X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=8d7a45ace544bcee33d23bf5240dc2a6160f89cc;hb=c3c305755d392741176209a0274a47897ac4d8a8;hp=b6dc45b18a0fbe02cd72ceda70d01a8034bc2756;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b6dc45b..8d7a45a 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.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
@@ -16,55 +16,106 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.schemes;
 
 import java.awt.*;
 
-public class ScoreColourScheme extends ResidueColourScheme {
-  public double min;
-  public double max;
-  public double[] scores;
-
-  public ScoreColourScheme( double[] scores,
-			   double min,
-			   double max) {
 
-    super();
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
+    public double min;
 
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-  }
+    /** DOCUMENT ME!! */
+    public double max;
 
+    /** DOCUMENT ME!! */
+    public double[] scores;
 
-    public Color findColour(String s,int j)
+    /**
+     * Creates a new ScoreColourScheme object.
+     *
+     * @param scores DOCUMENT ME!
+     * @param min DOCUMENT ME!
+     * @param max DOCUMENT ME!
+     */
+    public ScoreColourScheme(double[] scores, double min, double max)
     {
+        super();
+
+        this.scores = scores;
+        this.min = min;
+        this.max = max;
 
-      if (threshold > 0)
-      {
-         if (!aboveThreshold(s,j))
-             return Color.white;
-      }
+        // Make colours in constructor
+        // Why wasn't this done earlier?
+        int i, iSize=scores.length;
+        colors = new Color[scores.length];
+        for (i = 0; i < iSize; i++)
+        {
+          float red = (float) (scores[i] - (float) min) / (float) (max - min);
 
-	float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
-			    - (float)min)/(float)(max - min);
-	if (red > 1.0f)
-	    red = 1.0f;
+          if (red > 1.0f)
+          {
+            red = 1.0f;
+          }
 
-	if (red < 0.0f)
-	    red = 0.0f;
+          if (red < 0.0f)
+          {
+            red = 0.0f;
+          }
+          colors[i] = makeColour(red);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int j)
+    {
+        if (threshold > 0)
+        {
+            if (!aboveThreshold(s, j))
+            {
+                return Color.white;
+            }
+        }
 
-    char c = s.charAt(0);
+        char c = s.charAt(0);
 
-    if(jalview.util.Comparison.isGap((c)))
-        return Color.white;
+        if (jalview.util.Comparison.isGap((c)))
+        {
+            return Color.white;
+        }
 
-	// This isn';t great - pool of colours in here?
-	return makeColour(red);
+        currentColour = colors[ ResidueProperties.aaIndex[s.charAt(0)] ];
+
+        if(conservationColouring)
+         applyConservation(j);
+
+        return currentColour;
     }
-    public Color makeColour(float c) {
-	return new Color(c,(float)0.0,(float)1.0-c);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
+        return new Color(c, (float) 0.0, (float) 1.0 - c);
     }
 }
-