X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=3401cc4b31d676978eb35fa75ec243603051d7ee;hb=7bc213bae5828287329a3490faba291706599b03;hp=8f6e49f44740cad34fa0f08a384677204afa3b56;hpb=e13e34f4fce46de357b79344076ebfa7413ad86f;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 8f6e49f..3401cc4 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -82,11 +82,16 @@ public class APopupMenu
 
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null && sg.getSize()>0)
+    if (sg != null && sg.getSize(false)>0)
     {
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
+      if (!ap.av.alignment.getGroups().contains(sg))
+      {
+        groupMenu.remove(unGroupMenuItem);
+      }
+
     }
     else
     {
@@ -94,12 +99,7 @@ public class APopupMenu
       remove(editMenu);
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
-    {
-      groupMenu.remove(unGroupMenuItem);
-    }
-
-    if (seq != null && links!=null)
+    if (links!=null)
     {
       Menu linkMenu = new Menu("Link");
       MenuItem item;
@@ -109,13 +109,22 @@ public class APopupMenu
         link = links.elementAt(i).toString();
         final String target = link.substring(0, link.indexOf("|"));
         item = new MenuItem(target);
-        String id = seq.getName();
-        if(id.indexOf("|")>-1)
-             id = id.substring(id.lastIndexOf("|")+1);
 
-        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-               + id +
-               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+        final String url;
+
+        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        {
+          String id = seq.getName();
+          if (id.indexOf("|") > -1)
+            id = id.substring(id.lastIndexOf("|") + 1);
+
+          url = link.substring(link.indexOf("|") + 1,
+                               link.indexOf("$SEQUENCE_ID$"))
+              + id +
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+        }
+        else
+          url = link.substring(link.lastIndexOf("|")+1);
 
            item.addActionListener(new java.awt.event.ActionListener()
            {
@@ -128,18 +137,19 @@ public class APopupMenu
       }
       add(linkMenu);
 
-      item = new MenuItem("Show PDB Structure");
-      item.addActionListener(new java.awt.event.ActionListener()
-           {
-               public void actionPerformed(ActionEvent e)
-               {
-                  addPDB(seq);
-               }
-           });
-
-      add(item);
-
+      if(seq!=null)
+      {
+        item = new MenuItem("Show PDB Structure");
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            addPDB(seq);
+          }
+        });
 
+        add(item);
+      }
     }
   }
 
@@ -199,12 +209,14 @@ public class APopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();
       if (sg != null)
       {
-        for (int g = 0; g < sg.getSize(); g++)
+        for (int g = 0; g < sg.getSize(true); g++)
         {
           if (source == toggleCase)
-            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+           ((SequenceI) sg.getSequences(true).elementAt(g))
+          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
           else
-            sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),
+            ((SequenceI) sg.getSequences(true).elementAt(g))
+                .changeCase(source == toUpper, sg.getStartRes(),
                                            sg.getEndRes() + 1);
         }
         ap.seqPanel.seqCanvas.repaint();
@@ -323,7 +335,7 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -383,7 +395,7 @@ public class APopupMenu
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                                ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
           getGroup().getName());
@@ -411,7 +423,7 @@ public class APopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -422,7 +434,7 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                              ap.av.alignment.getWidth()));
 
     refresh();
@@ -445,7 +457,7 @@ public class APopupMenu
 
       Conservation c = new Conservation("Group",
                                         ResidueProperties.propHash, 3,
-                                        sg.sequences, 0,
+                                        sg.getSequences(true), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();