[Biojava-l] accessing the HSP alignment using biojava

[Tracy, Adam]

hello, and thank you for your contribution to biojava -

i'm following the example of how to parse blast alignments outlined on your
website here:
http://www.biojava.org/docs/bj_in_anger/ExtractSearchInformation.htm

now, i'm curious to access the consensus string that describes the
relationship between the subject and the query, for instance the middle row
below:

Query: 276 QSFQRVQGFKKMVDRWRNSHTRCMWQMTLSQRRNLYATLRMQDTMGQELALANKQLLMVR 455
           +SFQ+  G KK VDRWRNSHT C+WQM L QRRN YATLRMQDTM QELALA KQLLMVR
Sbjct: 120 ESFQKAMGLKKTVDRWRNSHTHCLWQMALGQRRNPYATLRMQDTMVQELALAKKQLLMVR 179

in the code snippet below, i can get the two sequence fragments from the
seqString() method called on the SymbolList items contained within the
SubHit's Alignment, but not the consensus string.  is there a protocol
defined in the API that might help me with this?  

  for (Iterator k = result.getHits().iterator(); k.hasNext(); ) {
    SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit) k.next(); 
    for (Iterator alignments = hit.getSubHits().iterator();
alignments.hasNext();) {
      SeqSimilaritySearchSubHit sh = (SeqSimilaritySearchSubHit)
alignments.next();
      Alignment al = sh.getAlignment(); 
      for (Iterator syms = al.symbolListIterator(); syms.hasNext();) {
        SymbolList sl = (SymbolList) syms.next();
        sl.seqString();  
      }
    }
  }

thank you for your time!

ant

--------
Adam Tracy | Staff Software Engineer | CIS Software Operations AFFYMETRIX,
INC. | 6550 Vallejo St. Suite 100 | Emeryville, CA 94608 | Tel: 510-428-8536