Merge branch 'develop' into merge/JAL-3127

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

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 7906ed1..4977107 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,24 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
 
 /**
  * DOCUMENT ME!
@@ -33,56 +36,29 @@ public class NucleotideColourScheme extends ResidueColourScheme
    */
   public NucleotideColourScheme()
   {
-    super(ResidueProperties.nucleotide, 0);
+    super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *                DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c)
+  @Override
+  public boolean isNucleotideSpecific()
   {
-    // System.out.println("called"); log.debug
-    return colors[ResidueProperties.nucleotideIndex[c]];
+    return true;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.Nucleotide.toString();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *                DOCUMENT ME!
-   * @param j
-   *                DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
    */
-  public Color findColour(char c, int j)
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
-    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;
+    return new NucleotideColourScheme();
   }
 }