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

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

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 08e699b..e23a497 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -1,65 +1,85 @@
+/*
+ * 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;
 
+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;
+  }
+}