Class: Bio::Blast::WU::Report_TBlast

Inherits:
Report show all
Defined in:
lib/bio/appl/blast/wublast.rb

Overview

WU-BLAST default output parser for TBLAST. All methods are equal to Bio::Blast::WU::Report. Only DELIMITER (and RS) is different.

Constant Summary

DELIMITER =

Delimter of each entry for TBLAST. Bio::FlatFile uses it.

RS = "\nTBLAST"
DELIMITER_OVERRUN =

(Integer) excess read size included in DELIMITER.

6

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 Report

#db, #exit_code, #exit_code_message, #expect, #fatal_errors, #notes, #notice, #parameter_matrix, #parameters, #query_record_number, #warnings

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