aaIndex replaces aaHash

[jalview.git] / src / jalview / schemes / ScoreColourScheme.java

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 225f8dd..8d7a45a 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,55 +1,121 @@
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
 package jalview.schemes;\r
 \r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-\r
-import java.util.*;\r
 import java.awt.*;\r
 \r
-public class ScoreColourScheme extends ResidueColourScheme {\r
-  public double min;\r
-  public double max;\r
-  public double[] scores;\r
-\r
-  public ScoreColourScheme( double[] scores,\r
-                          double min,\r
-                          double max) {\r
 \r
-    super();\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ScoreColourScheme extends ResidueColourScheme\r
+{\r
+    /** DOCUMENT ME!! */\r
+    public double min;\r
 \r
-    this.scores = scores;\r
-    this.min = min;\r
-    this.max = max;\r
-  }\r
+    /** DOCUMENT ME!! */\r
+    public double max;\r
 \r
+    /** DOCUMENT ME!! */\r
+    public double[] scores;\r
 \r
-    public Color findColour(String s,int j,Vector aa)\r
+    /**\r
+     * Creates a new ScoreColourScheme object.\r
+     *\r
+     * @param scores DOCUMENT ME!\r
+     * @param min DOCUMENT ME!\r
+     * @param max DOCUMENT ME!\r
+     */\r
+    public ScoreColourScheme(double[] scores, double min, double max)\r
     {\r
+        super();\r
+\r
+        this.scores = scores;\r
+        this.min = min;\r
+        this.max = max;\r
 \r
-      if (threshold > 0)\r
-      {\r
-         if (!aboveThreshold(aa,s,j))\r
-             return Color.white;\r
-      }\r
+        // Make colours in constructor\r
+        // Why wasn't this done earlier?\r
+        int i, iSize=scores.length;\r
+        colors = new Color[scores.length];\r
+        for (i = 0; i < iSize; i++)\r
+        {\r
+          float red = (float) (scores[i] - (float) min) / (float) (max - min);\r
 \r
-       float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]\r
-                           - (float)min)/(float)(max - min);\r
-       if (red > 1.0f)\r
-           red = 1.0f;\r
+          if (red > 1.0f)\r
+          {\r
+            red = 1.0f;\r
+          }\r
 \r
-       if (red < 0.0f)\r
-           red = 0.0f;\r
+          if (red < 0.0f)\r
+          {\r
+            red = 0.0f;\r
+          }\r
+          colors[i] = makeColour(red);\r
+        }\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param s DOCUMENT ME!\r
+     * @param j DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color findColour(String s, int j)\r
+    {\r
+        if (threshold > 0)\r
+        {\r
+            if (!aboveThreshold(s, j))\r
+            {\r
+                return Color.white;\r
+            }\r
+        }\r
 \r
-    char c = s.charAt(0);\r
+        char c = s.charAt(0);\r
 \r
-    if(jalview.util.Comparison.isGap((c)))\r
-        return Color.white;\r
+        if (jalview.util.Comparison.isGap((c)))\r
+        {\r
+            return Color.white;\r
+        }\r
 \r
-       // This isn';t great - pool of colours in here?\r
-       return makeColour(red);\r
+        currentColour = colors[ ResidueProperties.aaIndex[s.charAt(0)] ];\r
+\r
+        if(conservationColouring)\r
+         applyConservation(j);\r
+\r
+        return currentColour;\r
     }\r
-    public Color makeColour(float c) {\r
-       return new Color(c,(float)0.0,(float)1.0-c);\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param c DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color makeColour(float c)\r
+    {\r
+        return new Color(c, (float) 0.0, (float) 1.0 - c);\r
     }\r
 }\r
-\r