X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=1628f58d1c911e86b752e51252897843b2c850e4;hb=6bfaf3d3a82e4eece77dc1c2d83aede7c4dbb690;hp=eea181f476701e4d2a58abcf7b5068100d337692;hpb=eee02848424734a9466de35ff19636377652e59b;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index eea181f..1628f58 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -50,13 +50,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     JScrollPane scrollPane;
     AlignViewport av;
     Font font;
-    int fontSize;
+    FontMetrics fm;
     boolean fitToWindow = true;
     boolean showDistances = false;
     boolean showBootstrap = false;
     boolean markPlaceholders = false;
     int offx = 20;
-    int offy = 20;
+    int offy;
     float threshold;
     String longestName;
     int labelLength = -1;
@@ -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)
@@ -210,16 +210,16 @@ 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();
-            FontMetrics fm = g.getFontMetrics(font);
+
             int charWidth = fm.stringWidth(name) + 3;
-            int charHeight = fm.getHeight();
+            int charHeight = font.getSize();
 
-            Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
+            Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,
                     charWidth, charHeight);
 
             nameHash.put((SequenceI) node.element(), rect);
@@ -228,16 +228,16 @@ 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);
 
-                g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,
+                g.fillRect(xend + 10, ypos-charHeight/2, charWidth,
                     charHeight);
                 g.setColor(Color.white);
             }
 
-            g.drawString(name, xend + 10, ypos);
+            g.drawString(name, xend + 10, ypos+fm.getDescent());
             g.setColor(Color.black);
         }
         else
@@ -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);
             }
         }
     }
@@ -340,7 +340,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                 ((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);
     }
@@ -532,7 +532,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          FontMetrics fm = g.getFontMetrics(font);
+          fm = g.getFontMetrics(font);
 
           if (nameHash.size() == 0)
           {
@@ -558,25 +558,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getFontSize()
-    {
-        return fontSize;
-    }
 
     /**
      * DOCUMENT ME!
      *
      * @param fontSize DOCUMENT ME!
      */
-    public void setFontSize(int fontSize)
+    public void setFont(Font font)
     {
-        this.fontSize = fontSize;
-        font = new Font(font.getName(), font.getStyle(), fontSize);
+        this.font = font;
         repaint();
     }
 
@@ -597,7 +587,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
         g2.setFont(font);
 
-        labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
+        offy = font.getSize()+10;
+
+        fm = g2.getFontMetrics(font);
+
+        labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
 
         float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
 
@@ -609,7 +603,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                 ((SequenceNode) top.right()).count;
         }
 
-        float chunk = (float) (height - (offy * 2)) / top.count;
+        float chunk = (float) (height - (offy)) / top.count;
 
         drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
 
@@ -757,14 +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();