X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=86868948cbaabc6905181855e9ce8f6ac46c030c;hb=51bbc79eee43d019f9fcb14b7aa6e0a0c2c99f76;hp=9dc4c66aa729c9086b2d84d37a47f47432bea273;hpb=503ebba0021fa583fa7af58f9406f9234274fd7c;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 9dc4c66..8686894 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) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -21,6 +21,7 @@ package jalview.schemes;
 import java.awt.*;
 
 import jalview.datamodel.*;
+import jalview.analysis.AAFrequency;
 
 public class PIDColourScheme
     extends ResidueColourScheme
@@ -35,45 +36,54 @@ 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 = Character.toString(res -= ('a' - 'A'));
+      c -= ('a' - 'A');
     }
 
-
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j]==null)
     {
       return Color.white;
     }
 
+    if ( (threshold != 0) && !aboveThreshold(c, j))
+    {
+      return Color.white;
+    }
 
-
-    Color c = Color.white;
+    Color currentColour = Color.white;
 
     double sc = 0;
 
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
-        consensus[j].contains(s))
-    {
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
+    if(consensus.length<=j)
+      return Color.white;
 
-      if (!jalview.util.Comparison.isGap( res ))
+      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
+          consensus[j].contains(String.valueOf(c)))
       {
-        for (int i = 0; i < thresholds.length; i++)
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+        if (!jalview.util.Comparison.isGap(c))
         {
-          if (sc > thresholds[i])
+          for (int i = 0; i < thresholds.length; i++)
           {
-            c = pidColours[i];
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
 
-            break;
+              break;
+            }
           }
         }
       }
-    }
 
-    return c;
+    if(conservationColouring)
+      currentColour = applyConservation(currentColour, j);
+
+    return currentColour;
   }
 }