JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 26aea21..dd99f8a 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,37 +1,95 @@
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
-{\r
-  public NucleotideColourScheme() {\r
-  super(ResidueProperties.nucleotide,0);\r
-  }\r
-\r
-\r
-  public Color findColour(String n)\r
-  {\r
-    System.out.println("called");\r
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-  }\r
-\r
-\r
-  public Color findColour(String n, int j) {\r
-\r
-    if (threshold == 0 || aboveThreshold( n, j))\r
-      try\r
-      {\r
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        return Color.white;\r
-      }\r
-    else\r
-      return Color.white;\r
-\r
-  }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.datamodel.SequenceI;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+  /**
+   * Creates a new NucleotideColourScheme object.
+   */
+  public NucleotideColourScheme()
+  {
+    super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
+            0);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public Color findColour(char c)
+  {
+    // System.out.println("called"); log.debug
+    return colors[ResidueProperties.nucleotideIndex[c]];
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * @param j
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    Color currentColour;
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      try
+      {
+        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+      } catch (Exception ex)
+      {
+        return Color.white;
+      }
+    }
+    else
+    {
+      return Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}