+ /**\r
+ * Calculates the conservation values for given set of sequences\r
+ */\r
+ public void calculate()\r
+ {\r
+ Hashtable resultHash, residueHash, ht;\r
+ int count, thresh, j, jSize = sequences.size();\r
+ String sequence, res, type;\r
+ Enumeration enumeration, enumeration2;\r
+\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ resultHash = new Hashtable();\r
+ residueHash = new Hashtable();\r
+\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ // JBPNote - have to make sure elements of the sequences vector\r
+ // are tested like this everywhere...\r
+ if (sequences.elementAt(j) instanceof Sequence)\r
+ {\r
+ sequence = ((Sequence) sequences.elementAt(j)).getSequence();\r
+\r
+ if (sequence.length() > i)\r
+ {\r
+ res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));\r
+\r
+ if (residueHash.containsKey(res))\r
+ {\r
+ count = ((Integer) residueHash.get(res)).intValue();\r
+ count++;\r
+ residueHash.put(res, new Integer(count));\r
+ }\r
+ else\r
+ {\r
+ residueHash.put(res, new Integer(1));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (residueHash.containsKey("-"))\r
+ {\r
+ count = ((Integer) residueHash.get("-")).intValue();\r
+ count++;\r
+ residueHash.put("-", new Integer(count));\r
+ }\r
+ else\r
+ {\r
+ residueHash.put("-", new Integer(1));\r
+ }\r
+ }\r
+ }\r
+ }\r