class Bio::NeXML::SeqRow

Public Instance Methods

add_sequence( sequence ) click to toggle source

Add a sequence( row ) to the matrix.

  • Arguments :

sequence( required ) - a Bio::NeXML::Sequence object.

  • Returns : self.

    matrix.add_matrix( sequence )
    matrix.sequences               #=> [ .. sequence .. ]
    sequence.matrix                #=> matrix
    
# File lib/bio/db/nexml/matrix.rb, line 677
def add_sequence( sequence )
  # dummy for rdoc
end
delete_sequence( sequence ) click to toggle source

Remove a sequence( row ) from the matrix.

  • Arguments :

sequence( required ) - a Bio::NeXML::Sequence object.

  • Returns : the deleted object.

    matrix.delete_sequence( sequence )
    matrix.sequences               #=> [ .. .. ]
    sequence.matrix                #=> nil
    
# File lib/bio/db/nexml/matrix.rb, line 688
def delete_sequence( sequence )
  # dummy for rdoc
end
each_sequence() click to toggle source

Iterate over each sequence ( Bio::NeXML::Sequence object ) defined for the matrix. Returns an Enumerator if no block is provided.

# File lib/bio/db/nexml/matrix.rb, line 715
def each_sequence
  # dummy for rdoc
end
has_sequence?( sequence ) click to toggle source

Returns true if the given sequence( Bio::NeXML::Sequence object ) is defined for the matrix.

# File lib/bio/db/nexml/matrix.rb, line 709
def has_sequence?( sequence )
  # dummy for rdoc
end
number_of_sequences() click to toggle source

Returns the number of sequences defined for the matrix.

# File lib/bio/db/nexml/matrix.rb, line 720
def number_of_sequences
  # dummy for rdoc
end
sequences() click to toggle source

Returns an array of sequences ( Bio::NeXML::Sequence objects ) for the matrix.

matrix.sequences  #=> [ .. .. ]
# File lib/bio/db/nexml/matrix.rb, line 694
def sequences
  # dummy for rdoc
end
sequences=( sequences ) click to toggle source

Add sequences to the matirx. This function will override previous sequences if any.

  • Arguments :

sequences( required ) - an array of Bio::NeXML::Sequence object.

matrix.sequences = [ sequence ]
matrix.sequences    #=> [ sequence ]
sequence.matrix     #=> matrix
# File lib/bio/db/nexml/matrix.rb, line 704
def sequences=( sequences )
  # dummy for rdoc
end
to_xml() click to toggle source
# File lib/bio/db/nexml/matrix.rb, line 724
def to_xml
  node = @@writer.create_node( "row", @@writer.attributes( self, :id, :otu, :label ) )
  node << self.sequences.first.to_xml
  node
end