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.


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

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

Instance Attribute Details

#f0dbstatObject (readonly)

Returns the value of attribute f0dbstat


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

def f0dbstat
  @f0dbstat
end

#f0paramsObject

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

#databaseObject

Returns name (title or filename) of the database.


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# File 'lib/bio/appl/blast/format0.rb', line 452

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

#db_lenObject

Returns number of letters in database.


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# File 'lib/bio/appl/blast/format0.rb', line 462

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

#db_numObject

Returns number of sequences in database.


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# File 'lib/bio/appl/blast/format0.rb', line 467

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

#eff_spaceObject

Returns effective length of the database.


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# File 'lib/bio/appl/blast/format0.rb', line 405

def eff_space;   parse_params; @eff_space;   end

#expectObject

Returns e-value threshold specified when BLAST was executed.


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

def expect;      parse_params; @expect;      end

#gap_extendObject

Returns gap extend penalty value.


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# File 'lib/bio/appl/blast/format0.rb', line 402

def gap_extend;  parse_params; @gap_extend;  end

#gap_openObject

Returns gap open penalty value.


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# File 'lib/bio/appl/blast/format0.rb', line 400

def gap_open;    parse_params; @gap_open;    end

#matrixObject

Returns name of the matrix.


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

def matrix;      parse_params; @matrix;      end

#num_hitsObject

Returns number of hits.


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

def num_hits;    parse_params; @num_hits;    end

#posted_dateObject

Returns posted date of the database.


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# File 'lib/bio/appl/blast/format0.rb', line 457

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

#sc_matchObject

Returns the match score of the matrix.


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# File 'lib/bio/appl/blast/format0.rb', line 389

def sc_match
  parse_params
  (defined? @sc_match) ? @sc_match : nil
end

#sc_mismatchObject

Returns the mismatch score of the matrix.


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# File 'lib/bio/appl/blast/format0.rb', line 394

def sc_mismatch
  parse_params
  (defined? @sc_mismatch) ? @sc_mismatch : nil
end