JAL-1620 version bump and release notes

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

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 12f252d..442b90b 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,68 +1,132 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-\r
-public class ScoreColourScheme extends ResidueColourScheme {\r
-    public double min;\r
-    public double max;\r
-    public double[] scores;\r
-\r
-    public ScoreColourScheme(double[] scores, double min, double max) {\r
-        super();\r
-\r
-        this.scores = scores;\r
-        this.min = min;\r
-        this.max = max;\r
-    }\r
-\r
-    public Color findColour(String s, int j) {\r
-        if (threshold > 0) {\r
-            if (!aboveThreshold(s, j)) {\r
-                return Color.white;\r
-            }\r
-        }\r
-\r
-        float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -\r
-            (float) min) / (float) (max - min);\r
-\r
-        if (red > 1.0f) {\r
-            red = 1.0f;\r
-        }\r
-\r
-        if (red < 0.0f) {\r
-            red = 0.0f;\r
-        }\r
-\r
-        char c = s.charAt(0);\r
-\r
-        if (jalview.util.Comparison.isGap((c))) {\r
-            return Color.white;\r
-        }\r
-\r
-        // This isn';t great - pool of colours in here?\r
-        return makeColour(red);\r
-    }\r
-\r
-    public Color makeColour(float c) {\r
-        return new Color(c, (float) 0.0, (float) 1.0 - c);\r
-    }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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);
+  }
+}