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Bio::Blast::Record::Parameters Class Reference

Inheritance diagram for Bio::Blast::Record::Parameters:

Bio::Blast::Record::Blast Bio::Blast::Record::PSIBlast

List of all members.


Detailed Description

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)
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)

Definition at line 235 of file Record.py.


Public Member Functions

def __init__

Public Attributes

 blast_cutoff
 database_length
 dropoff_1st_pass
 effective_database_length
 effective_hsp_length
 effective_query_length
 effective_search_space
 effective_search_space_used
 frameshift
 gap_penalties
 gap_trigger
 gap_x_dropoff
 gap_x_dropoff_final
 hsps_gapped
 hsps_no_gap
 hsps_prelim_gapped
 hsps_prelim_gapped_attemped
 matrix
 num_good_extends
 num_hits
 num_seqs_better_e
 num_sequences
 query_length
 sc_match
 sc_mismatch
 threshold
 window_size

The documentation for this class was generated from the following file:

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