X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=9c10e7d8e1101c95b193233ff6c60c781de3b020;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=a688593eafc3f2f9ddb5e4f6908b52f6c7868541;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index a688593..9c10e7d 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -23,53 +23,122 @@ import java.awt.*;
 import java.util.*;
 
 
-public class ResidueColourScheme implements ColourSchemeI {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
     Color[] colors;
     int threshold = 0;
+
+    /** DOCUMENT ME!! */
     public Vector consensus;
 
-    public ResidueColourScheme(Color[] colors, int threshold) {
+    /**
+     * Creates a new ResidueColourScheme object.
+     *
+     * @param colors DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public ResidueColourScheme(Color[] colors, int threshold)
+    {
         this.colors = colors;
         this.threshold = threshold;
     }
 
-    public ResidueColourScheme() {
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
+    public ResidueColourScheme()
+    {
     }
 
-    public void setConsensus(Vector consensus) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector consensus)
+    {
         this.consensus = consensus;
     }
 
-    public Color findColour(String aa) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String aa)
+    {
         return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
     }
 
-    public Color findColour(String s, int j) {
-        if ((threshold == 0) || aboveThreshold(s, j)) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int j)
+    {
+        if ((threshold == 0) || aboveThreshold(s, j))
+        {
             return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
-        } else {
+        }
+        else
+        {
             return Color.white;
         }
     }
 
-    public int getThreshold() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getThreshold()
+    {
         return threshold;
     }
 
-    public void setThreshold(int ct) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct)
+    {
         threshold = ct;
     }
 
-    public boolean aboveThreshold(String s, int j) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean aboveThreshold(String s, int j)
+    {
         Hashtable hash = (Hashtable) consensus.elementAt(j);
 
         if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
-                hash.contains(s)) {
+                hash.contains(s))
+        {
             ////  resCount////////////////////                  ///////////////seq count////////////
             double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
                     "size")).intValue();
 
-            if (sc >= threshold) {
+            if (sc >= threshold)
+            {
                 return true;
             }
         }