set gap char modified

[jalview.git] / src / jalview / gui / RedundancyPanel.java

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 6cb2c22..93ffd9c 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -48,13 +48,14 @@ public class RedundancyPanel extends GSliderPanel
 \r
         undoButton.setEnabled(true);\r
 \r
-       if (ap.av.sel != null && ap.av.sel.size() > 1)\r
+        SequenceGroup sg = ap.av.getSelectionGroup();\r
+       if (sg != null && sg.getSize() > 1)\r
        {\r
 \r
-         del = ap.av.alignment.removeRedundancy(threshold, ap.av.sel.asVector());\r
+         del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
          for (int i = 0; i < del.size(); i++)\r
-           if (ap.av.sel.contains( (SequenceI) del.elementAt(i)))\r
-             ap.av.sel.removeElement( (SequenceI) del.elementAt(i));\r
+           if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
+             sg.deleteSequence( (SequenceI) del.elementAt(i));\r
 \r
          }\r
          else\r
@@ -69,13 +70,13 @@ public class RedundancyPanel extends GSliderPanel
             del = ap.av.alignment.removeRedundancy(threshold,s);\r
            for (int j=0; j < del.size(); j++)\r
            {\r
-               if (ap.av.sel.contains((SequenceI)del.elementAt(j)))\r
-               ap.av.sel.removeElement((SequenceI)del.elementAt(j));\r
+               if (sg.sequences.contains((SequenceI)del.elementAt(j)))\r
+               sg.deleteSequence((SequenceI)del.elementAt(j));\r
 \r
            }\r
          }\r
 \r
-         ap.RefreshPanels();\r
+         ap.repaint();\r
 \r
   }\r
 \r
@@ -84,7 +85,7 @@ public class RedundancyPanel extends GSliderPanel
       undoButton.setEnabled(false);\r
       ap.av.setAlignment( new Alignment(oldAlignment) );\r
       oldAlignment = null;\r
-      ap.RefreshPanels();\r
+      ap.repaint();\r
   }\r
 \r
 \r