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.

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)

Instance Methods [hide private]
Initialize the class.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]


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Initialize the class.
Overrides: object.__init__