Class | Bio::Sim4::Report::SeqDesc |
In: |
lib/bio/appl/sim4/report.rb
|
Parent: | Object |
Bio::Sim4::Report::SeqDesc stores sequence information of query or subject of sim4 report.
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 |
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 88: def initialize(seqid, seqdef, len, filename) 89: @entry_id = seqid 90: @definition = seqdef 91: @len = len 92: @filename = filename 93: 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.
# File lib/bio/appl/sim4/report.rb, line 106 106: 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