X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=db85cc842445951459e9a5166ec5e63a6f6694f1;hb=89350c76ad3884aa1394952979998ea58902063c;hp=13d1d55951c9218d2328a8954bd9a430572035e1;hpb=f831ddf7f52d6c4a1918e87d94877b22bd322648;p=jalview.git

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 13d1d55..db85cc8 100644
--- 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;
@@ -83,11 +84,12 @@ 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[]>();
-    AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+    seqMap = new IdentityHashMap<>();
+    AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+            ? alignment
             : alignment.getContext();
     if (alcontext == null)
     {
@@ -142,8 +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);
   }
@@ -154,8 +156,8 @@ public class TCoffeeColourScheme extends ResidueColourScheme
   @Override
   public boolean isApplicableTo(AnnotatedCollectionI ac)
   {
-    AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac : ac
-            .getContext();
+    AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
+            : ac.getContext();
     if (alcontext == null)
     {
       return false;