From 95ebd2cf76003f52476a7802c99831dfa98945f7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:48:22 +0000
Subject: [PATCH] Conservation colouring does what it should always have done

---
 src/jalview/schemes/ResidueColourScheme.java |   77 +++++++++-----------------
 1 file changed, 25 insertions(+), 52 deletions(-)

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 3c8e690..78ebab0 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -216,69 +216,42 @@ public class ResidueColourScheme implements ColourSchemeI
     *
     * @return DOCUMENT ME!
     */
-   void applyConservation(int i)
-   {
-       if ((conservation[i] != '*') && (conservation[i] != '+'))
-       {
-           int tmp = 10;
-           int t = 0;
-
-           if (!jalview.util.Comparison.isGap(conservation[i]))
-           {
-               t = conservation[i]-'0';
-           }
-
-           while (tmp >= t)
-           {
-               lighter(inc);
-               tmp--;
-           }
-       }
 
-   }
-
-    /**
-    * DOCUMENT ME!
-    *
-    * @param c DOCUMENT ME!
-    * @param inc DOCUMENT ME!
-    *
-    * @return DOCUMENT ME!
-    */
-   void lighter(int inc)
+   void applyConservation(int i)
    {
-       int red = currentColour.getRed();
-       int blue = currentColour.getBlue();
-       int green = currentColour.getGreen();
 
-       if (red < (255 - inc))
+     if ((conservation[i] != '*') && (conservation[i] != '+'))
+     {
+       if(jalview.util.Comparison.isGap(conservation[i]))
        {
-           red = red + inc;
+         currentColour = Color.white;
        }
        else
        {
-           red = 255;
-       }
+         float t = 11 - (conservation[i] - '0');
 
-       if (blue < (255 - inc))
-       {
-           blue = blue + inc;
-       }
-       else
-       {
-           blue = 255;
-       }
+         int red = currentColour.getRed();
+         int green = currentColour.getGreen();
+         int blue = currentColour.getBlue();
 
-       if (green < (255 - inc))
-       {
-           green = green + inc;
+         int dr = 255 - red;
+         int dg = 255 - green;
+         int db = 255 - blue;
+
+         dr *= t / 10f;
+         dg *= t / 10f;
+         db *= t / 10f;
+
+         red += (inc / 20f) * dr;
+         green += (inc / 20f) * dg;
+         blue += (inc / 20f) * db;
+
+         if (red > 255 || green > 255 || blue > 255)
+           currentColour = Color.white;
+         else
+           currentColour = new Color(red, green, blue);
        }
-       else
-       {
-           green = 255;
        }
-
-       currentColour = new Color(red, green, blue);
    }
 
 
-- 
1.7.10.2