Formatting

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

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 220aecc..134ed4c 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,51 +1,121 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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 java.awt.*;\r
 \r
-public class ScoreColourScheme extends ResidueColourScheme {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ScoreColourScheme\r
+    extends ResidueColourScheme\r
+{\r
+  /** DOCUMENT ME!! */\r
   public double min;\r
+\r
+  /** DOCUMENT ME!! */\r
   public double max;\r
-  public double[] scores;\r
 \r
-  public ScoreColourScheme( double[] scores,\r
-                          double min,\r
-                          double max) {\r
+  /** DOCUMENT ME!! */\r
+  public double[] scores;\r
 \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
-\r
 \r
-    public Color findColour(String s,int j)\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
-      if (threshold > 0)\r
+      if (red > 1.0f)\r
       {\r
-         if (!aboveThreshold(s,j))\r
-             return Color.white;\r
+        red = 1.0f;\r
       }\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
-\r
-       if (red < 0.0f)\r
-           red = 0.0f;\r
-\r
-    char c = s.charAt(0);\r
+      if (red < 0.0f)\r
+      {\r
+        red = 0.0f;\r
+      }\r
+      colors[i] = makeColour(red);\r
+    }\r
+  }\r
 \r
-    if(jalview.util.Comparison.isGap((c)))\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(char c, int j)\r
+  {\r
+    if (threshold > 0)\r
+    {\r
+      if (!aboveThreshold(c, j))\r
+      {\r
         return Color.white;\r
+      }\r
+    }\r
 \r
-       // This isn';t great - pool of colours in here?\r
-       return makeColour(red);\r
+    if (jalview.util.Comparison.isGap(c))\r
+    {\r
+      return Color.white;\r
     }\r
-    public Color makeColour(float c) {\r
-       return new Color(c,(float)0.0,(float)1.0-c);\r
+\r
+    Color currentColour = colors[ResidueProperties.aaIndex[c]];\r
+\r
+    if (conservationColouring)\r
+    {\r
+      currentColour = applyConservation(currentColour, j);\r
     }\r
-}\r
 \r
+    return currentColour;\r
+  }\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