fix aligned DNA codon translation bug(s) and generate AlignedCodonFrame mappings...

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

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 36b414f..3e91f21 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -174,7 +174,7 @@ public class ScalePanel
 \r
     }\r
 \r
-    ap.paintAlignment(true);\r
+    ap.paintAlignment(false);\r
   }\r
 \r
   /**\r
@@ -200,7 +200,7 @@ public class ScalePanel
 \r
     if (!stretchingGroup)\r
     {\r
-      ap.paintAlignment(true);\r
+      ap.paintAlignment(false);\r
 \r
       return;\r
     }\r
@@ -219,7 +219,7 @@ public class ScalePanel
       }\r
     }\r
     stretchingGroup = false;\r
-    ap.paintAlignment(true);\r
+    ap.paintAlignment(false);\r
   }\r
 \r
   /**\r
@@ -277,19 +277,22 @@ public class ScalePanel
         sg.setStartRes(res);\r
       }\r
 \r
+      int col;\r
       for (int i = min; i <= max; i++)\r
       {\r
-        if ( (i < sg.getStartRes()) || (i > sg.getEndRes()))\r
+        col = av.getColumnSelection().adjustForHiddenColumns(i);\r
+\r
+        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))\r
         {\r
-          av.getColumnSelection().removeElement(i);\r
+          av.getColumnSelection().removeElement(col);\r
         }\r
         else\r
         {\r
-          av.getColumnSelection().addElement(i);\r
+          av.getColumnSelection().addElement(col);\r
         }\r
       }\r
 \r
-      ap.paintAlignment(true);\r
+      ap.paintAlignment(false);\r
     }\r
   }\r
 \r