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.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(ary) ⇒ F0dbstat

Creates new F0dbstat class. Internal use only.



340
341
342
343
 
# File 'lib/bio/appl/blast/format0.rb', line 340

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

Instance Attribute Details

#f0dbstat ⇒ Object (readonly)

Returns the value of attribute f0dbstat.



344
345
346
 
# File 'lib/bio/appl/blast/format0.rb', line 344

def f0dbstat
  @f0dbstat
end

#f0params ⇒ Object

Returns the value of attribute f0params.



345
346
347
 
# File 'lib/bio/appl/blast/format0.rb', line 345

def f0params
  @f0params
end

Instance Method Details

#database ⇒ Object

Returns name (title or filename) of the database.



463
464
465
 
# File 'lib/bio/appl/blast/format0.rb', line 463

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

#db_len ⇒ Object

Returns number of letters in database.



473
474
475
 
# File 'lib/bio/appl/blast/format0.rb', line 473

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

#db_num ⇒ Object

Returns number of sequences in database.



478
479
480
 
# File 'lib/bio/appl/blast/format0.rb', line 478

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

#eff_space ⇒ Object

Returns effective length of the database.



416
 
# File 'lib/bio/appl/blast/format0.rb', line 416

def eff_space;   parse_params; @eff_space;   end

#expect ⇒ Object

Returns e-value threshold specified when BLAST was executed.



419
 
# File 'lib/bio/appl/blast/format0.rb', line 419

def expect;      parse_params; @expect;      end

#gap_extend ⇒ Object

Returns gap extend penalty value.



413
 
# File 'lib/bio/appl/blast/format0.rb', line 413

def gap_extend;  parse_params; @gap_extend;  end

#gap_open ⇒ Object

Returns gap open penalty value.



411
 
# File 'lib/bio/appl/blast/format0.rb', line 411

def gap_open;    parse_params; @gap_open;    end

#matrix ⇒ Object

Returns name of the matrix.



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

def matrix;      parse_params; @matrix;      end

#num_hits ⇒ Object

Returns number of hits.



422
 
# File 'lib/bio/appl/blast/format0.rb', line 422

def num_hits;    parse_params; @num_hits;    end

#posted_date ⇒ Object

Returns posted date of the database.



468
469
470
 
# File 'lib/bio/appl/blast/format0.rb', line 468

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

#sc_match ⇒ Object

Returns the match score of the matrix.



406
 
# File 'lib/bio/appl/blast/format0.rb', line 406

def sc_match;    parse_params; @sc_match;    end

#sc_mismatch ⇒ Object

Returns the mismatch score of the matrix.



408
 
# File 'lib/bio/appl/blast/format0.rb', line 408

def sc_mismatch; parse_params; @sc_mismatch; end