X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=1c6c4537fdba534388698c0bd9544f876ce97ce2;hb=e0d0ddec9ebf787eee7241f044426c81ea2a7992;hp=905255a11536bf27745f262fc94d1b4d7c3185a5;hpb=157004a864888ed2e690b907a28f715d3d42b666;p=jalview.git

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