Class: Bio::GFFbrowser::FastLineRecord

Inherits:

Record

• Object
• Record
• Bio::GFFbrowser::FastLineRecord

Includes:

FastLineParser

Defined in:

lib/bio/db/gff/gffrecord.rb

Overview

Using the fast line parser

Direct Known Subclasses

Bio::GFF::GFF3::FastParserFileRecord

Instance Method Summary

• #attributes ⇒ Object
• #comment ⇒ Object
• #end ⇒ Object
• #feature ⇒ Object (also: #feature_type)
• #get_attribute(name) ⇒ Object
• #id ⇒ Object (also: #entry_id)
• #initialize(fields) ⇒ FastLineRecord constructor

  A new instance of FastLineRecord.

• #phase ⇒ Object (also: #frame)
• #score ⇒ Object
• #seqid ⇒ Object (also: #seqname)
• #source ⇒ Object
• #start ⇒ Object
• #strand ⇒ Object

Methods included from FastLineParser

#parse_attributes_fast, #parse_line_fast

Methods included from Helpers::Logger

#debug, #error, #info, #log_sys_info, #warn

Constructor Details

#initialize(fields) ⇒ FastLineRecord

Returns a new instance of FastLineRecord.

# File 'lib/bio/db/gff/gffrecord.rb', line 15

def initialize fields
  @fields = fields
end

Instance Method Details

#attributes ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 60

def attributes 
  @attributes_ ||= parse_attributes_fast(@fields[GFF3_ATTRIBUTES])
end

#comment ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 19

def comment
  false
end

#end ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 39

def end
  @end_ ||= @fields[GFF3_END].to_i
end

#feature ⇒ Object Also known as: feature_type

# File 'lib/bio/db/gff/gffrecord.rb', line 51

def feature
  @feature_ ||= @fields[GFF3_TYPE]
end

#get_attribute(name) ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 64

def get_attribute name
  attributes[name]
end

#id ⇒ Object Also known as: entry_id

# File 'lib/bio/db/gff/gffrecord.rb', line 68

def id
  @id_ ||= attributes['ID']
end

#phase ⇒ Object Also known as: frame

# File 'lib/bio/db/gff/gffrecord.rb', line 29

def phase
  @phase_ ||= @fields[GFF3_PHASE].to_i
end

#score ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 43

def score
  @score_ ||= @fields[GFF3_SCORE].to_f
end

#seqid ⇒ Object Also known as: seqname

# File 'lib/bio/db/gff/gffrecord.rb', line 23

def seqid
  @seqid_ ||= @fields[GFF3_SEQID]
end

#source ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 56

def source
  @fields[GFF3_SOURCE]
end

#start ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 35

def start
  @start_ ||= @fields[GFF3_START].to_i
end

#strand ⇒ Object

# File 'lib/bio/db/gff/gffrecord.rb', line 47

def strand
  @fields[GFF3_STRAND]
end