Use font.getName, not font.getFontName

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index e90e6cc..9c10e7d 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -16,66 +16,133 @@
 * along with this program; if not, write to the Free Software\r
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
 */\r
-\r
 package jalview.schemes;\r
 \r
-import java.util.*;\r
 import java.awt.*;\r
 \r
-public class ResidueColourScheme implements ColourSchemeI{\r
-    Color    [] colors;\r
-    int       threshold = 0;\r
-    public Vector   consensus;\r
+import java.util.*;\r
 \r
-    public ResidueColourScheme(Color[] colors, int threshold) {\r
-        this.colors    = colors;\r
-       this.threshold = threshold;\r
+\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
+    /**\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
+    /**\r
+     * Creates a new ResidueColourScheme object.\r
+     */\r
     public ResidueColourScheme()\r
-    {   }\r
+    {\r
+    }\r
 \r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param consensus DOCUMENT ME!\r
+     */\r
     public void setConsensus(Vector consensus)\r
     {\r
-      this.consensus = consensus;\r
+        this.consensus = consensus;\r
     }\r
 \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
+        return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
     }\r
 \r
-    public Color findColour(String s, int j) {\r
-\r
-       if( threshold==0 || aboveThreshold(s,j))\r
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
-       else\r
-          return Color.white;\r
-\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
+        }\r
+        else\r
+        {\r
+            return Color.white;\r
+        }\r
     }\r
 \r
-    public int getThreshold() {\r
-       return threshold;\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
-       threshold = 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
+    /**\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
+        Hashtable hash = (Hashtable) consensus.elementAt(j);\r
 \r
-        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))\r
+        if ((((Integer) hash.get("maxCount")).intValue() != -1) &&\r
+                hash.contains(s))\r
         {\r
-               ////  resCount////////////////////                  ///////////////seq count////////////\r
-          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();\r
-\r
-          if (sc >= threshold)\r
-            return true;\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
+            {\r
+                return true;\r
+            }\r
         }\r
 \r
-       return false;\r
+        return false;\r
     }\r
 }\r