X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=cc050d57be5b29f5a76966ca16808c96ae06b283;hb=a2d2bfc9a2efd08446954c01dc5957560fdec9be;hp=312ae7d534ce8a8ce8bcc38419e4063788c9f262;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 312ae7d..cc050d5 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,8 +1,6 @@
 package jalview.schemes;
 
 import jalview.datamodel.*;
-import jalview.jbgui.*;
-
 import java.util.*;
 import java.awt.*;
 
@@ -16,45 +14,37 @@ public class PIDColourScheme extends ResidueColourScheme {
 	this.pidColours = ResidueProperties.pidColours;
 	this.thresholds = ResidueProperties.pidThresholds;
     }
-  public Color getColour(SequenceI seq, int j,Vector aa) {
-    Color c = Color.white;
-
-    String       s = seq.getSequence(j,j+1);
-
-    if (aa != null && j < aa.size()) {
-	c = findColour(seq,s,j,aa);
-    }
 
-    return c;
-  }
 
-  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;
 
-      if (aa != null) {
+
+      if (aa != null)
 	  hash = (Hashtable)aa.elementAt(j);
-      }
       else
         return c;
 
       String    max  = (String)hash.get("maxResidue");
 
       double sc = 0;
-      if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-	  sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));
-
-	  // MC Should be isGap
-	  if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-	      for (int i=0; i < thresholds.length; i++) {
-		  if (sc > thresholds[i]) {
-		      c = pidColours[i];
-		      break;
-		  }
-	      }
-	  } else {
-	      c = Color.white;
-	  }
+      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 (!jalview.util.Comparison.isGap((s.charAt(0))))
+        {
+          for (int i = 0; i < thresholds.length; i++)
+          {
+            if (sc > thresholds[i])
+            {
+              c = pidColours[i];
+              break;
+            }
+          }
+        }
+
       }
       return c;
   }