X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FCovariationColourScheme.java;h=4884283aa1024b9636932482a37f3cafa2489214;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=6cb095b32e8795a3237e21104bed3fa02384da1f;hpb=f831ddf7f52d6c4a1918e87d94877b22bd322648;p=jalview.git

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 6cb095b..4884283 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]);
   }
@@ -66,9 +65,9 @@ public class CovariationColourScheme extends ResidueColourScheme
 
     for (int x = 0; x < this.annotation._rnasecstr.length; x++)
     {
-      // System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
       // this.annotation._rnasecstr[x].getBegin());
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
       // pairs.put(this.annotation._rnasecstr[x].getBegin(),
       // this.annotation._rnasecstr[x].getEnd());
 
@@ -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());
       }
 
     }
@@ -104,7 +104,7 @@ public class CovariationColourScheme extends ResidueColourScheme
   @Override
   public Color findColour(char c)
   {
-    // System.out.println("called"); log.debug
+    // jalview.bin.Console.outPrintln("called"); log.debug
     // Generate a random pastel color
 
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
@@ -124,16 +124,16 @@ public class CovariationColourScheme extends ResidueColourScheme
   {
     Color currentColour = Color.white;
     String currentHelix = null;
-    // System.out.println(c + " " + j);
+    // jalview.bin.Console.outPrintln(c + " " + j);
     currentHelix = positionsToHelix.get(j);
-    // System.out.println(positionsToHelix.get(j));
+    // jalview.bin.Console.outPrintln(positionsToHelix.get(j));
 
     if (currentHelix != null)
     {
       currentColour = helixcolorhash.get(currentHelix);
     }
 
-    // System.out.println(c + " " + j + " helix " + currentHelix + " " +
+    // jalview.bin.Console.outPrintln(c + " " + j + " helix " + currentHelix + " " +
     // currentColour);
     return currentColour;
   }