Corrected hidden row feature render bug

[jalview.git] / src / jalview / gui / TreeCanvas.java

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e89f441..1628f58 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -195,7 +195,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 \r
             if (showDistances && (node.dist > 0))\r
             {\r
-                nodeLabel = new Format("%5.2f").form(node.dist);\r
+                nodeLabel = new Format("%-.2f").form(node.dist);\r
             }\r
 \r
             if (showBootstrap)\r
@@ -210,14 +210,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 \r
             if (!nodeLabel.equals(""))\r
             {\r
-                g.drawString(nodeLabel, xstart, ypos - 10);\r
+                g.drawString(nodeLabel, xstart+2, ypos - 2);\r
             }\r
 \r
             String name = (markPlaceholders && node.isPlaceholder())\r
                 ? (PLACEHOLDER + node.getName()) : node.getName();\r
 \r
             int charWidth = fm.stringWidth(name) + 3;\r
-            int charHeight = fm.getHeight();\r
+            int charHeight = font.getSize();\r
 \r
             Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,\r
                     charWidth, charHeight);\r
@@ -228,7 +228,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             SequenceGroup selected = av.getSelectionGroup();\r
 \r
             if ((selected != null) &&\r
-                    selected.sequences.contains((SequenceI) node.element()))\r
+                    selected.getSequences(false).contains((SequenceI) node.element()))\r
             {\r
                 g.setColor(Color.gray);\r
 \r
@@ -273,8 +273,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 \r
             if (showDistances && (node.dist > 0))\r
             {\r
-                g.drawString(new Format("%5.2f").form(node.dist), xstart,\r
-                    ypos - 5);\r
+                g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,\r
+                    ypos - 2);\r
             }\r
         }\r
     }\r
@@ -587,7 +587,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 \r
         g2.setFont(font);\r
 \r
-        offy = font.getSize()*2;\r
+        offy = font.getSize()+10;\r
 \r
         fm = g2.getFontMetrics(font);\r
 \r
@@ -751,14 +751,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 \r
                     SequenceGroup sg = new SequenceGroup(sequences,\r
                             "TreeGroup", cs, true, true, false, 0,\r
-                            av.alignment.getWidth());\r
+                            av.alignment.getWidth()-1);\r
 \r
 \r
                     if (  av.getGlobalColourScheme()!=null\r
                        && av.getGlobalColourScheme().conservationApplied())\r
                     {\r
                         Conservation c = new Conservation("Group",\r
-                                ResidueProperties.propHash, 3, sg.sequences,\r
+                                ResidueProperties.propHash, 3,\r
+                                sg.getSequences(false),\r
                                 sg.getStartRes(), sg.getEndRes());\r
 \r
                         c.calculate();\r