Formatting changes

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

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index bbc0edd..5d0d1f6 100755 (executable)
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -25,47 +25,88 @@ import java.awt.*;
 import java.util.Vector;\r
 \r
 \r
-public class ConservationColourScheme extends ResidueColourScheme {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ConservationColourScheme extends ResidueColourScheme\r
+{\r
+    /** DOCUMENT ME!! */\r
     public Conservation conserve;\r
+\r
+    /** DOCUMENT ME!! */\r
     public ColourSchemeI cs;\r
+\r
+    /** DOCUMENT ME!! */\r
     public int inc = 30;\r
 \r
-    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs) {\r
+    /**\r
+     * Creates a new ConservationColourScheme object.\r
+     *\r
+     * @param cons DOCUMENT ME!\r
+     * @param oldcs DOCUMENT ME!\r
+     */\r
+    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
+    {\r
         super();\r
         conserve = cons;\r
         cs = oldcs;\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
-        if (cs != null) {\r
+        if (cs != null)\r
+        {\r
             cs.setConsensus(consensus);\r
         }\r
     }\r
 \r
-    public Color findColour(String s, int i) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param s DOCUMENT ME!\r
+     * @param i DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color findColour(String s, int i)\r
+    {\r
         Color c = Color.white;\r
 \r
-        if (cs == null) {\r
+        if (cs == null)\r
+        {\r
             return c;\r
         }\r
 \r
         char ch = conserve.getConsSequence().getSequence().charAt(i);\r
 \r
-        if ((ch == '*') || (ch == '+')) {\r
+        if ((ch == '*') || (ch == '+'))\r
+        {\r
             c = cs.findColour(s, i);\r
-        } else {\r
+        }\r
+        else\r
+        {\r
             int tmp = 10;\r
             int t = 0;\r
 \r
-            if (!jalview.util.Comparison.isGap(ch)) {\r
+            if (!jalview.util.Comparison.isGap(ch))\r
+            {\r
                 t = Integer.parseInt(ch + "");\r
             }\r
 \r
             c = cs.findColour(s, i);\r
 \r
-            while (tmp >= t) {\r
+            while (tmp >= t)\r
+            {\r
                 c = lighter(c, inc);\r
                 tmp--;\r
             }\r
@@ -74,26 +115,44 @@ public class ConservationColourScheme extends ResidueColourScheme {
         return c;\r
     }\r
 \r
-    public Color lighter(Color c, int inc) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param c DOCUMENT ME!\r
+     * @param inc DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color lighter(Color c, int inc)\r
+    {\r
         int red = c.getRed();\r
         int blue = c.getBlue();\r
         int green = c.getGreen();\r
 \r
-        if (red < (255 - inc)) {\r
+        if (red < (255 - inc))\r
+        {\r
             red = red + inc;\r
-        } else {\r
+        }\r
+        else\r
+        {\r
             red = 255;\r
         }\r
 \r
-        if (blue < (255 - inc)) {\r
+        if (blue < (255 - inc))\r
+        {\r
             blue = blue + inc;\r
-        } else {\r
+        }\r
+        else\r
+        {\r
             blue = 255;\r
         }\r
 \r
-        if (green < (255 - inc)) {\r
+        if (green < (255 - inc))\r
+        {\r
             green = green + inc;\r
-        } else {\r
+        }\r
+        else\r
+        {\r
             green = 255;\r
         }\r
 \r