sequences are private in SequenceGroup

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 5ff10ce..6869964 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -187,7 +187,7 @@ public class SeqPanel
        SequenceGroup sg = av.selectionGroup;\r
        //Find the top and bottom of this group\r
        int min = av.alignment.getHeight(), max = 0;\r
-       for(int i=0; i<sg.getSize(); i++)\r
+       for(int i=0; i<sg.getSize(false); i++)\r
        {\r
          int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
          if(index > max)\r
@@ -223,7 +223,7 @@ public class SeqPanel
        else\r
        {\r
          // Now add any sequences between min and max\r
-         sg.sequences.removeAllElements();\r
+         sg.getSequences(false).removeAllElements();\r
          for (int i = min; i < max; i++)\r
          {\r
            sg.addSequence(av.alignment.getSequenceAt(i), false);\r
@@ -720,7 +720,7 @@ public class SeqPanel
 \r
         //Are we editing within a selection group?\r
         if (groupEditing\r
-            || (sg != null && sg.sequences.contains(seq)))\r
+            || (sg != null && sg.getSequences(false).contains(seq)))\r
         {\r
           fixedColumns = true;\r
 \r
@@ -771,7 +771,7 @@ public class SeqPanel
                  fixedRight--)\r
             {\r
               blank = true;\r
-              for (int s = 0; s < sg.getSize(); s++)\r
+              for (int s = 0; s < sg.getSize(false); s++)\r
               {\r
                 seq = sg.getSequenceAt(s);\r
                 for (int j = 0; j < startres - lastres; j++)\r
@@ -790,7 +790,7 @@ public class SeqPanel
 \r
             if (!blank)\r
             {\r
-              if(sg.getSize() == av.alignment.getHeight())\r
+              if(sg.getSize(false) == av.alignment.getHeight())\r
               {\r
                 //We can still insert gaps if the selectionGroup\r
                 //contains all the sequences\r
@@ -812,7 +812,7 @@ public class SeqPanel
             /// Are we able to delete?\r
             // ie are all columns blank?\r
 \r
-            for (int s = 0; s < sg.getSize(); s++)\r
+            for (int s = 0; s < sg.getSize(false); s++)\r
             {\r
               seq = sg.getSequenceAt(s);\r
 \r
@@ -835,7 +835,7 @@ public class SeqPanel
           }\r
 \r
 \r
-          for (int i = 0; i < sg.getSize(); i++)\r
+          for (int i = 0; i < sg.getSize(false); i++)\r
           {\r
             seq = sg.getSequenceAt(i);\r
 \r
@@ -1058,7 +1058,7 @@ public class SeqPanel
       }\r
     }\r
 \r
-    else if (!stretchGroup.sequences.contains(sequence)\r
+    else if (!stretchGroup.getSequences(false).contains(sequence)\r
              || stretchGroup.getStartRes() > res\r
              || stretchGroup.getEndRes() < res)\r
     {\r
@@ -1171,8 +1171,8 @@ public class SeqPanel
     {\r
       if (stretchGroup.cs instanceof ClustalxColourScheme)\r
       {\r
-        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
-            sequences,\r
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
+            stretchGroup.getSequences(true),\r
             stretchGroup.getWidth());\r
       }\r
 \r
@@ -1275,7 +1275,7 @@ public class SeqPanel
 \r
           Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 \r
-          if (stretchGroup.sequences.contains(nextSeq))\r
+          if (stretchGroup.getSequences(false).contains(nextSeq))\r
           {\r
               stretchGroup.deleteSequence(seq, false);\r
           }\r