fix feature creation for selected region beyond end of sequence bug: https://mantis...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a7e853a..bd55d50 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -1532,20 +1532,28 @@ public class PopupMenu extends JPopupMenu
     {
       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).getDatasetSequence();
       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).getDatasetSequence();
+        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))
     {