X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=9c10e7d8e1101c95b193233ff6c60c781de3b020;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=f16bccac39f58c3c8f22b7afa8594fd29f10c03c;hpb=341565559999a3c6a88f263e4ff0a6e8eacf09bd;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f16bcca..9c10e7d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,90 +1,148 @@
+/*
+* 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 java.util.*;
 import java.awt.*;
 
-public class ResidueColourScheme implements ColourSchemeI{
-    Color    [] colors;
-    int         threshold = 90;
+import java.util.*;
 
-    public ResidueColourScheme(Color[] colors, int threshold) {
-	this.colors    = colors;
-	this.threshold = threshold;
-    }
 
-    public ResidueColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+    Color[] colors;
+    int threshold = 0;
+
+    /** DOCUMENT ME!! */
+    public Vector consensus;
+
+    /**
+     * Creates a new ResidueColourScheme object.
+     *
+     * @param colors DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public ResidueColourScheme(Color[] colors, int threshold)
+    {
+        this.colors = colors;
+        this.threshold = threshold;
     }
 
-    public Color findColour(String aa)
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
+    public ResidueColourScheme()
     {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
     }
 
-    public Color findColour(SequenceI seq,String s, int j, Vector aa) {
-  try {
-	    return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
-	} catch (Exception e) {
-	    return Color.white;
-	}
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector consensus)
+    {
+        this.consensus = consensus;
     }
 
-    // aa should maybe be a class
-  /*  public Color getColour(SequenceI seq, int j,Vector aa) {
-
-	Color  c       = Color.white;
-	String s       = seq.getSequence(j,j+1);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String aa)
+    {
+        return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+    }
 
-	if (threshold > 0 && aa != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int j)
+    {
+        if ((threshold == 0) || aboveThreshold(s, j))
         {
-	    if (aboveThreshold(aa,seq,j,threshold))
-		c = findColour(seq,s,j,aa);
-	}
+            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
+        }
         else
-	    c = findColour(seq,s,j,aa);
-
-
-      return c;
-    }*/
-
-    public int getThreshold() {
-	return threshold;
+        {
+            return Color.white;
+        }
     }
 
-    public void setThreshold(int ct) {
-	threshold = ct;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getThreshold()
+    {
+        return threshold;
     }
 
-    public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {
-	String    s    = seq.getSequence(j,j+1);
-	Hashtable hash = (Hashtable)aa.elementAt(j);
-
-	if (j < aa.size()) {
-	    String maxRes = (String)hash.get("maxResidue");
-
-	    double sc = 0;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct)
+    {
+        threshold = ct;
+    }
 
-	    if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-		int maxCount = ((Integer)hash.get("maxCount")).intValue();
-		int resCount = ((Integer)hash.get(s)).intValue();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean aboveThreshold(String s, int j)
+    {
+        Hashtable hash = (Hashtable) consensus.elementAt(j);
 
-		sc = resCount * 100.0 / resCount;
+        if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
+                hash.contains(s))
+        {
+            ////  resCount////////////////////                  ///////////////seq count////////////
+            double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
+                    "size")).intValue();
 
-		// This should be isGap somewhere
-		if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-		    if (sc >= (double)threshold) {
-			return true;
-		    }
-		}
-	    }
-	}
-	return false;
-    }
+            if (sc >= threshold)
+            {
+                return true;
+            }
+        }
 
-    public boolean canThreshold() {
-	return true;
-    }
-    public boolean isUserDefinable() {
-	return false;
+        return false;
     }
 }