X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=f213abecf18b6bf8192d60d254a24a144dbf3249;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=ccc69c286b29259be84f278ddac2fd1bbab00b61;hpb=08fa75428822ee384d35eb67b1e23e33e83d8d9d;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index ccc69c2..f213abe 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -20,80 +20,89 @@
  */
 package jalview.schemes;
 
+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
-  public Color findColour(char c, int j, SequenceI seq)
+  public Color findColour(char c, int j, SequenceI seq,
+          String consensusResidue, float pid)
   {
+    /*
+     * make everything uppercase; note this does nothing
+     * if consensusResidue is already uppercase
+     */
+    consensusResidue = consensusResidue.toUpperCase();
     if ('a' <= c && c <= 'z')
     {
       c -= ('a' - 'A');
     }
 
-    if (consensus == null || j >= consensus.length || consensus[j] == null)
+    if (consensusResidue == null || Comparison.isGap(c))
     {
       return Color.white;
     }
 
-    if ((threshold != 0) && !aboveThreshold(c, j))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = Color.white;
-
-    double sc = 0;
-
-    if (consensus.length <= j)
-    {
-      return Color.white;
-    }
+    Color colour = Color.white;
 
     /*
      * test whether this is the consensus (or joint consensus) residue
      */
-    boolean matchesConsensus = consensus[j].getModalResidue().contains(
+    boolean matchesConsensus = consensusResidue.contains(
             String.valueOf(c));
     if (matchesConsensus)
     {
-      sc = consensus[j].getPercentageIdentity(ignoreGaps);
-
-      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 (sc > thresholds[i])
-          {
-            currentColour = pidColours[i];
-            break;
-          }
+          colour = pidColours[i];
+          break;
         }
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
+    return colour;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.PID.toString();
+  }
 
-    return currentColour;
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
+  {
+    return new PIDColourScheme();
+  }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
   }
 }