X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=3a5c066397dbc2182061da7d6529ff9551b77e02;hb=b9b1f47cc74bbec8c28b75776e1d00c258215dfb;hp=a6301fab9d8e5165f32a675abdc0282d92eaae21;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index a6301fa..3a5c066 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -20,27 +20,25 @@
  */
 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
 {
-  public Color[] pidColours;
+  private static final Color[] pidColours = { new Color(100, 100, 255),
+      new Color(153, 153, 255), new Color(204, 204, 255), };
 
-  public float[] thresholds;
+  private static final float[] thresholds = { 80, 60, 40, };
 
   SequenceGroup group;
 
   public PIDColourScheme()
   {
-    this.pidColours = ResidueProperties.pidColours;
-    this.thresholds = ResidueProperties.pidThresholds;
   }
 
   @Override
@@ -48,16 +46,15 @@ public class PIDColourScheme extends ResidueColourScheme
           String consensusResidue, float pid)
   {
     /*
-     * make everything uppercase; note this does nothing (fast)
-     * 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');
     }
 
-    if (consensusResidue == null)
+    if (consensusResidue == null || Comparison.isGap(c))
     {
       return Color.white;
     }
@@ -67,19 +64,15 @@ 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)
     {
-      if (!Comparison.isGap(c))
+      for (int i = 0; i < thresholds.length; i++)
       {
-        for (int i = 0; i < thresholds.length; i++)
+        if (pid > thresholds[i])
         {
-          if (pid > thresholds[i])
-          {
-            colour = pidColours[i];
-            break;
-          }
+          colour = pidColours[i];
+          break;
         }
       }
     }
@@ -98,8 +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();
   }