isGap method implemented in utils

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d91d49f..d0546dc 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -36,9 +36,10 @@ public class Blosum62ColourScheme extends ResidueColourScheme
     this.av = av;\r
   }\r
 \r
-  public Color findColour(SequenceI seq, String s, int j, Vector aa)\r
+  public Color findColour(String s, int j, Vector aa)\r
   {\r
-      if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
+\r
+      if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
       {\r
         String max = av.getVisibleConsensus().charAt(j) + "";\r
 \r

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