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)
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Creates a new object. It is designed to be called internally from Bio::Sim4::Report object. Users shall not use it directly.
# File lib/bio/appl/sim4/report.rb, line 88 def initialize(seqid, seqdef, len, filename) @entry_id = seqid @definition = seqdef @len = len @filename = filename end
parse(str, str2 = nil)
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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.
# File lib/bio/appl/sim4/report.rb, line 106 def self.parse(str, str2 = nil) /^seq[12] \= (.*)(?: \((.*)\))?\,\s*(\d+)\s*bp\s*$/ =~ str seqid = $2 filename = $1 len = $3.to_i if str2 then seqdef = str2.sub(/^\>\s*/, '') seqid =seqdef.split(/\s+/, 2)[0] unless seqid else seqdef = (seqid or filename) seqid = filename unless seqid end self.new(seqid, seqdef, len, filename) end