From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 14 Dec 2004 17:34:50 +0000 (+0000)
Subject: PID Colour scheme now operational!
X-Git-Tag: Release_2_0~824
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=1032f8a608bb97dd7817390aa56293dba3fe3806

PID Colour scheme now operational!
---

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 0a28c33..e587fee 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -14,45 +14,39 @@ 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) {
       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 (!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;
       }
       return c;
   }