- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- else\r
- {\r
- start = -1;\r
- end = -1;\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
-\r
- Sequence newSeq = null;\r
-\r
- if ( (start != -1) && (end != -1))\r
- {\r
- newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString())\r
- .toString(), start, end);\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString())\r
- .toString(), 1,\r
- seqhash.get(headers.elementAt(i).toString())\r
- .toString().length());\r
- seqs.addElement(newSeq);\r
- }\r