X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=eae76e16821a3d75e273da6f69900f8152711283;hb=4d959452a9c486b6d94291d8e819036ec19b09ef;hp=e8d71568bdbb0129f0ea6c174fc9d8ad4112f47f;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index e8d7156..eae76e1 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,63 +1,126 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-
-import java.util.*;
-import java.awt.*;
-
-public class ScoreColourScheme extends ResidueColourScheme {
-  public double min;
-  public double max;
-  public double[] scores;
-
-  public ScoreColourScheme( double[] scores,
-			   double min,
-			   double max) {
-
-    super();
-
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-  }
-
-  public Color getColour(SequenceI seq, int j, Vector aa) {
-      Color c = Color.white;
-      String s = seq.getSequence(j,j+1);
-
-      if (threshold > 0)
-      {
-	  if (aboveThreshold(aa,seq,j,threshold))
-	      c = findColour(seq,s,j,aa);
-      }
-      else if ( !s.equals("-")  && !s.equals(".") && !s.equals(" ") )
-	  c = findColour(seq,s,j,aa);
-     //  else
-	//  c = Color.white;
-
-      return c;
-  }
-
-    public Color findColour(SequenceI seq,String s,int j,Vector aa)
-    {
-
-	float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
-			    - (float)min)/(float)(max - min);
-	if (red > (float)1.0)
-	    red = (float)1.0;
-
-	if (red < (float)0.0)
-	    red = (float)0.0;
-
-    if(s.equals(" ")|| s.equals(".")  || s.equals("-"))
-        return Color.white;
-
-	// This isn';t great - pool of colours in here?
-	return makeColour(red);
-    }
-    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);
+  }
+}