X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=b83244d61ea9d2a8857ff451c5e46076a4db6e81;hb=e25f63a72efddff9e071abdeff0ae5599431e4f8;hp=c435f7dc264687811c7001b68c8d62b6800d1c23;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index c435f7d..b83244d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -179,6 +179,9 @@ public class ResidueColourScheme implements ColourSchemeI
      */
     public void setConsensus(Vector vconsensus)
     {
+      if(vconsensus==null)
+        return;
+
        int i, iSize=vconsensus.size();
        consensus = new Hashtable[iSize];
        for(i=0; i<iSize; i++)
@@ -213,69 +216,47 @@ 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(t==0)
+         {
+           currentColour = Color.white;
+           return;
+         }
 
-       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);
    }