X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=77ec3739f8d769bfa8e6516d75c1cdcf6b60bacd;hb=c51dbe7933683b64548f5353e67561d2b5e377f7;hp=4ae0ed2df8511ef2135639c49462856c54467428;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 4ae0ed2..77ec373 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -65,6 +65,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -210,7 +211,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   Menu menu1 = new Menu();
 
   public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
-          Vector<String> links)
+          List<String> links)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -243,6 +244,24 @@ public class APopupMenu extends java.awt.PopupMenu implements
     SequenceGroup sg = ap.av.getSelectionGroup();
     if (sg != null && sg.getSize() > 0)
     {
+      if (sg.isNucleotide())
+      {
+        conservationColour.setEnabled(false);
+        clustalColour.setEnabled(false);
+        BLOSUM62Colour.setEnabled(false);
+        zappoColour.setEnabled(false);
+        taylorColour.setEnabled(false);
+        hydrophobicityColour.setEnabled(false);
+        helixColour.setEnabled(false);
+        strandColour.setEnabled(false);
+        turnColour.setEnabled(false);
+        buriedColour.setEnabled(false);
+      }
+      else
+      {
+        purinePyrimidineColour.setEnabled(false);
+        nucleotideColour.setEnabled(false);
+      }
       editGroupName.setLabel(MessageManager.formatMessage(
               "label.name_param", new Object[] { sg.getName() }));
       showText.setState(sg.getDisplayText());
@@ -801,9 +820,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
         return;
       }
 
-      int rsize = 0, gSize = sg.getSize();
-      SequenceI[] rseqs, seqs = new SequenceI[gSize];
-      SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+      int gSize = sg.getSize();
+      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      List<SequenceFeature> features = new ArrayList<SequenceFeature>();
 
       for (int i = 0; i < gSize; i++)
       {
@@ -811,25 +830,17 @@ public class APopupMenu extends java.awt.PopupMenu implements
         int end = sg.findEndRes(sg.getSequenceAt(i));
         if (start <= end)
         {
-          seqs[rsize] = sg.getSequenceAt(i);
-          features[rsize] = new SequenceFeature(null, null, null, start,
-                  end, "Jalview");
-          rsize++;
+          seqs.add(sg.getSequenceAt(i));
+          features.add(new SequenceFeature(null, null, null, start, end,
+                  "Jalview"));
         }
       }
-      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))
       {
         ap.alignFrame.sequenceFeatures.setState(true);
         ap.av.setShowSequenceFeatures(true);
-        ;
         ap.highlightSearchResults(null);
       }
     }