X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=86868948cbaabc6905181855e9ce8f6ac46c030c;hb=ca26cdb914e0a8885bb0a3986750481bde71383a;hp=253515434b247888b857816e7cb27e0f76579065;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 2535154..8686894 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,89 @@
 /*
-* 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) 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 java.awt.*;
+
 import jalview.datamodel.*;
+import jalview.analysis.AAFrequency;
 
-import java.awt.*;
+public class PIDColourScheme
+    extends ResidueColourScheme
+{
+  public Color[] pidColours;
+  public float[] thresholds;
+  SequenceGroup group;
 
-import java.util.*;
+  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');
+    }
 
-public class PIDColourScheme extends ResidueColourScheme {
-    public Color[] pidColours;
-    public float[] thresholds;
-    SequenceGroup group;
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j]==null)
+    {
+      return Color.white;
+    }
 
-    public PIDColourScheme() {
-        this.pidColours = ResidueProperties.pidColours;
-        this.thresholds = ResidueProperties.pidThresholds;
+    if ( (threshold != 0) && !aboveThreshold(c, j))
+    {
+      return Color.white;
     }
 
-    public Color findColour(String s, int j) {
-        if ((threshold != 0) && !aboveThreshold(s, j)) {
-            return Color.white;
-        }
+    Color currentColour = Color.white;
 
-        Color c = Color.white;
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
+    double sc = 0;
 
-        double sc = 0;
+    if(consensus.length<=j)
+      return Color.white;
 
-        if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
-                hash.contains(s)) {
-            sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
-                    "size")).intValue();
+      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
+          consensus[j].contains(String.valueOf(c)))
+      {
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
 
-            // MC Should be isGap
-            if (!jalview.util.Comparison.isGap((s.charAt(0)))) {
-                for (int i = 0; i < thresholds.length; i++) {
-                    if (sc > thresholds[i]) {
-                        c = pidColours[i];
+        if (!jalview.util.Comparison.isGap(c))
+        {
+          for (int i = 0; i < thresholds.length; i++)
+          {
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
 
-                        break;
-                    }
-                }
+              break;
             }
+          }
         }
+      }
 
-        return c;
-    }
+    if(conservationColouring)
+      currentColour = applyConservation(currentColour, j);
+
+    return currentColour;
+  }
 }