X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAInteractionColourScheme.java;h=86104175e25d3be505564d4f7b4284aca54b50b4;hb=994a386819147f73fa47f3c29ba6c438f0e4b15a;hp=2738f229aeb6f2a89a04c455e320d9d4570200fe;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 2738f22..8610417 100644
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -18,68 +18,63 @@
  * 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();
+  }
+}