class Bio::NeXML::SeqRow
Public Instance Methods
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
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
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
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
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
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
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
# 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