable();
 
-  public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,
-                    String label)
+  public TreeCanvas(AlignViewport av, ScrollPane scroller)
   {
     this.av = av;
-    this.tree = tree;
+    font = av.getFont();
     scrollPane = scroller;
     addMouseListener(this);
-    tree.findHeight(tree.getTopNode());
-    longestName = label;
     setLayout(null);
 
     PaintRefresher.Register(this, av.alignment);
@@ -93,6 +88,30 @@ public class TreeCanvas
   {
     this.tree = tree;
     tree.findHeight(tree.getTopNode());
+
+    // Now have to calculate longest name based on the leaves
+    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    boolean has_placeholders = false;
+    longestName = "";
+
+    for (int i = 0; i < leaves.size(); i++)
+    {
+      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+
+      if (lf.isPlaceholder())
+      {
+        has_placeholders = true;
+      }
+
+      if (longestName.length() < ( (Sequence) lf.element()).getName()
+          .length())
+      {
+        longestName = TreeCanvas.PLACEHOLDER +
+            ( (Sequence) lf.element()).getName();
+      }
+    }
+
+    setMarkPlaceholders(has_placeholders);
   }
 
   public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,
@@ -140,7 +159,7 @@ public class TreeCanvas
       String nodeLabel = "";
       if (showDistances && node.dist > 0)
       {
-        nodeLabel = new Format("%5.2f").form(node.dist);
+        nodeLabel = new Format("%-.2f").form(node.dist);
       }
       if (showBootstrap)
       {
@@ -152,7 +171,7 @@ public class TreeCanvas
       }
       if (!nodeLabel.equals(""))
       {
-        g.drawString(nodeLabel, xstart, ypos - 10);
+        g.drawString(nodeLabel, xstart+2, ypos - 2);
       }
 
       String name = (markPlaceholders && node.isPlaceholder()) ?
@@ -161,7 +180,7 @@ public class TreeCanvas
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
 
-      Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
+      Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
                                      charWidth, charHeight);
 
       nameHash.put( (SequenceI) node.element(), rect);
@@ -208,7 +227,7 @@ public class TreeCanvas
 
       if (showDistances && node.dist > 0)
       {
-        g.drawString(new Format("%5.2f").form(node.dist), xstart, ypos - 5);
+        g.drawString(new Format("%-.2f").form(node.dist), xstart+2, ypos - 2);
       }
 
     }
@@ -260,7 +279,7 @@ public class TreeCanvas
       top.count = ( (SequenceNode) top.left()).count +
           ( (SequenceNode) top.right()).count;
     }
-    float chunk = (float) (height - offy * 2) / top.count;
+    float chunk = (float) (height - offy) / top.count;
 
     pickNode(pickBox, top, chunk, wscale, width, offx, offy);
   }
@@ -276,9 +295,9 @@ public class TreeCanvas
     if (node.left() == null && node.right() == null)
     {
       float height = node.height;
-      float dist = node.dist;
+      //float dist = node.dist;
 
-      int xstart = (int) ( (height - dist) * scale) + offx;
+      //int xstart = (int) ( (height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
@@ -332,9 +351,12 @@ public class TreeCanvas
   public void paint(Graphics g)
   {
 
-    font = new Font("Verdana", Font.PLAIN, fontSize);
+    if(tree==null)
+      return;
+
     g.setFont(font);
 
+
     FontMetrics fm = g.getFontMetrics(font);
 
     if (nameHash.size() == 0)
@@ -358,19 +380,10 @@ public class TreeCanvas
     scrollPane.validate();
   }
 
-  public int getFontSize()
-  {
-    return fontSize;
-  }
-
-  public void setFontSize(int fontSize)
-  {
-    this.fontSize = fontSize;
-    repaint();
-  }
 
   public void draw(Graphics g, int width, int height)
   {
+    offy = font.getSize()+10;
 
     g.setColor(Color.white);
     g.fillRect(0, 0, width, height);
@@ -386,7 +399,7 @@ public class TreeCanvas
       top.count = ( (SequenceNode) top.left()).count +
           ( (SequenceNode) top.right()).count;
     }
-    float chunk = (float) (height - offy * 2) / top.count;
+    float chunk = (float) (height - offy) / top.count;
 
     drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
 
@@ -480,9 +493,25 @@ public class TreeCanvas
               sequences.addElement(s1);
           }
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
-              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));
+          ColourSchemeI cs = null;
 
+          if (av.getGlobalColourScheme() != null)
+          {
+            if (av.getGlobalColourScheme() instanceof UserColourScheme)
+            {
+              cs = new UserColourScheme(
+                  ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+
+            }
+            else
+              cs = ColourSchemeProperty.getColour(sequences,
+                                                  av.alignment.getWidth(),
+                                                  ColourSchemeProperty.getColourName(
+                                                      av.getGlobalColourScheme()));
+
+              cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                                                   av.getIgnoreGapsConsensus());
+          }
 
           SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
                                                cs, true, true,