abovePIDThreshold added to viewport

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