X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=e1dbf4696706b9cd4b8c96bb4a6cf7f76d8a04cf;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=34c47ed82707f796192366a7accbe291c5beab78;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 34c47ed..e1dbf46 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,94 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.schemes;
 
-import jalview.datamodel.*;
-import java.util.*;
 import java.awt.*;
 
-public class PIDColourScheme extends ResidueColourScheme {
-    public Color[] pidColours;
-    public float[] thresholds;
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-    SequenceGroup group;
+public class PIDColourScheme
+    extends ResidueColourScheme
+{
+  public Color[] pidColours;
+  public float[] thresholds;
+  SequenceGroup group;
+
+  public PIDColourScheme()
+  {
+    this.pidColours = ResidueProperties.pidColours;
+    this.thresholds = ResidueProperties.pidThresholds;
+  }
 
-    public PIDColourScheme() {
-	this.pidColours = ResidueProperties.pidColours;
-	this.thresholds = ResidueProperties.pidThresholds;
+  public Color findColour(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      c -= ('a' - 'A');
     }
 
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j] == null)
+    {
+      return Color.white;
+    }
 
+    if ( (threshold != 0) && !aboveThreshold(c, j))
+    {
+      return Color.white;
+    }
 
-  public Color findColour(String s, int j) {
+    Color currentColour = Color.white;
 
-    if( threshold!=0 && !aboveThreshold(s,j))
+    double sc = 0;
+
+    if (consensus.length <= j)
+    {
       return Color.white;
+    }
 
-    Color     c    = Color.white;
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);
+    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=
+          -1) &&
+        consensus[j].contains(String.valueOf(c)))
+    {
+      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
 
-      double sc = 0;
-      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
+      if (!jalview.util.Comparison.isGap(c))
       {
-        sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
-        // MC Should be isGap
-        if (!jalview.util.Comparison.isGap((s.charAt(0))))
+        for (int i = 0; i < thresholds.length; i++)
         {
-          for (int i = 0; i < thresholds.length; i++)
+          if (sc > thresholds[i])
           {
-            if (sc > thresholds[i])
-            {
-              c = pidColours[i];
-              break;
-            }
+            currentColour = pidColours[i];
+
+            break;
           }
         }
-
       }
-      return c;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
   }
 }