X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=66f180be4c72186c75934d0e2cb817a4dd865b8f;hb=133e5d7be0ca295fd4ac4ccfa6c82165c795ea80;hp=e587feec2a55f9cb876a94a0d95426b458dd4e7a;hpb=1032f8a608bb97dd7817390aa56293dba3fe3806;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e587fee..66f180b 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,53 +1,80 @@
+/*
+ * 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
+ */
 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.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(String s, int j)
+  {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z')
+    {
+      s = String.valueOf(res -= ('a' - 'A'));
     }
 
 
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {
-      Color     c    = Color.white;
-      Hashtable hash = null;
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
+      return Color.white;
+    }
 
+    currentColour = Color.white;
 
-      if (aa != null)
-	  hash = (Hashtable)aa.elementAt(j);
-      else
-        return c;
+    double sc = 0;
 
-      String    max  = (String)hash.get("maxResidue");
+    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+        consensus[j].contains(s))
+    {
+      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( res ))
       {
-
-        sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
-        // MC Should be isGap
-        if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
+        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;
           }
         }
-        else
-          c = Color.white;
       }
-      return c;
+    }
+
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
   }
 }