X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FCovariationColourScheme.java;h=dc7971b9e3582b2add896656a7601d8de0608b90;hb=a3bed79406073da41d03e8278733e4beae172e6e;hp=3637ce3b9982405a63811190b9963a56227d74d3;hpb=373586a0c940f2345179d1135738f245e29a98b8;p=jalview.git

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 3637ce3..dc7971b 100644
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -20,10 +20,9 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
 
 import java.awt.Color;
@@ -38,9 +37,9 @@ import java.util.Map;
  */
 public class CovariationColourScheme extends ResidueColourScheme
 {
-  public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
+  public Map<String, Color> helixcolorhash = new Hashtable<>();
 
-  public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+  public Map<Integer, String> positionsToHelix = new Hashtable<>();
 
   int numHelix = 0;
 
@@ -51,8 +50,8 @@ public class CovariationColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
     return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
   }
@@ -77,10 +76,11 @@ public class CovariationColourScheme extends ResidueColourScheme
       positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
               this.annotation._rnasecstr[x].getFeatureGroup());
 
-      if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+      if (Integer.parseInt(
+              this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
       {
-        numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
-                .getFeatureGroup());
+        numHelix = Integer
+                .parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
       }
 
     }
@@ -149,4 +149,10 @@ public class CovariationColourScheme extends ResidueColourScheme
   {
     return "Covariation";
   }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
 }