GPL license added

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 0a28c33..34c47ed 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,3 +1,22 @@
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
+\r
 package jalview.schemes;\r
 \r
 import jalview.datamodel.*;\r
@@ -14,45 +33,34 @@ public class PIDColourScheme extends ResidueColourScheme {
        this.pidColours = ResidueProperties.pidColours;\r
        this.thresholds = ResidueProperties.pidThresholds;\r
     }\r
- /* public Color getColour(SequenceI seq, int j,Vector aa) {\r
-    Color c = Color.white;\r
 \r
-    String       s = seq.getSequence(j,j+1);\r
 \r
-    if (aa != null && j < aa.size()) {\r
-       c = findColour(seq,s,j,aa);\r
-    }\r
 \r
-    return c;\r
-  }\r
-*/\r
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
-      Color     c    = Color.white;\r
-      Hashtable hash = null;\r
+  public Color findColour(String s, int j) {\r
 \r
-      if (aa != null) {\r
-         hash = (Hashtable)aa.elementAt(j);\r
-      }\r
-      else\r
-        return c;\r
+    if( threshold!=0 && !aboveThreshold(s,j))\r
+      return Color.white;\r
 \r
-      String    max  = (String)hash.get("maxResidue");\r
+    Color     c    = Color.white;\r
+      Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
 \r
       double sc = 0;\r
-      if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {\r
-         sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));\r
-\r
-         // MC Should be isGap\r
-         if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {\r
-             for (int i=0; i < thresholds.length; i++) {\r
-                 if (sc > thresholds[i]) {\r
-                     c = pidColours[i];\r
-                     break;\r
-                 }\r
-             }\r
-         } else {\r
-             c = Color.white;\r
-         }\r
+      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
+      {\r
+        sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
+        // MC Should be isGap\r
+        if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
+        {\r
+          for (int i = 0; i < thresholds.length; i++)\r
+          {\r
+            if (sc > thresholds[i])\r
+            {\r
+              c = pidColours[i];\r
+              break;\r
+            }\r
+          }\r
+        }\r
+\r
       }\r
       return c;\r
   }\r