Class: Bio::Blast::Default::Report::F0dbstat

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/blast/format0.rb

Overview

Stores format0 database statistics. Internal use only. Users must not use the class.

Direct Known Subclasses

Bl2seq::Report::F0dbstat, WU::Report::F0dbstat

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (F0dbstat) initialize(ary)

Creates new F0dbstat class. Internal use only.



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# File 'lib/bio/appl/blast/format0.rb', line 322

def initialize(ary)
  @f0dbstat = ary
  @hash = {}
end

Instance Attribute Details

- (Object) f0dbstat (readonly)

Returns the value of attribute f0dbstat



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# File 'lib/bio/appl/blast/format0.rb', line 326

def f0dbstat
  @f0dbstat
end

- (Object) f0params

Returns the value of attribute f0params



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# File 'lib/bio/appl/blast/format0.rb', line 327

def f0params
  @f0params
end

Instance Method Details

- (Object) database

Returns name (title or filename) of the database.



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# File 'lib/bio/appl/blast/format0.rb', line 445

def database
  unless defined?(@database);    parse_dbstat; end; @database
end

- (Object) db_len

Returns number of letters in database.



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# File 'lib/bio/appl/blast/format0.rb', line 455

def db_len
  unless defined?(@db_len);      parse_dbstat; end; @db_len
end

- (Object) db_num

Returns number of sequences in database.



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# File 'lib/bio/appl/blast/format0.rb', line 460

def db_num
  unless defined?(@db_num);      parse_dbstat; end; @db_num
end

- (Object) eff_space

Returns effective length of the database.



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# File 'lib/bio/appl/blast/format0.rb', line 398

def eff_space;   parse_params; @eff_space;   end

- (Object) expect

Returns e-value threshold specified when BLAST was executed.



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# File 'lib/bio/appl/blast/format0.rb', line 401

def expect;      parse_params; @expect;      end

- (Object) gap_extend

Returns gap extend penalty value.



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# File 'lib/bio/appl/blast/format0.rb', line 395

def gap_extend;  parse_params; @gap_extend;  end

- (Object) gap_open

Returns gap open penalty value.



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# File 'lib/bio/appl/blast/format0.rb', line 393

def gap_open;    parse_params; @gap_open;    end

- (Object) matrix

Returns name of the matrix.



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# File 'lib/bio/appl/blast/format0.rb', line 386

def matrix;      parse_params; @matrix;      end

- (Object) num_hits

Returns number of hits.



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# File 'lib/bio/appl/blast/format0.rb', line 404

def num_hits;    parse_params; @num_hits;    end

- (Object) posted_date

Returns posted date of the database.



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# File 'lib/bio/appl/blast/format0.rb', line 450

def posted_date
  unless defined?(@posted_date); parse_dbstat; end; @posted_date
end

- (Object) sc_match

Returns the match score of the matrix.



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# File 'lib/bio/appl/blast/format0.rb', line 388

def sc_match;    parse_params; @sc_match;    end

- (Object) sc_mismatch

Returns the mismatch score of the matrix.



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# File 'lib/bio/appl/blast/format0.rb', line 390

def sc_mismatch; parse_params; @sc_mismatch; end