X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=b905c452ba87dcce2683ded2f74c2ec0fdc5cd36;hb=d640a8ce605b836b2e6eb1771994d3baef5c31a0;hp=c435f7dc264687811c7001b68c8d62b6800d1c23;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index c435f7d..b905c45 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -41,7 +41,7 @@ public class ResidueColourScheme implements ColourSchemeI
     int threshold = 0;
 
     /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
-    protected String ignoreGaps = "pid_gaps";
+    protected String ignoreGaps = AAFrequency.PID_GAPS;
 
     /** Consenus as a hashtable array */
     Hashtable [] consensus;
@@ -52,12 +52,6 @@ public class ResidueColourScheme implements ColourSchemeI
    /** DOCUMENT ME!! */
    int inc = 30;
 
-   /**
-    * The colour to be calculated, manipulated and returned
-    */
-   Color currentColour = null;
-
-
 
     /**
      * Creates a new ResidueColourScheme object.
@@ -83,15 +77,15 @@ public class ResidueColourScheme implements ColourSchemeI
     */
    public Color findColour(String aa)
    {
-       return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+       return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
    }
 
 
 
    public Color findColour(String s, int j)
    {
-
-       int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+       Color currentColour;
+       int index = ResidueProperties.aaIndex[s.charAt(0)];
 
        if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
        {
@@ -103,7 +97,7 @@ public class ResidueColourScheme implements ColourSchemeI
        }
 
        if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
 
        return currentColour;
@@ -129,9 +123,9 @@ public class ResidueColourScheme implements ColourSchemeI
     {
         threshold = ct;
         if(ignoreGaps)
-          this.ignoreGaps = "pid_nogaps";
+          this.ignoreGaps = AAFrequency.PID_NOGAPS;
         else
-          this.ignoreGaps = "pid_gaps";
+          this.ignoreGaps = AAFrequency.PID_GAPS;
     }
 
     /**
@@ -144,13 +138,25 @@ public class ResidueColourScheme implements ColourSchemeI
      */
     public boolean aboveThreshold(String s, int j)
     {
-        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
-                consensus[j].contains(s))
+      char c = s.charAt(0);
+      if ('a' <= c && c <= 'z')
         {
-            if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
-            {
-                return true;
-            }
+          // TO UPPERCASE !!!
+          //Faster than toUpperCase
+          c -= ('a' - 'A');
+          s = String.valueOf(c);
+        }
+
+        if (consensus == null || consensus[j] == null)
+          return false;
+
+        if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+            consensus[j].contains(s))
+        {
+          if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+          {
+            return true;
+          }
         }
 
         return false;
@@ -177,15 +183,16 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @param consensus DOCUMENT ME!
      */
-    public void setConsensus(Vector vconsensus)
+    public void setConsensus(Hashtable [] consensus)
     {
-       int i, iSize=vconsensus.size();
-       consensus = new Hashtable[iSize];
-       for(i=0; i<iSize; i++)
-        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+      if(consensus==null)
+        return;
+
+      this.consensus = consensus;
     }
 
 
+
     public void setConservation(Conservation cons)
     {
       if(cons==null)
@@ -213,69 +220,47 @@ 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)
+   Color applyConservation(Color currentColour, 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)
+         {
+           return Color.white;
+         }
 
-       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);
+       return currentColour;
    }