Sequence is char []

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 9bd092e..8686894 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -36,12 +36,11 @@ public class PIDColourScheme
     this.thresholds = ResidueProperties.pidThresholds;\r
   }\r
 \r
-  public Color findColour(String s, int j)\r
+  public Color findColour(char c, int j)\r
   {\r
-    char res = s.charAt(0);\r
-    if ('a' <= res && res <= 'z')\r
+    if ('a' <= c && c <= 'z')\r
     {\r
-      s = String.valueOf(res -= ('a' - 'A'));\r
+      c -= ('a' - 'A');\r
     }\r
 \r
     if (consensus == null\r
@@ -51,7 +50,7 @@ public class PIDColourScheme
       return Color.white;\r
     }\r
 \r
-    if ( (threshold != 0) && !aboveThreshold(s, j))\r
+    if ( (threshold != 0) && !aboveThreshold(c, j))\r
     {\r
       return Color.white;\r
     }\r
@@ -64,11 +63,11 @@ public class PIDColourScheme
       return Color.white;\r
 \r
       if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&\r
-          consensus[j].contains(s))\r
+          consensus[j].contains(String.valueOf(c)))\r
       {\r
         sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
 \r
-        if (!jalview.util.Comparison.isGap(res))\r
+        if (!jalview.util.Comparison.isGap(c))\r
         {\r
           for (int i = 0; i < thresholds.length; i++)\r
           {\r