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
1062 def initialize(seqid, start, endpos)
1063   @seqid = seqid
1064   @start = start ? start.to_i : nil
1065   @end = endpos ? endpos.to_i : nil
1066 end

parse(str) click to toggle source

parses given string and returns SequenceRegion class

     # File lib/bio/db/gff.rb
1069 def self.parse(str)
1070   _, seqid, start, endpos =
1071     str.chomp.split(/\s+/, 4).collect { |x| unescape(x) }
1072   self.new(seqid, start, endpos)
1073 end

Public Instance Methods

==(other) click to toggle source

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

     # File lib/bio/db/gff.rb
1093 def ==(other)
1094   if other.class == self.class and
1095       other.seqid == self.seqid and
1096       other.start == self.start and
1097       other.end == self.end then
1098     true
1099   else
1100     false
1101   end
1102 end

to_s() click to toggle source

string representation

     # File lib/bio/db/gff.rb
1085 def to_s
1086   i = escape_seqid(column_to_s(@seqid))
1087   s = escape_seqid(column_to_s(@start))
1088   e = escape_seqid(column_to_s(@end))
1089   "##sequence-region #{i} #{s} #{e}\n"
1090 end