X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=fba1188907a1aff1907043ce0f7c5866fe45ef19;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=e238d797d83860d17a6cd62b2317c885e426a601;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e238d79..fba1188 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,121 +1,132 @@
-/*
-* 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);
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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);
+  }
+}