updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

[jalview.git] / src / jalview / schemes / PIDColourScheme.java

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index eadf09b..d9fd7bd 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,48 +1,83 @@
-package jalview.schemes;\r
-\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class PIDColourScheme extends ResidueColourScheme {\r
-    public Color[] pidColours;\r
-    public float[] thresholds;\r
-\r
-    SequenceGroup group;\r
-\r
-    public PIDColourScheme() {\r
-       this.pidColours = ResidueProperties.pidColours;\r
-       this.thresholds = ResidueProperties.pidThresholds;\r
-    }\r
-\r
-\r
-\r
-  public Color findColour(String s, int j) {\r
-\r
-    if( threshold!=0 && !aboveThreshold(s,j))\r
-      return Color.white;\r
-\r
-    Color     c    = Color.white;\r
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
-\r
-      double sc = 0;\r
-      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
-      {\r
-        sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
-        // MC Should be isGap\r
-        if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
-        {\r
-          for (int i = 0; i < thresholds.length; i++)\r
-          {\r
-            if (sc > thresholds[i])\r
-            {\r
-              c = pidColours[i];\r
-              break;\r
-            }\r
-          }\r
-        }\r
-\r
-      }\r
-      return c;\r
-  }\r
-}\r
+/*
+ * 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.*;
+
+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)
+  {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z')
+    {
+      s = String.valueOf(res -= ('a' - 'A'));
+    }
+
+
+    if ( (threshold != 0) && !aboveThreshold(s, j))
+    {
+      return Color.white;
+    }
+
+    currentColour = Color.white;
+
+    double sc = 0;
+
+    if(consensus.length<=j)
+      return Color.white;
+
+      if ( (Integer.parseInt(consensus[j].get("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;
+            }
+          }
+        }
+      }
+
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
+  }
+}