formatting

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 666834e..642eb05 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -36,6 +36,7 @@ import java.util.Map;
 public class ResidueColourScheme implements ColourSchemeI
 {
   final int[] symbolIndex;
+
   boolean conservationColouring = false;
 
   Color[] colors = null;
@@ -58,13 +59,16 @@ 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 +76,17 @@ 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 +98,7 @@ 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 +106,8 @@ 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 +123,7 @@ public class ResidueColourScheme implements ColourSchemeI
 
     return currentColour;
   }
+
   /**
    * Get the percentage threshold for this colour scheme
    *