Class Parameters
source code
- Known Subclasses:
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Holds information about the parameters.
Members: matrix Name of the matrix. gap_penalties
Tuple of (open, extend) penalties. (floats) sc_match Match
score for nucleotide-nucleotide comparison sc_mismatch Mismatch
penalty for nucleotide-nucleotide comparison num_hits Number
of hits to the database. (int) num_sequences Number of sequences.
(int) num_good_extends Number of extensions. (int) num_seqs_better_e
Number of sequences better than e-value. (int) hsps_no_gap
Number of HSP's better, without gapping. (int) hsps_prelim_gapped
Number of HSP's gapped in prelim test. (int) hsps_prelim_gapped_attemped
Number of HSP's attempted in prelim. (int) hsps_gapped Total
number of HSP's gapped. (int) query_length Length of the query.
(int) query_id Identifier of the query sequence. (str)
database_length Number of letters in the database. (int)
effective_hsp_length Effective HSP length. (int)
effective_query_length Effective length of query. (int)
effective_database_length Effective length of database. (int)
effective_search_space Effective search space. (int)
effective_search_space_used Effective search space used. (int)
frameshift Frameshift window. Tuple of (int, float) threshold
Threshold. (int) window_size Window size. (int)
dropoff_1st_pass Tuple of (score, bits). (int, float) gap_x_dropoff
Tuple of (score, bits). (int, float) gap_x_dropoff_final Tuple of
(score, bits). (int, float) gap_trigger Tuple of (score, bits).
(int, float) blast_cutoff Tuple of (score, bits). (int,
float)