- // TODO: verify pfam format requires spaces and not tab characters -
- // if not upgrade to use stevesoft regex and look for whitespace.
- StringTokenizer str = new StringTokenizer(line, " ");
- String id = "";
-
- if (str.hasMoreTokens())
- {
- id = str.nextToken();
-
- StringBuffer tempseq;
-
- if (seqhash.containsKey(id))
- {
- tempseq = (StringBuffer) seqhash.get(id);
- }
- else
- {
- tempseq = new StringBuffer();
- seqhash.put(id, tempseq);
- }
-
- if (!(headers.contains(id)))
- {
- headers.addElement(id);
- }
- if (str.hasMoreTokens())
- {
- tempseq.append(str.nextToken());
- }
- }