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

new(data)

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 243
243:       def initialize(data)
244:         @definition, *data = data.split(/\n/)
245:         @data = {}
246:         @sequence = ''
247: 
248:         pat = /;\s+([^:]+):\s+(.*)/
249: 
250:         data.each do |x|
251:           if pat.match(x)
252:             @data[$1] = $2
253:           else
254:             @sequence += x
255:           end
256:         end
257:       end

Public Instance methods

entry_id()

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 274
274:       def entry_id
275:         @definition[/\S+/]
276:       end
length()

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 280
280:       def length
281:         @data['sq_len'].to_i
282:       end
moltype()

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

[Source]

     # File lib/bio/appl/fasta/format10.rb, line 285
285:       def moltype
286:         @data['sq_type']
287:       end
start()

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 291
291:       def start
292:         @data['al_start'].to_i
293:       end
stop()

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 297
297:       def stop
298:         @data['al_stop'].to_i
299:       end

[Validate]