class Bio::Sim4::Report::SeqDesc

Bio::Sim4::Report::SeqDesc stores sequence information of query or subject of sim4 report.

Attributes

definition [R]

definition of the sequence

entry_id [R]

identifier of the sequence

filename [R]

filename of the sequence

len [R]

sequence length of the sequence

Public Class Methods

new (seqid, seqdef, len, filename)

Source

   # File lib/bio/appl/sim4/report.rb
88 def initialize(seqid, seqdef, len, filename)
89   @entry_id   = seqid
90   @definition = seqdef
91   @len        = len
92   @filename   = filename
93 end

Creates a new object. It is designed to be called internally from Bio::Sim4::Report object. Users shall not use it directly.

parse (str, str2 = nil)

Source

    # File lib/bio/appl/sim4/report.rb
106 def self.parse(str, str2 = nil)
107   /^seq[12] \= (.*)(?: \((.*)\))?\,\s*(\d+)\s*bp\s*$/ =~ str
108   seqid = $2
109   filename = $1
110   len = $3.to_i
111   if str2 then
112     seqdef = str2.sub(/^\>\s*/, '')
113     seqid  =seqdef.split(/\s+/, 2)[0] unless seqid
114   else
115     seqdef = (seqid or filename)
116     seqid = filename unless seqid
117   end
118   self.new(seqid, seqdef, len, filename)
119 end

Parses part of sim4 result text and creates new SeqDesc object. It is designed to be called internally from Bio::Sim4::Report object. Users shall not use it directly.