- count++;\r
-\r
- StringTokenizer str = new StringTokenizer(line, " ");\r
-\r
- id = str.nextToken();\r
- id = id.substring(1);\r
-\r
- com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(\r
- "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
-\r
- // JBPNote At the moment - we don't get rid of the friendly names but this\r
- // behaviour is probably wrong in the long run.\r
- if (dbId.search(id))\r
- {\r
- String dbid = dbId.stringMatched(1);\r
- String idname = dbId.stringMatched(2);\r
-\r
- if ((idname.length() > 0) &&\r
- (idname.indexOf("_") > -1))\r
- {\r
- id = idname; // use the friendly name - apparently no dbid\r
- }\r
- else if (dbid.length() > 1)\r
- {\r
- id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise\r
- }\r
- }\r
-\r
- if (id.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(id, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- id = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r