X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=7462bc802faf9b61bd3a0c86c0877ebbe3a9bb0f;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=e002999e066602c75d9a9fa596b81dc267f77e54;hpb=2e531bf4493e93059becb2cd2238d8dfabd72ea2;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index e002999..7462bc8 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -422,13 +422,14 @@ public class AnnotationLabels extends JPanel
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
-       if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
+      if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
               && PAEContactMatrix.PAEMATRIX
                       .equals(aa[selectedRow].getCalcId()))
       {
         final PAEContactMatrix cm = (PAEContactMatrix) av
                 .getContactMatrix(aa[selectedRow]);
-        if (cm.getNewick()!=null && cm.getNewick().length()>0)
+        if (cm != null && cm.getNewick() != null
+                && cm.getNewick().length() > 0)
         {
           item = new JMenuItem("Show Tree for Matrix");
           item.addActionListener(new ActionListener()
@@ -438,7 +439,7 @@ public class AnnotationLabels extends JPanel
             public void actionPerformed(ActionEvent e)
             {
 
-                ap.alignFrame.showContactMapTree(aa[selectedRow],cm);
+              ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
 
             }
           });
@@ -1123,7 +1124,8 @@ public class AnnotationLabels extends JPanel
         }
         olY = y;
         // look ahead to next annotation
-        for (nexAA=i+1; nexAA<aa.length && !aa[nexAA].visible; nexAA++)
+        for (nexAA = i + 1; nexAA < aa.length
+                && !aa[nexAA].visible; nexAA++)
           ;
         y += aa[i].height;
         if (clip)
@@ -1273,7 +1275,8 @@ public class AnnotationLabels extends JPanel
         {
           if (vertBar)
           {
-            g.drawLine(width-3, y + offset-fontHeight, width-3, (int)(y - 1.5*aa[i].height-offset-fontHeight));
+            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);
 
           }