Remove all gaps must check jSize

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index aeee116..3ab3132 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -397,13 +397,26 @@ public class AlignFrame
       return;\r
     }\r
 \r
+\r
     SequenceGroup sg = viewport.getSelectionGroup();\r
+    boolean allSequences = false;\r
+    if(sg.sequences.size()==viewport.alignment.getHeight())\r
+          allSequences = true;\r
+\r
     for (int i = 0; i < sg.sequences.size(); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.getAlignment().findIndex(seq);\r
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 \r
+      // If the cut affects all sequences, remove highlighted columns\r
+      if (allSequences)\r
+      {\r
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+                                                     sg.getEndRes() + 1);\r
+      }\r
+\r
+\r
       if (seq.getSequence().length() < 1)\r
       {\r
         viewport.getAlignment().deleteSequence(seq);\r
@@ -579,7 +592,7 @@ public class AlignFrame
         }\r
         j++;\r
       }\r
-      while(j < end);\r
+      while(j < end && j < jSize) ;\r
     }\r
 \r
     viewport.updateConservation();\r