Doesn't draw the white box at the end of a line

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 905255a..1c6c453 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -20,23 +20,24 @@ public class AlignViewport
   boolean showColourText=false;\r
   boolean showBoxes=true;\r
   boolean wrapAlignment=false;\r
-  boolean renderGaps = false;\r
-  boolean groupEdit    = false;\r
-  boolean groupDefiningMode = true;\r
+  boolean renderGaps = true;\r
 \r
   ColourSchemeI globalColourScheme = null;\r
+  boolean conservationColourSelected = false;\r
+\r
+  SequenceGroup rubberbandGroup = null;\r
 \r
   RendererI renderer = new SequenceRenderer(this);\r
 \r
   int             charHeight;\r
-  int          charWidth;\r
+  int             charWidth;\r
   int             chunkWidth;\r
   int             chunkHeight;\r
 \r
   Font            font = new Font("SansSerif",Font.PLAIN,10);\r
   AlignmentI      alignment;\r
 \r
-  Selection       sel    = new Selection();\r
+  Selection       sel    = new Selection(this);\r
   ColumnSelection colSel = new ColumnSelection();\r
 \r
   OutputGenerator og;\r
@@ -114,6 +115,25 @@ public class AlignViewport
     return consensus;\r
   }\r
 \r
+  public SequenceGroup getRubberbandGroup()\r
+  {\r
+    return rubberbandGroup;\r
+  }\r
+\r
+  public void setRubberbandGroup(SequenceGroup sg)\r
+  {\r
+    rubberbandGroup = sg;\r
+  }\r
+\r
+ public boolean getConservationSelected()\r
+ {\r
+   return conservationColourSelected;\r
+ }\r
+\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+   conservationColourSelected = b;\r
+ }\r
 \r
   public int getStartRes() {\r
     return startRes;\r
@@ -254,15 +274,7 @@ public class AlignViewport
   public boolean getShowBoxes() {\r
     return showBoxes;\r
   }\r
- // public CommandParser getCommandLog() {\r
- ///   return log;\r
- // }\r
-  public boolean getGroupEdit() {\r
-    return groupEdit;\r
-  }\r
-  public void setGroupEdit(boolean state) {\r
-    groupEdit = state;\r
-  }\r
+\r
   public char getGapCharacter() {\r
     return getAlignment().getGapCharacter();\r
   }\r