From d9929c98ecb8fa9aa65cf5e2c07fc8cbf8fc91df Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 15 Feb 2005 10:46:52 +0000
Subject: [PATCH] abovePIDThreshold added to viewport

---
 src/jalview/gui/AlignViewport.java |   19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3620bc0..c1708ea 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -23,8 +23,10 @@ public class AlignViewport
   boolean renderGaps = true;
   boolean showSequenceFeatures = true;
 
+  boolean colourAppliesToAllGroups = true;
   ColourSchemeI globalColourScheme = null;
   boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
 
   SequenceGroup rubberbandGroup = null;
 
@@ -134,6 +136,16 @@ public class AlignViewport
    conservationColourSelected = b;
  }
 
+ public boolean getAbovePIDThreshold()
+ {
+   return abovePIDThreshold;
+ }
+
+ public void setAbovePIDThreshold(boolean b)
+ {
+   abovePIDThreshold = b;
+ }
+
   public int getStartRes() {
     return startRes;
   }
@@ -339,4 +351,11 @@ public class AlignViewport
 	return renderer;
     }
 
+  public void setColourAppliesToAllGroups(boolean b)
+  {   colourAppliesToAllGroups = b; }
+
+  public boolean getColourAppliesToAllGroups()
+  {return colourAppliesToAllGroups; }
+
+
 }
-- 
1.7.10.2