X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=eae76e16821a3d75e273da6f69900f8152711283;hb=994a386819147f73fa47f3c29ba6c438f0e4b15a;hp=b69e536cfa30384bf30b07eb992fdea38795d9f0;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b69e536..eae76e1 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,110 +1,126 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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;
-    }
-
-    /**
-     * 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;
-            }
-        }
-
-        float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
-            (float) min) / (float) (max - min);
-
-        if (red > 1.0f)
-        {
-            red = 1.0f;
-        }
-
-        if (red < 0.0f)
-        {
-            red = 0.0f;
-        }
-
-        char c = s.charAt(0);
-
-        if (jalview.util.Comparison.isGap((c)))
-        {
-            return Color.white;
-        }
-
-        // This isn';t great - pool of colours in here?
-        return makeColour(red);
-    }
-
-    /**
-     * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+  public double min;
+
+  public double max;
+
+  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 iSize = scores.length;
+    colors = new Color[scores.length];
+    for (int i = 0; i < iSize; i++)
+    {
+      /*
+       * scale score between min and max to the range 0.0 - 1.0
+       */
+      float score = (float) (scores[i] - (float) min) / (float) (max - min);
+
+      if (score > 1.0f)
+      {
+        score = 1.0f;
+      }
+
+      if (score < 0.0f)
+      {
+        score = 0.0f;
+      }
+      colors[i] = makeColour(score);
+    }
+  }
+
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    if (Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+    return super.findColour(c);
+  }
+
+  /**
+   * 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);
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return "Score";
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
+  {
+    return new ScoreColourScheme(symbolIndex, scores, min, max);
+  }
+}