Merge branch 'test_paolo_JAL-1065' into Tcoffee_JAL-1065

[jalview.git] / src / jalview / schemes / ColourSchemeI.java

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index e8e5828..273273f 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -19,11 +19,14 @@ package jalview.schemes;
 
 import java.awt.Color;
 
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
+
 public interface ColourSchemeI
 {
   public Color findColour(char c);
 
-  public Color findColour(char c, int j, int sequenceIndex);
+  public Color findColour(char c, int j, SequenceI seq);
 
   public void setConsensus(java.util.Hashtable[] h);
 
@@ -39,4 +42,6 @@ public interface ColourSchemeI
 
   public void setThreshold(int ct, boolean ignoreGaps);
 
+  public void alignmentChanged(AnnotatedCollectionI alignment);
+
 }