Class Bio::GFF::GFF3::SequenceRegion
In: lib/bio/db/gff.rb
Parent: Object

Stores meta-data "#sequence-region seqid start end".

Methods

==   new   parse   to_s  

Included Modules

Escape

Attributes

end  [RW]  end position
seqid  [RW]  sequence ID
start  [RW]  start position

Public Class methods

creates a new SequenceRegion class

[Source]

      # File lib/bio/db/gff.rb, line 1060
1060:         def initialize(seqid, start, endpos)
1061:           @seqid = seqid
1062:           @start = start ? start.to_i : nil
1063:           @end = endpos ? endpos.to_i : nil
1064:         end

parses given string and returns SequenceRegion class

[Source]

      # File lib/bio/db/gff.rb, line 1067
1067:         def self.parse(str)
1068:           dummy, seqid, start, endpos =
1069:             str.chomp.split(/\s+/, 4).collect { |x| unescape(x) }
1070:           self.new(seqid, start, endpos)
1071:         end

Public Instance methods

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

[Source]

      # File lib/bio/db/gff.rb, line 1091
1091:         def ==(other)
1092:           if other.class == self.class and
1093:               other.seqid == self.seqid and
1094:               other.start == self.start and
1095:               other.end == self.end then
1096:             true
1097:           else
1098:             false
1099:           end
1100:         end

string representation

[Source]

      # File lib/bio/db/gff.rb, line 1083
1083:         def to_s
1084:           i = escape_seqid(column_to_s(@seqid))
1085:           s = escape_seqid(column_to_s(@start))
1086:           e = escape_seqid(column_to_s(@end))
1087:           "##sequence-region #{i} #{s} #{e}\n"
1088:         end

[Validate]