X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=cc050d57be5b29f5a76966ca16808c96ae06b283;hb=a2d2bfc9a2efd08446954c01dc5957560fdec9be;hp=e587feec2a55f9cb876a94a0d95426b458dd4e7a;hpb=1032f8a608bb97dd7817390aa56293dba3fe3806;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e587fee..cc050d5 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,7 +16,7 @@ public class PIDColourScheme extends ResidueColourScheme {
     }
 
 
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {
+  public Color findColour(String s, int j,Vector aa) {
       Color     c    = Color.white;
       Hashtable hash = null;
 
@@ -31,10 +31,9 @@ public class PIDColourScheme extends ResidueColourScheme {
       double sc = 0;
       if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
       {
-
         sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
         // MC Should be isGap
-        if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
+        if (!jalview.util.Comparison.isGap((s.charAt(0))))
         {
           for (int i = 0; i < thresholds.length; i++)
           {
@@ -45,8 +44,7 @@ public class PIDColourScheme extends ResidueColourScheme {
             }
           }
         }
-        else
-          c = Color.white;
+
       }
       return c;
   }