Class: Bio::Blast::Bl2seq::Report

Inherits:
Default::Report show all
Defined in:
lib/bio/appl/bl2seq/report.rb

Overview

Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser. It inherits Bio::Blast::Default::Report. Most of its methods are the same as Bio::Blast::Default::Report, but it lacks many methods.

Defined Under Namespace

Classes: F0dbstat, HSP, Hit, Iteration

Constant Summary

DELIMITER =

Delimiter of each entry. Bio::FlatFile uses it. In Bio::Blast::Bl2seq::Report, it it nil (1 entry 1 file).

RS = nil
DELIMITER_OVERRUN =
nil

Instance Attribute Summary

Attributes inherited from Default::Report

#db_len, #db_num, #eff_space, #entry_overrun, #expect, #gap_extend, #gap_open, #iterations, #matrix, #num_hits, #posted_date, #sc_match, #sc_mismatch

Method Summary

Methods inherited from Default::Report

#converged?, #db, #each_hit, #each_iteration, #entropy, #gapped_entropy, #gapped_kappa, #gapped_lambda, #hits, #initialize, #kappa, #lambda, #message, open, #pattern, #pattern_positions, #program, #query_def, #query_len, #reference, #references, #to_s, #version, #version_date, #version_number

Constructor Details

This class inherits a constructor from Bio::Blast::Default::Report