X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=52a6066db16bd0b27de610615574664aa6938374;hb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;hp=c01a6f3d3aa35108b41bc60a16c5d5193f995fcd;hpb=c2e6335a319d61b641fb6fcbb0a4a5dc88a58014;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c01a6f3..52a6066 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -428,9 +428,9 @@ public class AnnotationLabels extends JPanel
       {
         final PAEContactMatrix cm = (PAEContactMatrix) av
                 .getContactMatrix(aa[selectedRow]);
-        if (cm.getNewickString()!=null && cm.getNewickString().length()>0)
+        if (cm!=null && cm.getNewick()!=null && cm.getNewick().length()>0)
         {
-          item = new JMenuItem("Show Matrix");
+          item = new JMenuItem("Show Tree for Matrix");
           item.addActionListener(new ActionListener()
           {
 
@@ -1087,6 +1087,7 @@ public class AnnotationLabels extends JPanel
     g.translate(0, getScrollOffset());
     g.setColor(Color.black);
     SequenceI lastSeqRef = null;
+    String lastLabel = null;
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
@@ -1111,6 +1112,7 @@ public class AnnotationLabels extends JPanel
     {
       hasHiddenRows = false;
       int olY = 0;
+      int nexAA = 0;
       for (int i = 0; i < aa.length; i++)
       {
         visible = true;
@@ -1120,6 +1122,9 @@ public class AnnotationLabels extends JPanel
           continue;
         }
         olY = y;
+        // look ahead to next annotation
+        for (nexAA=i+1; nexAA<aa.length && !aa[nexAA].visible; nexAA++)
+          ;
         y += aa[i].height;
         if (clip)
         {
@@ -1167,6 +1172,24 @@ public class AnnotationLabels extends JPanel
         }
         String label = aa[i].label;
         boolean vertBar = false;
+        if ((lastLabel != null && lastLabel.equals(label)))
+        {
+          label = aa[i].description;
+        }
+        else
+        {
+          if (nexAA < aa.length && label.equals(aa[nexAA].label)) // &&
+                                                                  // aa[nexY].sequenceRef==aa[i].sequenceRef)
+          {
+            lastLabel = label;
+            // next label is the same as this label
+            label = aa[i].description;
+          }
+          else
+          {
+            lastLabel = label;
+          }
+        }
         if (aa[i].sequenceRef != null)
         {
           if (aa[i].sequenceRef != lastSeqRef)
@@ -1250,8 +1273,8 @@ public class AnnotationLabels extends JPanel
         {
           if (vertBar)
           {
-            g.drawLine(20, y + offset, 20, y - aa[i].height);
-            g.drawLine(20, y + offset, x - 20, y + offset);
+            g.drawLine(width-3, y + offset-fontHeight, width-3, (int)(y - 1.5*aa[i].height-offset-fontHeight));
+            // g.drawLine(20, y + offset, x - 20, y + offset);
 
           }
           g.drawString(label, x, y + offset);