Class Bio::Fasta::Report::Hit::Query
In: lib/bio/appl/fasta/format10.rb
Parent: Object

Methods

entry_id   length   moltype   new   start   stop  

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 333
333:       def initialize(data)
334:         @definition, *data = data.split(/\n/)
335:         @data = {}
336:         @sequence = ''
337: 
338:         pat = /;\s+([^:]+):\s+(.*)/
339: 
340:         data.each do |x|
341:           if pat.match(x)
342:             @data[$1] = $2
343:           else
344:             @sequence += x
345:           end
346:         end
347:       end

Public Instance methods

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 364
364:       def entry_id
365:         @definition[/\S+/]
366:       end

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 370
370:       def length
371:         @data['sq_len'].to_i
372:       end

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 375
375:       def moltype
376:         @data['sq_type']
377:       end

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 381
381:       def start
382:         @data['al_start'].to_i
383:       end

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 387
387:       def stop
388:         @data['al_stop'].to_i
389:       end

[Validate]