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