X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=943d2fa3a715364e85ebdee75a943a4352dfb4e0;hb=5b29190f1ea9500d3ad9f690ffb359f6aab17b80;hp=666834e9dc90c2008a67cbeb46a4ac838b57b87a;hpb=ac33424148b2a4de29b3ca43f941162e8ba0384c;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 666834e..943d2fa 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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;
 
@@ -36,6 +37,7 @@ import java.util.Map;
 public class ResidueColourScheme implements ColourSchemeI
 {
   final int[] symbolIndex;
+
   boolean conservationColouring = false;
 
   Color[] colors = null;
@@ -58,13 +60,16 @@ public class ResidueColourScheme implements ColourSchemeI
 
   /**
    * Creates a new ResidueColourScheme object.
-   * @param final int[] index table into colors (ResidueProperties.naIndex or ResidueProperties.aaIndex)
+   * 
+   * @param final int[] index table into colors (ResidueProperties.naIndex or
+   *        ResidueProperties.aaIndex)
    * @param colors
    *          colours for symbols in sequences
    * @param threshold
    *          threshold for conservation shading
    */
-  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, int threshold)
+  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+          int threshold)
   {
     symbolIndex = aaOrnaIndex;
     this.colors = colours;
@@ -72,14 +77,17 @@ public class ResidueColourScheme implements ColourSchemeI
   }
 
   /**
-   * Creates a new ResidueColourScheme object with a lookup table for indexing the colour map
+   * Creates a new ResidueColourScheme object with a lookup table for indexing
+   * the colour map
    */
   public ResidueColourScheme(int[] aaOrNaIndex)
   {
     symbolIndex = aaOrNaIndex;
   }
+
   /**
-   * Creates a new ResidueColourScheme object - default constructor for non-sequence dependent colourschemes
+   * Creates a new ResidueColourScheme object - default constructor for
+   * non-sequence dependent colourschemes
    */
   public ResidueColourScheme()
   {
@@ -91,8 +99,7 @@ public class ResidueColourScheme implements ColourSchemeI
    */
   public Color findColour(char c)
   {
-    return colors == null ? Color.white
-            : colors[symbolIndex[c]];
+    return colors == null ? Color.white : colors[symbolIndex[c]];
   }
 
   @Override
@@ -100,7 +107,8 @@ public class ResidueColourScheme implements ColourSchemeI
   {
     Color currentColour;
 
-    if (colors!=null && symbolIndex!=null && (threshold == 0) || aboveThreshold(c, j))
+    if (colors != null && symbolIndex != null && (threshold == 0)
+            || aboveThreshold(c, j))
     {
       currentColour = colors[symbolIndex[c]];
     }
@@ -116,6 +124,7 @@ public class ResidueColourScheme implements ColourSchemeI
 
     return currentColour;
   }
+
   /**
    * Get the percentage threshold for this colour scheme
    *