class Bio::Fasta::Report::Hit::Query

Attributes

data[R]

Returns a Hash containing ‘sq_len’, ‘sq_offset’, ‘sq_type’, ‘al_start’, ‘al_stop’, and ‘al_display_start’ values. You can access most of these values by Report::Hit#query_* methods.

definition[R]

Returns the definition of the entry as a String. You can access this value by Report::Hit#query_def method.

sequence[R]

Returns the sequence (with gaps) as a String. You can access this value by the Report::Hit#query_seq method.

Public Class Methods

new(data) click to toggle source

    # File lib/bio/appl/fasta/format10.rb
334 def initialize(data)
335   @definition, *data = data.split(/\n/)
336   @data = {}
337   @sequence = ''
338 
339   pat = /;\s+([^:]+):\s+(.*)/
340 
341   data.each do |x|
342     if pat.match(x)
343       @data[$1] = $2
344     else
345       @sequence += x
346     end
347   end
348 end

Public Instance Methods

entry_id() click to toggle source

Returns the first word in the definition as a String. You can get this value by Report::Hit#query_id method.

    # File lib/bio/appl/fasta/format10.rb
365 def entry_id
366   @definition[/\S+/]
367 end

length() click to toggle source

Returns the sequence length. You can access this value by the Report::Hit#query_len method.

    # File lib/bio/appl/fasta/format10.rb
371 def length
372   @data['sq_len'].to_i
373 end

moltype() click to toggle source

Returns ‘p’ for protein sequence, ‘D’ for nucleotide sequence.

    # File lib/bio/appl/fasta/format10.rb
376 def moltype
377   @data['sq_type']
378 end

start() click to toggle source

Returns alignment start position. You can also access this value by Report::Hit#query_start method for shortcut.

    # File lib/bio/appl/fasta/format10.rb
382 def start
383   @data['al_start'].to_i
384 end

stop() click to toggle source

Returns alignment end position. You can access this value by Report::Hit#query_end method for shortcut.

    # File lib/bio/appl/fasta/format10.rb
388 def stop
389   @data['al_stop'].to_i
390 end