Formatting changes

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

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