X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=e1dbf4696706b9cd4b8c96bb4a6cf7f76d8a04cf;hb=7000ea3223f2f6a390f56341ba26850d2a137ae0;hp=8061e67c3bc0282028234031ab76fa7c97e307b3;hpb=09429083519f2ed29b9cee54ab3baa9bdbde8655;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8061e67..e1dbf46 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -20,8 +20,8 @@ package jalview.schemes;
 
 import java.awt.*;
 
+import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.analysis.AAFrequency;
 
 public class PIDColourScheme
     extends ResidueColourScheme
@@ -36,54 +36,58 @@ public class PIDColourScheme
     this.thresholds = ResidueProperties.pidThresholds;
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
-    char res = s.charAt(0);
-    if ('a' <= res && res <= 'z')
+    if ('a' <= c && c <= 'z')
     {
-      s = String.valueOf(res -= ('a' - 'A'));
+      c -= ('a' - 'A');
     }
 
     if (consensus == null
         || j >= consensus.length
-        || consensus[j]==null)
+        || consensus[j] == null)
     {
       return Color.white;
     }
 
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if ( (threshold != 0) && !aboveThreshold(c, j))
     {
       return Color.white;
     }
 
-    currentColour = Color.white;
+    Color currentColour = Color.white;
 
     double sc = 0;
 
-    if(consensus.length<=j)
+    if (consensus.length <= j)
+    {
       return Color.white;
+    }
 
-      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
-          consensus[j].contains(s))
-      {
-        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=
+          -1) &&
+        consensus[j].contains(String.valueOf(c)))
+    {
+      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
 
-        if (!jalview.util.Comparison.isGap(res))
+      if (!jalview.util.Comparison.isGap(c))
+      {
+        for (int i = 0; i < thresholds.length; i++)
         {
-          for (int i = 0; i < thresholds.length; i++)
+          if (sc > thresholds[i])
           {
-            if (sc > thresholds[i])
-            {
-              currentColour = pidColours[i];
+            currentColour = pidColours[i];
 
-              break;
-            }
+            break;
           }
         }
       }
+    }
 
-    if(conservationColouring)
-         applyConservation(j);
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }