X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=3401cc4b31d676978eb35fa75ec243603051d7ee;hb=df9b85c1cf39894039018499fe802406cc37f209;hp=1c9b3cd94091c3bb1a19283843fe2472ba0dfccc;hpb=bf2bf43c980b18a26b724d2a2d51dddc1a79a185;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1c9b3cd..3401cc4 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -82,7 +82,7 @@ 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());
@@ -209,12 +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();
@@ -333,7 +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();
   }
 
@@ -393,7 +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());
@@ -421,7 +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();
   }
@@ -432,7 +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();
@@ -455,7 +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();