X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=134ed4cb64cc2695c54647b6346832f48562eb1c;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=e238d797d83860d17a6cd62b2317c885e426a601;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e238d79..134ed4c 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,121 +1,121 @@
 /*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+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)
+  /** 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++)
     {
-        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);
-        }
+      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)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    if (threshold > 0)
     {
-        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);
+      if (!aboveThreshold(c, j))
+      {
+        return Color.white;
+      }
+    }
 
-        return currentColour;
+    if (jalview.util.Comparison.isGap(c))
+    {
+      return Color.white;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color makeColour(float c)
+    Color currentColour = colors[ResidueProperties.aaIndex[c]];
+
+    if (conservationColouring)
     {
-        return new Color(c, (float) 0.0, (float) 1.0 - c);
+      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);
+  }
 }