Jalview 2.6 source licence

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 5f2a977..f4b3903 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
 
@@ -152,7 +151,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
-      displayNonconserved.setState(sg.getShowunconserved());
+      displayNonconserved.setState(sg.getShowNonconserved());
       if (!ap.av.alignment.getGroups().contains(sg))
       {
         groupMenu.remove(unGroupMenuItem);
@@ -285,6 +284,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         }
       }
     }
+    // TODO: add group link menu entry here
     if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
@@ -586,18 +586,28 @@ 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,
-                "Jalview");
+        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))
@@ -982,7 +992,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   public void showNonconserved_itemStateChanged()
   {
-    getGroup().setShowunconserved(this.displayNonconserved.getState());
+    getGroup().setShowNonconserved(this.displayNonconserved.getState());
     refresh();
   }