Any character non aa or nucleotide is a space

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8cea507..8686894 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -21,6 +21,7 @@ package jalview.schemes;
 import java.awt.*;\r
 \r
 import jalview.datamodel.*;\r
+import jalview.analysis.AAFrequency;\r
 \r
 public class PIDColourScheme\r
     extends ResidueColourScheme\r
@@ -35,36 +36,54 @@ 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
-    if ( (threshold != 0) && !aboveThreshold(s, j))\r
+    if ('a' <= c && c <= 'z')\r
+    {\r
+      c -= ('a' - 'A');\r
+    }\r
+\r
+    if (consensus == null\r
+        || j >= consensus.length\r
+        || consensus[j]==null)\r
+    {\r
+      return Color.white;\r
+    }\r
+\r
+    if ( (threshold != 0) && !aboveThreshold(c, j))\r
     {\r
       return Color.white;\r
     }\r
 \r
-    Color c = Color.white;\r
+    Color currentColour = Color.white;\r
 \r
     double sc = 0;\r
 \r
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
-        consensus[j].contains(s))\r
-    {\r
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
+    if(consensus.length<=j)\r
+      return Color.white;\r
 \r
-      if (!jalview.util.Comparison.isGap( (s.charAt(0))))\r
+      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&\r
+          consensus[j].contains(String.valueOf(c)))\r
       {\r
-        for (int i = 0; i < thresholds.length; i++)\r
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
+\r
+        if (!jalview.util.Comparison.isGap(c))\r
         {\r
-          if (sc > thresholds[i])\r
+          for (int i = 0; i < thresholds.length; i++)\r
           {\r
-            c = pidColours[i];\r
+            if (sc > thresholds[i])\r
+            {\r
+              currentColour = pidColours[i];\r
 \r
-            break;\r
+              break;\r
+            }\r
           }\r
         }\r
       }\r
-    }\r
 \r
-    return c;\r
+    if(conservationColouring)\r
+      currentColour = applyConservation(currentColour, j);\r
+\r
+    return currentColour;\r
   }\r
 }\r