From d4ede6b61d4abab78200f334d8df07879dfe6741 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 24 Jan 2005 17:27:00 +0000
Subject: [PATCH] returns color.white if the underlying colourscheme is null

---
 src/jalview/schemes/ConservationColourScheme.java |   14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index ab5a808..f6726bb 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -83,12 +83,9 @@ public class ConservationColourScheme extends ResidueColourScheme {
 
            int tmp = 10;
            int t = 0;
-           try
-             {t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));}
-             catch(NumberFormatException ex){
-               System.out.println("fix this bug, conserveColourScheme");
-               t=0;
-             }
+           if( !jalview.util.Comparison.isGap( conserve.getConsSequence().getSequence().charAt(i) ))
+               t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));
+
            c = findColour(null,s,i);
 
             while (tmp >= t) {
@@ -105,7 +102,10 @@ public class ConservationColourScheme extends ResidueColourScheme {
    }
 
   public Color findColour(DrawableSequence seq, String s, int j) {
-    return cs.findColour( s, -1, null);
+    if(cs!=null)
+      return cs.findColour( s, -1, null);
+    else
+      return Color.white;
   }
   public boolean fullConservation(int j) {
     String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
-- 
1.7.10.2