X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAInteractionColourScheme.java;h=491d3ea24268cad17ae1a00f830010b99c0bca2e;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=2738f229aeb6f2a89a04c455e320d9d4570200fe;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 2738f22..491d3ea 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -18,68 +18,68 @@
  * 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.datamodel.SequenceI;
 
 import java.awt.Color;
 
+public class RNAInteractionColourScheme extends ResidueColourScheme
+{
+  public RNAInteractionColourScheme()
+  {
+    super();
+  }
 
-public class RNAInteractionColourScheme extends ResidueColourScheme{
-	 public RNAInteractionColourScheme()
-	  {
-	    super();
-	  }
+  /**
+   * 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!
-	   * 
-	   * @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;
+    }
 
-	  /**
-	   * 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);
+    }
 
-	    if (conservationColouring)
-	    {
-	      currentColour = applyConservation(currentColour, j);
-	    }
-
-	    return currentColour;
-	  }
-	}
+    return currentColour;
+  }
+}