X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=1628f58d1c911e86b752e51252897843b2c850e4;hb=ef36c8bbd6c5eef95e4d1a2cff57ea772af5110b;hp=e89f4417cd4232ea2673a82c2628208e94f1e412;hpb=fdcfb775a9b255c4c09c9509bf35e7352b5d1f3a;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e89f441..1628f58 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -195,7 +195,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
             if (showDistances && (node.dist > 0))
             {
-                nodeLabel = new Format("%5.2f").form(node.dist);
+                nodeLabel = new Format("%-.2f").form(node.dist);
             }
 
             if (showBootstrap)
@@ -210,14 +210,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
             if (!nodeLabel.equals(""))
             {
-                g.drawString(nodeLabel, xstart, ypos - 10);
+                g.drawString(nodeLabel, xstart+2, ypos - 2);
             }
 
             String name = (markPlaceholders && node.isPlaceholder())
                 ? (PLACEHOLDER + node.getName()) : node.getName();
 
             int charWidth = fm.stringWidth(name) + 3;
-            int charHeight = fm.getHeight();
+            int charHeight = font.getSize();
 
             Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,
                     charWidth, charHeight);
@@ -228,7 +228,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             SequenceGroup selected = av.getSelectionGroup();
 
             if ((selected != null) &&
-                    selected.sequences.contains((SequenceI) node.element()))
+                    selected.getSequences(false).contains((SequenceI) node.element()))
             {
                 g.setColor(Color.gray);
 
@@ -273,8 +273,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
             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).trim(), xstart+2,
+                    ypos - 2);
             }
         }
     }
@@ -587,7 +587,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
         g2.setFont(font);
 
-        offy = font.getSize()*2;
+        offy = font.getSize()+10;
 
         fm = g2.getFontMetrics(font);
 
@@ -751,14 +751,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
                     SequenceGroup sg = new SequenceGroup(sequences,
                             "TreeGroup", cs, true, true, false, 0,
-                            av.alignment.getWidth());
+                            av.alignment.getWidth()-1);
 
 
                     if (  av.getGlobalColourScheme()!=null
                        && av.getGlobalColourScheme().conservationApplied())
                     {
                         Conservation c = new Conservation("Group",
-                                ResidueProperties.propHash, 3, sg.sequences,
+                                ResidueProperties.propHash, 3,
+                                sg.getSequences(false),
                                 sg.getStartRes(), sg.getEndRes());
 
                         c.calculate();