X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=7f4bebeae89016568d89bbe635c565f09fc6a1fe;hb=0bdaa0deb6ee514912d2ed730e19f618bc44cb69;hp=312ae7d534ce8a8ce8bcc38419e4063788c9f262;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 312ae7d..7f4bebe 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,61 +1,89 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 jalview.jbgui.*;
-
-import java.util.*;
 import java.awt.*;
 
-public class PIDColourScheme extends ResidueColourScheme {
-    public Color[] pidColours;
-    public float[] thresholds;
+import jalview.datamodel.*;
+import jalview.analysis.AAFrequency;
 
-    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 getColour(SequenceI seq, int j,Vector aa) {
-    Color c = Color.white;
 
-    String       s = seq.getSequence(j,j+1);
+    if (consensus == null ||
+        j >= consensus.length)
+    {
+      return Color.white;
+    }
 
-    if (aa != null && j < aa.size()) {
-	c = findColour(seq,s,j,aa);
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
+      return Color.white;
     }
 
-    return c;
-  }
+    currentColour = Color.white;
 
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {
-      Color     c    = Color.white;
-      Hashtable hash = null;
+    double sc = 0;
 
-      if (aa != null) {
-	  hash = (Hashtable)aa.elementAt(j);
-      }
-      else
-        return c;
-
-      String    max  = (String)hash.get("maxResidue");
-
-      double sc = 0;
-      if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-	  sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));
-
-	  // MC Should be isGap
-	  if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-	      for (int i=0; i < thresholds.length; i++) {
-		  if (sc > thresholds[i]) {
-		      c = pidColours[i];
-		      break;
-		  }
-	      }
-	  } else {
-	      c = Color.white;
-	  }
+    if(consensus.length<=j)
+      return Color.white;
+
+      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
+          consensus[j].contains(s))
+      {
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+        if (!jalview.util.Comparison.isGap(res))
+        {
+          for (int i = 0; i < thresholds.length; i++)
+          {
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
+
+              break;
+            }
+          }
+        }
       }
-      return c;
+
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
   }
 }