X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=b0a5caa81f8f172cb75d9d326521c5cd65fb63a0;hb=09b64bea954c283bde1d21c0a230f51f1ae89373;hp=48f7c38ddf548767396174229857af10b5128cdb;hpb=744374dec356da1937728980b81dc60656366276;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 48f7c38..b0a5caa 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -6,7 +6,7 @@ import java.awt.*;
 
 public class ResidueColourScheme implements ColourSchemeI{
     Color    [] colors;
-    int         threshold = 90;
+    int       threshold = 0;
 
     public ResidueColourScheme(Color[] colors, int threshold) {
 	this.colors    = colors;
@@ -21,31 +21,15 @@ public class ResidueColourScheme implements ColourSchemeI{
       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;
-	}
-    }
-
-    // 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);
-
-	if (threshold > 0 && aa != null)
-        {
-	    if (aboveThreshold(aa,seq,j,threshold))
-		c = findColour(seq,s,j,aa);
-	}
-        else
-	    c = findColour(seq,s,j,aa);
+    public Color findColour(String s, int j, Vector aa) {
 
+       if( threshold==0 || aboveThreshold(aa,s,j))
+          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
+       else
+          return Color.white;
 
-      return c;
     }
+
     public int getThreshold() {
 	return threshold;
     }
@@ -54,51 +38,21 @@ public class ResidueColourScheme implements ColourSchemeI{
 	threshold = ct;
     }
 
-    public Vector  getColours(SequenceI s, Vector aa) {
-	Vector colours = new Vector();
-
-	for (int j = 0; j < s.getLength(); j++)
-	    colours.addElement(getColour(s,j,aa));
-
-	return colours;
-    }
-
-    public Vector getColours(SequenceGroup sg, Vector aa) {
-	Vector colours = new Vector();
-
-	for (int j = 0; j < sg.getSize(); j++) {
-	    SequenceI s = sg.getSequenceAt(j);
-
-	    for (int i = 0; i < s.getLength();i++) {
-		colours.addElement(getColour(s,i,aa));
-	    }
-	}
-	return colours;
-    }
+    public boolean aboveThreshold(Vector aa,String s, int j)
+    {
 
-    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;
+        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();
 
-	    if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-		int maxCount = ((Integer)hash.get("maxCount")).intValue();
-		int resCount = ((Integer)hash.get(s)).intValue();
+          if (sc >= threshold)
+            return true;
 
-		sc = resCount * 100.0 / resCount;
+        }
 
-		// This should be isGap somewhere
-		if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-		    if (sc >= (double)threshold) {
-			return true;
-		    }
-		}
-	    }
-	}
 	return false;
     }