X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=65a23754a8e6c4055f99d8f6c95f2f574f6bc029;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=34c47ed82707f796192366a7accbe291c5beab78;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 34c47ed..65a2375 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,95 @@
-/*
-* 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;
-
-    SequenceGroup group;
-
-    public PIDColourScheme() {
-	this.pidColours = ResidueProperties.pidColours;
-	this.thresholds = ResidueProperties.pidThresholds;
-    }
-
-
-
-  public Color findColour(String s, int j) {
-
-    if( threshold!=0 && !aboveThreshold(s,j))
-      return Color.white;
-
-    Color     c    = Color.white;
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);
-
-      double sc = 0;
-      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
-      {
-        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++)
-          {
-            if (sc > thresholds[i])
-            {
-              c = pidColours[i];
-              break;
-            }
-          }
-        }
-
-      }
-      return c;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+  public Color[] pidColours;
+
+  public float[] thresholds;
+
+  SequenceGroup group;
+
+  public PIDColourScheme()
+  {
+    this.pidColours = ResidueProperties.pidColours;
+    this.thresholds = ResidueProperties.pidThresholds;
+  }
+
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    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;
+    }
+
+    Color currentColour = Color.white;
+
+    double sc = 0;
+
+    if (consensus.length <= j)
+    {
+      return Color.white;
+    }
+
+    if ((Integer
+            .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
+            && consensus[j].contains(String.valueOf(c)))
+    {
+      sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
+
+      if (!jalview.util.Comparison.isGap(c))
+      {
+        for (int i = 0; i < thresholds.length; i++)
+        {
+          if (sc > thresholds[i])
+          {
+            currentColour = pidColours[i];
+
+            break;
+          }
+        }
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}