Bio::AlignIO nexml
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Summary
Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
Package variables
No package variables defined.
Included modules
Bio::Nexml::Factory
Bio::Phylo::IO qw ( parse unparse )
Inherit
Bio::AlignIO
Synopsis
Do not use this module directly. Use it via the Bio::AlignIO class.
Description
This object can transform Bio::SimpleAlign objects to and from
NeXML format. For more information on NeXML, visit http://www.nexml.org.
Methods
_initialize
No description
Code
next_alnDescriptionCode
rewindDescriptionCode
docDescriptionCode
_parse
No description
Code
write_alnDescriptionCode
Methods description
next_alncode    nextTop
 Title   : next_aln
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args :
See Bio::Align::AlignI
rewindcodeprevnextTop
 Title   : rewind
Usage : $alnio->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_alncodeprevnextTop
 Title   : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in nexml format
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
See Bio::Align::AlignI
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);  
  $self->{_doc} = undef;
}
next_alndescriptionprevnextTop
sub next_aln {
	my ($self) = @_;
    unless ( $self->{'_parsed'} ) {
    	#use a parse function to load all the alignment objects found in the nexml file at once
$self->_parse; } return $self->{'_alns'}->[ $self->{'_alnsiter'}++ ];
}
rewinddescriptionprevnextTop
sub rewind {
    my $self = shift;
    $self->{'_alniter'} = 0;
}
docdescriptionprevnextTop
sub doc {
	my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_doc'} = $value;
	}
	return $obj->{'_doc'};
}
_parsedescriptionprevnextTop
sub _parse {
	my ($self) = @_;

    $self->{'_parsed'}   = 1;
    $self->{'_alnsiter'} = 0;
    my $fac = Bio::Nexml::Factory->new();
	
	$self->doc(parse(
 	'-file'       => $self->{'_file'},
 	'-format'     => 'nexml',
 	'-as_project' => '1'
 	));

	$self->{'_alns'} = $fac->create_bperl_aln($self);
 	if(@{ $self->{'_alns'} } == 0)
 	{
 		self->debug("no seqs in $self->{_file}");
 	}
}
write_alndescriptionprevnextTop
sub write_aln {
	my ($self, $aln) = @_;
	
    my $fac = Bio::Nexml::Factory->new();
    my $taxa = $fac->create_bphylo_taxa($aln);
	my ($matrix) = $fac->create_bphylo_aln($aln, $taxa);
	$matrix->set_taxa($taxa);
	
	$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
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/
AUTHORSTop
Chase Miller
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 _