Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 812dca7..db85cc8 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -83,10 +84,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme
 
     // assume only one set of TCOFFEE scores - but could have more than one
     // potentially.
-    List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> annots = new ArrayList<>();
     // Search alignment to get all tcoffee annotation and pick one set of
     // annotation to use to colour seqs.
-    seqMap = new IdentityHashMap<SequenceI, Color[]>();
+    seqMap = new IdentityHashMap<>();
     AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
             ? alignment
             : alignment.getContext();
@@ -143,8 +144,8 @@ public class TCoffeeColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     return new TCoffeeColourScheme(sg);
   }