Blast.txt
=========


Parsers
-------

BLAST parsers are built with an event-oriented design described in
Parser.txt.


Scanners
--------

BLAST Scanners produce the following events:
SECTION NAME                      COMMENTS
    EVENT NAME

header
    version
    reference
    query_info
    database_info

descriptions
    round                         psi blast
    model_sequences               psi blast
    nonmodel_sequences            psi blast
    converged                     psi blast
    description
    no_hits

alignment
    multalign                     master-slave
    title                         pairwise
    length                        pairwise
  hsp
    score                         pairwise
    identities                    pairwise
    strand                        pairwise, blastn
    frame                         pairwise, blastx, tblastn, tblastx
    query                         pairwise
    align                         pairwise
    sbjct                         pairwise

database_report
    database
    posted_date
    num_letters_in_database
    num_sequences_in_database
    num_letters_searched          RESERVED.  Currently unused.  I've never
    num_sequences_searched        RESERVED.  seen it, but it's in blastool.c..
    ka_params
    gapped                        not blastp
    ka_params_gap                 gapped mode (not tblastx)

parameters
    matrix
    gap_penalties                 gapped mode (not tblastx)
    num_hits                      
    num_sequences                 
    num_extends                   
    num_good_extends              
    num_seqs_better_e
    hsps_no_gap                   gapped (not tblastx) and not blastn
    hsps_prelim_gapped            gapped (not tblastx) and not blastn
    hsps_prelim_gap_attempted     gapped (not tblastx) and not blastn
    hsps_gapped                   gapped (not tblastx) and not blastn
    query_length
    database_length
    effective_hsp_length
    effective_query_length
    effective_database_length
    effective_search_space
    effective_search_space_used
    frameshift                    blastx or tblastn or tblastx
    threshold
    window_size
    dropoff_1st_pass
    gap_x_dropoff
    gap_x_dropoff_final           gapped (not tblastx) and not blastn
    gap_trigger
    blast_cutoff