X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=25a7a934a52b84f84ffb9322bd3c84a851dcf299;hb=1660a4fe03b8dda74b008ae4de2d804f8044a463;hp=5f2a977d892c19dffa7ba0d63de13d50589cb142;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 5f2a977..25a7a93 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -285,6 +285,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         }
       }
     }
+    // TODO: add group link menu entry here
     if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
@@ -586,18 +587,29 @@ public class APopupMenu extends java.awt.PopupMenu implements
         return;
       }
 
-      int gSize = sg.getSize();
-      SequenceI[] seqs = new SequenceI[gSize];
-      SequenceFeature[] features = new SequenceFeature[gSize];
-
+      
+      int rsize=0,gSize = sg.getSize();
+      SequenceI[] rseqs,seqs = new SequenceI[gSize];
+      SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
+      
       for (int i = 0; i < gSize; i++)
       {
-        seqs[i] = sg.getSequenceAt(i);
         int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
         int end = sg.findEndRes(sg.getSequenceAt(i));
-        features[i] = new SequenceFeature(null, null, null, start, end,
+        if (start<=end)
+        {
+          seqs[rsize] = sg.getSequenceAt(i);
+          features[rsize] = new SequenceFeature(null, null, null, start, end,
                 "Jalview");
+          rsize++;
+        }
       }
+      rseqs = new SequenceI[rsize];
+      tfeatures = new SequenceFeature[rsize];
+      System.arraycopy(seqs,0,rseqs, 0, rsize);
+      System.arraycopy(features, 0, tfeatures, 0, rsize);
+      features = tfeatures;
+      seqs = rseqs;
 
       if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
               features, true, ap))