Bio::SeqIO nexml
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Summary
Bio::SeqIO::nexml - NeXML sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::Nexml::Factory
Bio::Phylo::IO qw ( parse unparse )
Bio::Seq
Bio::Seq::SeqFactory
Inherit
Bio::SeqIO
Synopsis
Do not use this module directly. Use it via the Bio::SeqIO class.
Description
This object can transform Bio::Seq objects to and from NeXML format.
For more information on the NeXML standard, visit http://www.nexml.org.
Methods
_initialize
No description
Code
next_seqDescriptionCode
rewindDescriptionCode
docDescriptionCode
_parse
No description
Code
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
rewindcodeprevnextTop
 Title   : rewind
Usage : $seqio->rewind
Function: Resets the stream
Returns : none
Args : none
doccodeprevnextTop
 Title   : doc
Usage : $treeio->doc
Function: Returns the biophylo nexml document object
Returns : Bio::Phylo::Project
Args : none or Bio::Phylo::Project object
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq(@seq)
Function: Writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of 1 or more Bio::PrimarySeqI objects
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args); 
  $self->{_doc} = undef;
}
next_seqdescriptionprevnextTop
sub next_seq {
	my ($self) = @_;
    unless ( $self->{'_parsed'} ) {
    	#use a parse function to load all the sequence objects found in the nexml file at once
$self->_parse; } return $self->{'_seqs'}->[ $self->{'_seqiter'}++ ];
}
rewinddescriptionprevnextTop
sub rewind {
    my $self = shift;
    $self->{'_seqiter'} = 0;
}
docdescriptionprevnextTop
sub doc {
	my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_doc'} = $value;
	}
	return $obj->{'_doc'};
}
_parsedescriptionprevnextTop
sub _parse {
	my ($self) = @_;
	my $fac = Bio::Nexml::Factory->new();
	
    $self->{'_parsed'}   = 1;
    $self->{'_seqiter'} = 0;
	
	$self->doc(Bio::Phylo::IO->parse(
 	'-file'       => $self->{'_file'},
 	'-format'     => 'nexml',
 	'-as_project' => '1'
 	));
 
 	
 		
 	$self->{'_seqs'} = $fac->create_bperl_seq($self);
 		
 	
 	unless(@{ $self->{'_seqs'} } == 0)
 	{
# 		self->debug("no seqs in $self->{_file}");
}
}
write_seqdescriptionprevnextTop
sub write_seq {
	
	my ($self, $bp_seq) = @_;
	
	my $fac = Bio::Nexml::Factory->new();
	my $taxa = $fac->create_bphylo_taxa($bp_seq);
	my ($seq) = $fac->create_bphylo_seq($bp_seq, $taxa);
	
	my $matrix = Bio::Phylo::Factory->create_matrix('-type' => $seq->get_type());
	$matrix->insert($seq);
	$matrix->set_taxa($taxa);
	
	#set matrix label
my $feat = ($bp_seq->get_SeqFeatures())[0]; $matrix->set_name($feat->get_tag_values('matrix_label')); $self->doc(Bio::Phylo::Factory->create_project()); $self->doc->insert($matrix); my $ret = $self->_print($self->doc->to_xml()); $self->flush; return $ret } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Chase MillerTop
Email: chmille4@gmail.com
CONTRIBUTORSTop
Mark Jensen, maj@fortinbras.us
Rutger Vos, rutgeraldo@gmail.com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _