Remove all gaps must check jSize

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d154e2e..2f7e5a8 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -680,6 +680,9 @@ public class AlignFrame extends GAlignFrame
                 HistoryItem.HIDE));\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
@@ -687,6 +690,13 @@ public class AlignFrame extends GAlignFrame
             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(), sg.getEndRes()+1);\r
+            }\r
+\r
+\r
             if (seq.getSequence().length() < 1)\r
             {\r
                 seqsdeleted = true;\r
@@ -936,7 +946,7 @@ public class AlignFrame extends GAlignFrame
 \r
                 j++;\r
             }\r
-            while (j < end);\r
+            while (j < end && j < jSize);\r
         }\r
 \r
         viewport.updateConservation();\r