class Bio::GFF::GFF3::SequenceRegion

Stores meta-data “##sequence-region seqid start end”.

Attributes

end [RW]

end position

seqid [RW]

sequence ID

start [RW]

start position

Public Class Methods

new (seqid, start, endpos)

Source

     # File lib/bio/db/gff.rb
1068 def initialize(seqid, start, endpos)
1069   @seqid = seqid
1070   @start = start ? start.to_i : nil
1071   @end = endpos ? endpos.to_i : nil
1072 end

creates a new SequenceRegion class

parse (str)

Source

     # File lib/bio/db/gff.rb
1075 def self.parse(str)
1076   _, seqid, start, endpos =
1077     str.chomp.split(/\s+/, 4).collect { |x| unescape(x) }
1078   self.new(seqid, start, endpos)
1079 end

parses given string and returns SequenceRegion class

Public Instance Methods

== (other)

Source

     # File lib/bio/db/gff.rb
1099 def ==(other)
1100   if other.class == self.class and
1101       other.seqid == self.seqid and
1102       other.start == self.start and
1103       other.end == self.end then
1104     true
1105   else
1106     false
1107   end
1108 end

Returns true if self == other. Otherwise, returns false.

to_s ()

Source

     # File lib/bio/db/gff.rb
1091 def to_s
1092   i = escape_seqid(column_to_s(@seqid))
1093   s = escape_seqid(column_to_s(@start))
1094   e = escape_seqid(column_to_s(@end))
1095   "##sequence-region #{i} #{s} #{e}\n"
1096 end

string representation