JAL-1483 cut and paste from SW score model to allow scores based on sequences to...

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 590ca18..4f78145 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -160,11 +160,17 @@ public interface AlignViewportI
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
 
+  void setSequenceColour(SequenceI seq, Color col);
+
+  Color getSequenceColour(SequenceI seq);
+
+  void updateSequenceIdColours();
 
   SequenceGroup getSelectionGroup();
 
   SequenceI[] getSequenceSelection();
 
+  void clearSequenceColours();
 
   CigarArray getViewAsCigars(boolean selectedRegionOnly);
 
@@ -178,5 +184,7 @@ public interface AlignViewportI
 
   char getGapCharacter();
 
+  void setColumnSelection(ColumnSelection cs);
+
 
 }