From c9f0ef34e578218c8ffabaac9c405fd86d1196e2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:21:35 +0000
Subject: [PATCH] ColourScheme no longer requires sequence

---
 src/jalview/gui/SequenceRenderer.java   |   35 +++----------------------------
 src/jalview/gui/UserDefinedColours.java |    2 +-
 2 files changed, 4 insertions(+), 33 deletions(-)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e8cf340..82124ce 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -27,9 +27,10 @@ public class SequenceRenderer implements RendererI
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
    Color c = Color.white;
-
+try{
      if (cs != null)
-       c = cs.findColour(seq, seq.getSequence(i, i + 1), i, av.getConsensus(false));
+       c = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
+   }catch(Exception ex){}
 
     return c;
   }
@@ -54,8 +55,6 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;
     int curWidth = width;
 
-  //  int threshold = 80;
-
     while (i <= end && i < length)
     {
       color = color.white;
@@ -69,34 +68,6 @@ public class SequenceRenderer implements RendererI
            color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
 
 
-    //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);
-    //  String    s     = (String)hash.get("maxResidue");
-    //  int       count = ((Integer)hash.get("maxCount")).intValue();
-  //    int       max   = ((Integer)hash.get("size")).intValue();
-   //   int       nongap = ((Integer)hash.get("nongap")).intValue();
-   //   float     frac  = (float)(count*1.0/(1.0*nongap));
-
-      //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);
-    /*  if (!seq.getSequence().substring(i,i+1).equals(s) ||
-	  s.equals("-") ||
-	  s.equals(".") ||
-	  s.equals(" "))
-      {
-	c = Color.white;
-      } else {
-	if (frac > 0.9) {
-	  c = Color.red;
-	} else if (frac > 0.8) {
-	  c = Color.orange;
-	} else if (frac > 0.7) {
-	  c = Color.pink;
-	} else if (frac > 0.5) {
-	  c = Color.yellow;
-	} else if (frac> 0.3) {
-	    c = Color.lightGray;
-	}
-      }*/
-
       if (color != currentColor || color != null)
       {
         g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 1fcc923..28f0474 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -61,7 +61,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
       cs = ap.av.getGlobalColourScheme();
 
     if(cs!=null)
-      col = cs.findColour(null, aa, -1, null);
+      col = cs.findColour( aa, -1, null);
 
     button.setBackground(  col );
     oldColours.addElement( col );
-- 
1.7.10.2