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) click to toggle source

creates a new SequenceRegion class

# File lib/bio/db/gff.rb, line 1059
def initialize(seqid, start, endpos)
  @seqid = seqid
  @start = start ? start.to_i : nil
  @end = endpos ? endpos.to_i : nil
end
parse(str) click to toggle source

parses given string and returns SequenceRegion class

# File lib/bio/db/gff.rb, line 1066
def self.parse(str)
  _, seqid, start, endpos =
    str.chomp.split(/\s+/, 4).collect { |x| unescape(x) }
  self.new(seqid, start, endpos)
end

Public Instance Methods

==(other) click to toggle source

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

# File lib/bio/db/gff.rb, line 1090
def ==(other)
  if other.class == self.class and
      other.seqid == self.seqid and
      other.start == self.start and
      other.end == self.end then
    true
  else
    false
  end
end
to_s() click to toggle source

string representation

# File lib/bio/db/gff.rb, line 1082
def to_s
  i = escape_seqid(column_to_s(@seqid))
  s = escape_seqid(column_to_s(@start))
  e = escape_seqid(column_to_s(@end))
  "##sequence-region #{i} #{s} #{e}\n"
end