X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=86868948cbaabc6905181855e9ce8f6ac46c030c;hb=f78ed026becc8e143d5b5953fce6c0961428d2a7;hp=e09745a0c315399fcfbac91a366b1daf9cd6683f;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e09745a..8686894 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -36,21 +36,26 @@ 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)
+    {
+      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;
 
@@ -58,11 +63,11 @@ public class PIDColourScheme
       return Color.white;
 
       if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
-          consensus[j].contains(s))
+          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++)
           {
@@ -77,7 +82,7 @@ public class PIDColourScheme
       }
 
     if(conservationColouring)
-         applyConservation(j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }