Package Bio :: Package Blast :: Module Record :: Class Parameters
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Class Parameters

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object --+
Known Subclasses:

Holds information about the parameters.

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)

Instance Methods [hide private]
x.__init__(...) initializes x; see help(type(x)) for signature
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

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Inherited from object: __class__

Method Details [hide private]


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x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)