class Array

Ruby core Array class, with additional methods.

Method to create a RGFA::ByteArray from an Array

Extensions to the Array core class.

Method to create a numeric array from an array

Public Instance Methods

default_gfa_datatype() click to toggle source

@!macro gfa_datatype

# File lib/rgfa/field_writer.rb, line 90
def default_gfa_datatype
  (all?{|i|i.kind_of?(Integer)} or all?{|i|i.kind_of?(Float)}) ? :B : :J
end

rgfa_field_array?() click to toggle source

Is this possibly a {RGFA::FieldArray} instance?

(i.e. are the two last elements a datatype symbol and a zero byte?) @return [Boolean]

# File lib/rgfa/field_array.rb, line 71
def rgfa_field_array?
  self[-1] == "\0" and
    RGFA::Line::OPTFIELD_DATATYPE.include?(self[-2].to_sym)
end

to_byte_array() click to toggle source

Create a RGFA::ByteArray from an Array instance @return [RGFA::ByteArray] the byte array

# File lib/rgfa/byte_array.rb, line 55
def to_byte_array
  RGFA::ByteArray.new(self)
end

to_cigar() click to toggle source

Create a {RGFA::CIGAR} instance from the content of the array. @return [RGFA::CIGAR]

# File lib/rgfa/cigar.rb, line 139
def to_cigar
  RGFA::CIGAR.new(self)
end

to_cigar_operation() click to toggle source

Create a {RGFA::CIGAR::Operation} instance from the content of the array. @return [RGFA::CIGAR::Operation]

# File lib/rgfa/cigar.rb, line 144
def to_cigar_operation
  RGFA::CIGAR::Operation.new(Integer(self[0]), self[1].to_sym)
end

to_gfa_field(datatype: default_gfa_datatype) click to toggle source

@!macro to_gfa_field

# File lib/rgfa/field_writer.rb, line 70
def to_gfa_field(datatype: default_gfa_datatype)
  case datatype
  when :B
    to_numeric_array.to_s
  when :J
    to_json
  when :cig
    to_cigar.to_s
  when :cgs
    map{|cig|cig.to_cigar.to_s}.join(",")
  when :lbs
    map{|os|os.to_oriented_segment.to_s}.join(",")
  when :H
    to_byte_array.to_s
  else
    map(&:to_s).join(",")
  end
end

to_numeric_array(validate: true) click to toggle source

Create a numeric array from an Array instance @param validate [Boolean] (default: true)

if +true+, validate the range of the numeric values, according
to the array subtype

@raise [RGFA::NumericArray::ValueError] if validate is set and

any value is not compatible with the subtype

@return [RGFA::NumericArray] the numeric array

# File lib/rgfa/numeric_array.rb, line 148
def to_numeric_array(validate: true)
  na = RGFA::NumericArray.new(self)
  na.validate! if validate
  na
end

to_oriented_segment() click to toggle source

Create and validate a segment end from an array @!macro segment_info_validation_errors @return [RGFA::OrientedSegment]

# File lib/rgfa/segment_info.rb, line 145
def to_oriented_segment
  to_segment_info(RGFA::OrientedSegment)
end

to_rgfa(validate: 2) click to toggle source

Converts an Array of strings or RGFA::Line instances into a RGFA instance. @return [RGFA] @!macro validate

# File lib/rgfa.rb, line 369
def to_rgfa(validate: 2)
  gfa = RGFA.new(validate: validate)
  each {|line| gfa << line}
  gfa.validate! if validate >= 1
  return gfa
end

to_rgfa_field_array(datatype=nil) click to toggle source

Create a {RGFA::FieldArray} from an array @param datatype [RGFA::Line::OPTFIELD_DATATYPE, nil] the datatype to use

# File lib/rgfa/field_array.rb, line 78
def to_rgfa_field_array(datatype=nil)
  if self.rgfa_field_array?
    RGFA::FieldArray.new(self[-2].to_sym, self[0..-3])
  elsif datatype.nil?
    raise RGFA::FieldArray::Error, "no datatype specified"
  else
    RGFA::FieldArray.new(datatype, self)
  end
end

to_rgfa_line(validate: 2) click to toggle source

Parses an array containing the fields of a RGFA file line and creates an object of the correct record type child class of {RGFA::Line} @note

This method modifies the content of the array; if you still
need the array, you must create a copy before calling it

@return [subclass of RGFA::Line] @raise [RGFA::Error] if the fields do not comply to the RGFA specification @param validate [Integer] (defaults to: 2)

see RGFA::Line#initialize

# File lib/rgfa/line.rb, line 723
def to_rgfa_line(validate: 2)
  RGFA::Line.subclass(shift).new(self, validate: validate)
end

to_segment_end() click to toggle source

Create and validate a segment end from an array @!macro segment_info_validation_errors @return [RGFA::SegmentEnd]

# File lib/rgfa/segment_info.rb, line 138
def to_segment_end
  to_segment_info(RGFA::SegmentEnd)
end

validate_gfa_field!(datatype, fieldname=nil) click to toggle source

@!macro validate_gfa_field

# File lib/rgfa/field_validator.rb, line 116
def validate_gfa_field!(datatype, fieldname=nil)
  begin
    case datatype
    when :J
      return
    when :Z
      return
    when :lbs
      map!(&:to_oriented_segment).each(&:validate!)
      return
    when :cig
      to_cigar.validate!
      return
    when :cgs
      map(&:to_cigar).each(&:validate!)
      return
    when :B
      to_numeric_array.validate!
      return
    when :H
      to_byte_array.validate!
      return
    end
  rescue => err
    raise RGFA::FieldParser::FormatError,
      "Invalid content for field #{fieldname}\n"+
      "Content: #{self.inspect}\n"+
      "Datatype: #{datatype}\n"+
      "Error: #{err}"
  end
  raise RGFA::FieldParser::FormatError,
      "Wrong type (#{self.class}) for field #{fieldname}\n"+
      "Content: #{self.inspect}\n"+
      "Datatype: #{datatype}"
end

Protected Instance Methods

to_segment_info(subclass) click to toggle source

# File lib/rgfa/segment_info.rb, line 151
def to_segment_info(subclass)
  return self if self.kind_of?(subclass)
  # support converting from gfa gem GraphVertex objects:
  if respond_to?(:segment) and respond_to?(:orient)
    return RGFA::OrientedSegment.new([segment.to_sym, orient.to_sym])
  end
  se = subclass.new(map {|e| e.kind_of?(String) ? e.to_sym : e})
  se.validate!
  return se
end