Formatting

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index eadf09b..e1dbf46 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,48 +1,94 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
 package jalview.schemes;\r
 \r
-import jalview.datamodel.*;\r
-import java.util.*;\r
 import java.awt.*;\r
 \r
-public class PIDColourScheme extends ResidueColourScheme {\r
-    public Color[] pidColours;\r
-    public float[] thresholds;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+\r
+public class PIDColourScheme\r
+    extends ResidueColourScheme\r
+{\r
+  public Color[] pidColours;\r
+  public float[] thresholds;\r
+  SequenceGroup group;\r
+\r
+  public PIDColourScheme()\r
+  {\r
+    this.pidColours = ResidueProperties.pidColours;\r
+    this.thresholds = ResidueProperties.pidThresholds;\r
+  }\r
 \r
-    SequenceGroup group;\r
+  public Color findColour(char c, int j)\r
+  {\r
+    if ('a' <= c && c <= 'z')\r
+    {\r
+      c -= ('a' - 'A');\r
+    }\r
 \r
-    public PIDColourScheme() {\r
-       this.pidColours = ResidueProperties.pidColours;\r
-       this.thresholds = ResidueProperties.pidThresholds;\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 currentColour = Color.white;\r
 \r
-  public Color findColour(String s, int j) {\r
+    double sc = 0;\r
 \r
-    if( threshold!=0 && !aboveThreshold(s,j))\r
+    if (consensus.length <= j)\r
+    {\r
       return Color.white;\r
+    }\r
 \r
-    Color     c    = Color.white;\r
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
+    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=\r
+          -1) &&\r
+        consensus[j].contains(String.valueOf(c)))\r
+    {\r
+      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
 \r
-      double sc = 0;\r
-      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
+      if (!jalview.util.Comparison.isGap(c))\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
+        for (int i = 0; i < thresholds.length; i++)\r
         {\r
-          for (int i = 0; i < thresholds.length; i++)\r
+          if (sc > thresholds[i])\r
           {\r
-            if (sc > thresholds[i])\r
-            {\r
-              c = pidColours[i];\r
-              break;\r
-            }\r
+            currentColour = pidColours[i];\r
+\r
+            break;\r
           }\r
         }\r
-\r
       }\r
-      return c;\r
+    }\r
+\r
+    if (conservationColouring)\r
+    {\r
+      currentColour = applyConservation(currentColour, j);\r
+    }\r
+\r
+    return currentColour;\r
   }\r
 }\r