X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=af1d752897a78d10b230306775b536db3ce67e06;hb=04011072920c5e2587a8d549869ee47e28ad7d81;hp=47bebbea18725d2e5cc5dbd88284e6ddc988600b;hpb=8a5c39442bced20fc95272efe6d3176719ca3f15;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 47bebbe..af1d752 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;
 
@@ -62,6 +60,7 @@ public class TreeCanvas
   public TreeCanvas(AlignViewport av, ScrollPane scroller)
   {
     this.av = av;
+    font = av.getFont();
     scrollPane = scroller;
     addMouseListener(this);
     setLayout(null);
@@ -160,7 +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)
       {
@@ -172,7 +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()) ?
@@ -181,7 +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);
@@ -189,7 +188,7 @@ public class TreeCanvas
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
       if (selected != null &&
-          selected.sequences.contains( (SequenceI) node.element()))
+          selected.getSequences(false).contains( (SequenceI) node.element()))
       {
         g.setColor(Color.gray);
 
@@ -228,7 +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);
       }
 
     }
@@ -280,7 +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);
   }
@@ -296,9 +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;
@@ -352,9 +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)
@@ -378,19 +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);
@@ -406,7 +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);
 
@@ -530,7 +523,8 @@ public class TreeCanvas
             {
             Conservation c = new Conservation("Group",
                                               ResidueProperties.propHash, 3,
-                                              sg.sequences, sg.getStartRes(),
+                                              sg.getSequences(false),
+                                              sg.getStartRes(),
                                               sg.getEndRes());
 
             c.calculate();