X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=acf2ae5ec8282b8015cfdaa4a93d7c2b6bfbe24e;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=b6dc45b18a0fbe02cd72ceda70d01a8034bc2756;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b6dc45b..acf2ae5 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,70 +1,121 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* 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();
-
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-  }
-
-
-    public Color findColour(String s,int j)
-    {
-
-      if (threshold > 0)
-      {
-         if (!aboveThreshold(s,j))
-             return Color.white;
-      }
-
-	float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
-			    - (float)min)/(float)(max - min);
-	if (red > 1.0f)
-	    red = 1.0f;
-
-	if (red < 0.0f)
-	    red = 0.0f;
-
-    char c = s.charAt(0);
-
-    if(jalview.util.Comparison.isGap((c)))
-        return Color.white;
-
-	// This isn';t great - pool of colours in here?
-	return makeColour(red);
-    }
-    public Color makeColour(float c) {
-	return new Color(c,(float)0.0,(float)1.0-c);
-    }
-}
-
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* 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
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* 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.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
+    public double min;
+
+    /** DOCUMENT ME!! */
+    public double max;
+
+    /** DOCUMENT ME!! */
+    public double[] scores;
+
+    /**
+     * 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;
+
+        // 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);
+
+          if (red > 1.0f)
+          {
+            red = 1.0f;
+          }
+
+          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);
+
+        if (jalview.util.Comparison.isGap((c)))
+        {
+            return Color.white;
+        }
+
+        currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];
+
+        if(conservationColouring)
+         applyConservation(j);
+
+        return currentColour;
+    }
+
+    /**
+     * 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);
+    }
+}