Merge branch 'develop' into merge/JAL-3127

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

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 42f4feb..8610417 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -1,82 +1,80 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
+package jalview.schemes;
 
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 
+public class RNAInteractionColourScheme extends ResidueColourScheme
+{
+  public RNAInteractionColourScheme()
+  {
+    super();
+  }
 
-public class RNAInteractionColourScheme extends ResidueColourScheme{
-        public RNAInteractionColourScheme()
-         {
-           super();
-         }
+  @Override
+  public Color findColour(char c)
+  {
+    // FIXME this is just a copy of NucleotideColourScheme
+    return colors[ResidueProperties.nucleotideIndex[c]];
+  }
 
-         /**
-          * 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]];
-         }
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    // FIXME this is just a copy of NucleotideColourScheme
+    Color currentColour = Color.white;
+    try
+    {
+      currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+    } catch (Exception ex)
+    {
+    }
 
-         /**
-          * 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;
-           }
+    return currentColour;
+  }
 
-           if (conservationColouring)
-           {
-             currentColour = applyConservation(currentColour, j);
-           }
+  @Override
+  public boolean isNucleotideSpecific()
+  {
+    return true;
+  }
 
-           return currentColour;
-         }
-       }
+  @Override
+  public String getSchemeName()
+  {
+    return "RNA Interaction type";
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
+  {
+    return new RNAInteractionColourScheme();
+  }
+}