From b78278b3ee2cb653c439fa207b78a469d53ce697 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:25:25 +0000
Subject: [PATCH] isGap method implemented in utils

---
 src/jalview/schemes/Blosum62ColourScheme.java |    5 ++--
 src/jalview/schemes/ScoreColourScheme.java    |   32 ++++++++++---------------
 2 files changed, 15 insertions(+), 22 deletions(-)

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d91d49f..d0546dc 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -36,9 +36,10 @@ public class Blosum62ColourScheme extends ResidueColourScheme
     this.av = av;
   }
 
-  public Color findColour(SequenceI seq, String s, int j, Vector aa)
+  public Color findColour(String s, int j, Vector aa)
   {
-      if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
+
+      if (!jalview.util.Comparison.isGap((s.charAt(0))))
       {
         String max = av.getVisibleConsensus().charAt(j) + "";
 
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 89e94fd..225f8dd 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -22,35 +22,27 @@ public class ScoreColourScheme extends ResidueColourScheme {
     this.max = max;
   }
 
- /* public Color getColour(SequenceI seq, int j, Vector aa) {
-      Color c = Color.white;
-      String s = seq.getSequence(j,j+1);
+
+    public Color findColour(String s,int j,Vector aa)
+    {
 
       if (threshold > 0)
       {
-	  if (aboveThreshold(aa,seq,j,threshold))
-	      c = findColour(seq,s,j,aa);
+         if (!aboveThreshold(aa,s,j))
+             return Color.white;
       }
-      else if ( !s.equals("-")  && !s.equals(".") && !s.equals(" ") )
-	  c = findColour(seq,s,j,aa);
-     //  else
-	//  c = Color.white;
-
-      return c;
-  }*/
-
-    public Color findColour(SequenceI seq,String s,int j,Vector aa)
-    {
 
 	float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
 			    - (float)min)/(float)(max - min);
-	if (red > (float)1.0)
-	    red = (float)1.0;
+	if (red > 1.0f)
+	    red = 1.0f;
+
+	if (red < 0.0f)
+	    red = 0.0f;
 
-	if (red < (float)0.0)
-	    red = (float)0.0;
+    char c = s.charAt(0);
 
-    if(s.equals(" ")|| s.equals(".")  || s.equals("-"))
+    if(jalview.util.Comparison.isGap((c)))
         return Color.white;
 
 	// This isn';t great - pool of colours in here?
-- 
1.7.10.2