- if (flag) {\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++) {\r
- int start = -1;\r
- int end = -1;\r
-\r
- if (seqhash.get(headers.elementAt(i)) != null) {\r
- if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
- .length()) {\r
- maxLength = seqhash.get(headers.elementAt(i)).toString()\r
- .length();\r
- }\r
-\r
- String head = headers.elementAt(i).toString();\r
- start = 1;\r
- end = seqhash.get(headers.elementAt(i)).toString().length();\r
-\r
- if (head.indexOf("/") > 0) {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2) {\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2) {\r
- start = Integer.valueOf(st.nextToken())\r
- .intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- } else {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- } else {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
-\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString())\r
- .toString(), start, end);\r
-\r
- seqs.addElement(newSeq);\r
- } else {\r
- System.err.println(\r
- "Clustal File Reader: Can't find sequence for " +\r
- headers.elementAt(i));\r