isGap method implemented in utils, and optimized

[jalview.git] / src / jalview / schemes / PIDColourScheme.java

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e587fee..cc050d5 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,7 +16,7 @@ public class PIDColourScheme extends ResidueColourScheme {
     }\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
       Color     c    = Color.white;\r
       Hashtable hash = null;\r
 \r
@@ -31,10 +31,9 @@ public class PIDColourScheme extends ResidueColourScheme {
       double sc = 0;\r
       if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
       {\r
-\r
         sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
         // MC Should be isGap\r
-        if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
+        if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
         {\r
           for (int i = 0; i < thresholds.length; i++)\r
           {\r
@@ -45,8 +44,7 @@ public class PIDColourScheme extends ResidueColourScheme {
             }\r
           }\r
         }\r
-        else\r
-          c = Color.white;\r
+\r
       }\r
       return c;\r
   }\r