- public void verdict(boolean consflag, float percentageGaps) {\r
- String consString = "";\r
-\r
- for (int i = start; i <= end; i++) {\r
- int[] gapcons = countConsNGaps(i);\r
- boolean cons = (gapcons[0] == 1) ? true : false;\r
- int totGaps = gapcons[1];\r
- float pgaps = ((float) totGaps * 100) / (float) sequences.size();\r
-\r
- // System.out.println("percentage gaps = "+pgaps+"\n");\r
- if (percentageGaps > pgaps) {\r
- Hashtable resultHash = (Hashtable) total.elementAt(i - start);\r
+ /**\r
+ * Calculates the conservation sequence\r
+ *\r
+ * @param consflag if true, poitiveve conservation; false calculates negative conservation\r
+ * @param percentageGaps commonly used value is 25\r
+ */\r
+ public void verdict(boolean consflag, float percentageGaps)\r
+ {\r
+ StringBuffer consString = new StringBuffer();\r
+ String type;\r
+ Integer result;\r
+ int[] gapcons;\r
+ int totGaps, count;\r
+ float pgaps;\r
+ Hashtable resultHash ;\r
+ Enumeration enumeration;\r
+\r
+\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ gapcons = countConsNGaps(i);\r
+ totGaps = gapcons[1];\r
+ pgaps = ((float) totGaps * 100) / (float) sequences.size();\r
+\r
+ if (percentageGaps > pgaps)\r
+ {\r
+ resultHash = (Hashtable) total.elementAt(i - start);\r