JAL-3675 release notes for JAL-3750 JAL-3751

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index f213abe..3a5c066 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -20,14 +20,13 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-import java.util.Map;
 
 public class PIDColourScheme extends ResidueColourScheme
 {
@@ -47,10 +46,9 @@ public class PIDColourScheme extends ResidueColourScheme
           String consensusResidue, float pid)
   {
     /*
-     * make everything uppercase; note this does nothing
-     * if consensusResidue is already uppercase
+     * compare as upper case; note consensusResidue is 
+     * always computed as uppercase
      */
-    consensusResidue = consensusResidue.toUpperCase();
     if ('a' <= c && c <= 'z')
     {
       c -= ('a' - 'A');
@@ -66,8 +64,7 @@ public class PIDColourScheme extends ResidueColourScheme
     /*
      * test whether this is the consensus (or joint consensus) residue
      */
-    boolean matchesConsensus = consensusResidue.contains(
-            String.valueOf(c));
+    boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
     if (matchesConsensus)
     {
       for (int i = 0; i < thresholds.length; i++)
@@ -94,8 +91,8 @@ public class PIDColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
     return new PIDColourScheme();
   }