Class: Array

Inherits:
Object show all
Defined in:
lib/rgfa.rb,
lib/rgfa/line.rb,
lib/rgfa/cigar.rb,
lib/rgfa/byte_array.rb,
lib/rgfa/field_array.rb,
lib/rgfa/field_writer.rb,
lib/rgfa/segment_info.rb,
lib/rgfa/numeric_array.rb,
lib/rgfa/field_validator.rb

Overview

Method to create a numeric array from an array

Instance Method Summary collapse

Instance Method Details

#default_gfa_datatype ⇒ RGFA::Line::FIELD_DATATYPE

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Optional field GFA datatype to use, if none is provided

Returns:



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# 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? ⇒ Boolean

Is this possibly a RGFA::FieldArray instance?

(i.e. are the two last elements a datatype symbol and a zero byte?)

Returns:

  • (Boolean) 


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# 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 ⇒ RGFA::ByteArray

Create a RGFA::ByteArray from an Array instance

Returns:



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# File 'lib/rgfa/byte_array.rb', line 55

def to_byte_array
  RGFA::ByteArray.new(self)
end

#to_cigar ⇒ RGFA::CIGAR

Create a RGFA::CIGAR instance from the content of the array.

Returns:



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# File 'lib/rgfa/cigar.rb', line 139

def to_cigar
  RGFA::CIGAR.new(self)
end

#to_cigar_operation ⇒ RGFA::CIGAR::Operation

Create a RGFA::CIGAR::Operation instance from the content of the array.

Returns:



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# 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) ⇒ String

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Representation of the data for GFA fields; this method does not (in general) validate the string. The method can be overwritten for a given class, and may take the #default_gfa_datatype into consideration.

Returns:



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# 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) ⇒ RGFA::NumericArray

Create a numeric array from an Array instance

Parameters:

  • validate (Boolean) (defaults to: true) —

    (default: true) if true, validate the range of the numeric values, according to the array subtype

Returns:

Raises:



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# 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 ⇒ RGFA::OrientedSegment

Create and validate a segment end from an array

Returns:

Raises:



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# File 'lib/rgfa/segment_info.rb', line 145

def to_oriented_segment
  to_segment_info(RGFA::OrientedSegment)
end

#to_rgfa(validate: 2) ⇒ RGFA

Converts an Array of strings or RGFA::Line instances into a RGFA instance.

Parameters:

  • validate (Integer) (defaults to: 2) —

    (defaults to: 2) the validation level; see “Validation level” under RGFA::Line#initialize.

Returns:



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# 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) ⇒ Object

Create a RGFA::FieldArray from an array

Parameters:



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# 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) ⇒ subclass 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

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

Parameters:

  • validate (Integer) (defaults to: 2) —

    (defaults to: 2) see RGFA::Line#initialize

Returns:

Raises:

  • (RGFA::Error) —

    if the fields do not comply to the RGFA specification



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# 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 ⇒ RGFA::SegmentEnd

Create and validate a segment end from an array

Returns:

Raises:



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# File 'lib/rgfa/segment_info.rb', line 138

def to_segment_end
  to_segment_info(RGFA::SegmentEnd)
end

#validate_gfa_field!(datatype, fieldname = nil) ⇒ void

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

This method returns an undefined value.

Validates the object according to the provided datatype

Parameters:

Raises:



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# 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