sequences are private in SequenceGroup

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1c9b3cd..3401cc4 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -82,7 +82,7 @@ public class APopupMenu
 \r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
-    if (sg != null && sg.getSize()>0)\r
+    if (sg != null && sg.getSize(false)>0)\r
     {\r
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
@@ -209,12 +209,14 @@ public class APopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       if (sg != null)\r
       {\r
-        for (int g = 0; g < sg.getSize(); g++)\r
+        for (int g = 0; g < sg.getSize(true); g++)\r
         {\r
           if (source == toggleCase)\r
-            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+           ((SequenceI) sg.getSequences(true).elementAt(g))\r
+          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
           else\r
-            sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),\r
+            ((SequenceI) sg.getSequences(true).elementAt(g))\r
+                .changeCase(source == toUpper, sg.getStartRes(),\r
                                            sg.getEndRes() + 1);\r
         }\r
         ap.seqPanel.seqCanvas.repaint();\r
@@ -333,7 +335,7 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
     refresh();\r
   }\r
 \r
@@ -393,7 +395,7 @@ public class APopupMenu
 \r
     if (abovePIDColour.getState())\r
     {\r
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
@@ -421,7 +423,7 @@ public class APopupMenu
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new PIDColourScheme();\r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                              ap.av.alignment.getWidth()));\r
     refresh();\r
   }\r
@@ -432,7 +434,7 @@ public class APopupMenu
 \r
     sg.cs = new Blosum62ColourScheme();\r
 \r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
                                              ap.av.alignment.getWidth()));\r
 \r
     refresh();\r
@@ -455,7 +457,7 @@ public class APopupMenu
 \r
       Conservation c = new Conservation("Group",\r
                                         ResidueProperties.propHash, 3,\r
-                                        sg.sequences, 0,\r
+                                        sg.getSequences(true), 0,\r
                                         ap.av.alignment.getWidth());\r
 \r
       c.calculate();\r