From 1efc6eee5c3eff789274b47a46707ba2d0923288 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 14 Apr 2005 16:52:43 +0000
Subject: [PATCH] blosum colour now displayed ok

---
 src/jalview/schemes/ConservationColourScheme.java |   35 ++++++---------------
 1 file changed, 9 insertions(+), 26 deletions(-)

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index f8db803..cef65c2 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -24,7 +24,6 @@ import jalview.analysis.*;
 
 public class ConservationColourScheme extends ResidueColourScheme {
   public Conservation conserve;
-  boolean byResidue = true;
   public ColourSchemeI cs;
   public int inc = 30;
   int colourThreshold =  7;
@@ -38,24 +37,21 @@ public class ConservationColourScheme extends ResidueColourScheme {
   }
 
 
-   public Color findColour(String s, int i, java.util.Vector whatever)
+   public Color findColour(String s, int i, java.util.Vector v)
    {
-     Color c = null;
+     Color c = Color.white;
+     if(cs == null)
+       return c;
+
      if (colourThreshold > 0 && conserve.getConsSequence() != null)
      {
-       if (conserve.getConsSequence().getSequence().charAt(i)=='*'
-           || conserve.getConsSequence().getSequence().charAt(i)=='+')
+       if (conserve.getConsSequence().getSequence().charAt(i) == '*'
+           || conserve.getConsSequence().getSequence().charAt(i) == '+')
        {
-         if (byResidue)
-           c = findColour(s, i);
-         else
-           c = Color.red;
+           c = cs.findColour(s, i, v);
        }
        else
        {
-         if (byResidue)
-         {
-
            int tmp = 10;
            int t = 0;
            if (!jalview.util.Comparison.isGap(conserve.getConsSequence().
@@ -63,30 +59,17 @@ public class ConservationColourScheme extends ResidueColourScheme {
              t = Integer.parseInt(conserve.getConsSequence().getSequence().
                                   substring(i, i + 1));
 
-           c = findColour(s, i);
-
+           c = cs.findColour(s, i, v);
            while (tmp >= t)
            {
-             //      c = c.darker();
              c = lighter(c, inc);
              tmp--;
            }
-         }
-         else
-           c = Color.yellow;
        }
      }
      return c;
    }
 
-  public Color findColour(String s, int j) {
-    if(cs!=null)
-      return cs.findColour( s, j, null);
-    else
-      return Color.white;
-  }
-
-
 
   public Color lighter(Color c, int inc) {
     int red = c.getRed();
-- 
1.7.10.2