X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=134ed4cb64cc2695c54647b6346832f48562eb1c;hb=712d1fca4bfa7e91d667e9931fb67fbc99a5f369;hp=89e94fde391669525c0cbfc00a5c471ec34b3476;hpb=341565559999a3c6a88f263e4ff0a6e8eacf09bd;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 89e94fd..134ed4c 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,63 +1,121 @@
+/*
+ * 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 jalview.datamodel.*;
-import jalview.jbgui.*;
-
-import java.util.*;
 import java.awt.*;
 
-public class ScoreColourScheme extends ResidueColourScheme {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme
+    extends ResidueColourScheme
+{
+  /** DOCUMENT ME!! */
   public double min;
+
+  /** DOCUMENT ME!! */
   public double max;
-  public double[] scores;
 
-  public ScoreColourScheme( double[] scores,
-			   double min,
-			   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;
-  }
 
- /* public Color getColour(SequenceI seq, int j, Vector aa) {
-      Color c = Color.white;
-      String s = seq.getSequence(j,j+1);
+    // 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 (threshold > 0)
+      if (red > 1.0f)
       {
-	  if (aboveThreshold(aa,seq,j,threshold))
-	      c = findColour(seq,s,j,aa);
+        red = 1.0f;
       }
-      else if ( !s.equals("-")  && !s.equals(".") && !s.equals(" ") )
-	  c = findColour(seq,s,j,aa);
-     //  else
-	//  c = Color.white;
 
-      return c;
-  }*/
+      if (red < 0.0f)
+      {
+        red = 0.0f;
+      }
+      colors[i] = makeColour(red);
+    }
+  }
 
-    public Color findColour(SequenceI seq,String s,int j,Vector aa)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    if (threshold > 0)
     {
-
-	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("-"))
+      if (!aboveThreshold(c, j))
+      {
         return Color.white;
+      }
+    }
 
-	// This isn';t great - pool of colours in here?
-	return makeColour(red);
+    if (jalview.util.Comparison.isGap(c))
+    {
+      return Color.white;
     }
-    public Color makeColour(float c) {
-	return new Color(c,(float)0.0,(float)1.0-c);
+
+    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);
+  }
+}