X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=4e696cf54c9551bc0566766278d80eb4b02446c9;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=b62ca18c2ae3de626ff321620608ede68fe8134d;hpb=ac4bbf6dd2bfccdaae9067fb4765c73600dea729;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b62ca18..4e696cf 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,55 +1,129 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-
-import java.util.*;
-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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+/**
+ * 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(int symbolIndex[], double[] scores, double min,
+          double max)
+  {
+    super(symbolIndex);
+
+    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!
+   */
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    if (threshold > 0)
+    {
+      if (!aboveThreshold(c, j))
+      {
+        return Color.white;
+      }
+    }
+
+    if (jalview.util.Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+
+    Color currentColour = colors[ResidueProperties.aaIndex[c]];
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, 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);
+  }
+}