X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=c11e1ecee6b18adcc25a1f55878a8262f8cde1b6;hb=279f73359584dd952a06668b034d2ed98818e315;hp=89e94fde391669525c0cbfc00a5c471ec34b3476;hpb=341565559999a3c6a88f263e4ff0a6e8eacf09bd;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 89e94fd..c11e1ec 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) 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 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) {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
+    public double min;
+
+    /** DOCUMENT ME!! */
+    public double max;
 
-    super();
+    /** DOCUMENT ME!! */
+    public double[] scores;
 
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-  }
+    /**
+     * 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();
 
- /* public Color getColour(SequenceI seq, int j, Vector aa) {
-      Color c = Color.white;
-      String s = seq.getSequence(j,j+1);
+        this.scores = scores;
+        this.min = min;
+        this.max = max;
 
-      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;
+        // 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);
 
-      return c;
-  }*/
+          if (red > 1.0f)
+          {
+            red = 1.0f;
+          }
+
+          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(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 > (float)1.0)
-	    red = (float)1.0;
+        char c = s.charAt(0);
 
-	if (red < (float)0.0)
-	    red = (float)0.0;
+        if (jalview.util.Comparison.isGap((c)))
+        {
+            return Color.white;
+        }
 
-    if(s.equals(" ")|| s.equals(".")  || s.equals("-"))
-        return Color.white;
+        currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];
 
-	// This isn';t great - pool of colours in here?
-	return makeColour(red);
+        if(conservationColouring)
+         applyConservation(j);
+
+        return currentColour;
     }
-    public Color makeColour(float c) {
-	return new Color(c,(float)0.0,(float)1.0-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);
     }
 }
-