NAME

       Bio::NexmlIO - stream handler for NeXML documents

SYNOPSIS

           #Instantiate a Bio::Nexml object and link it to a file
           my $in_nexml = Bio::Nexml->new(-file => 'nexml_doc.xml', -format => 'Nexml');

               #Read in some data
               my $bptree1 = $in_nexml->next_tree();
               my $bpaln1  = $in_nexml->next_aln();
               my $bpseq1  = $in_nexml->next_seq();

               #Use/manipulate data
               ...

               #Write data to nexml file
               my $out_nexml = Bio::Nexml->new(-file => '>new_nexml_doc.xml', -format => 'Nexml');
               $out_nexml->to_xml();

DESCRIPTION

       Bio::NexmlIO is an I/O handler for a NeXML document.  A NeXML document can represent three
       different data types: simple sequences, alignments, and trees. NexmlIO has four main
       methods next_tree, next_seq, next_aln, and write. NexmlIO returns bioperl seq, tree, and
       aln objects which can be manipulated then passed to the write method of a new NexmlIO
       instance to allow the creation of a NeXML document.

       Each bioperl object contains all the information necessary to recreate a Bio::Phylo::Taxa
       object, so each time a bioperl object is converted to a biophylo object, the bioperl
       object is checked to see if its associated taxa has already been created (against a hash
       using the NexmlIO_ID and Taxa_ID to create a unique string). If not, it is created; if so,
       that taxa object is used to link the Bio::Phylo tree or matrix.

       For more information on the NeXML format, see <http://www.nexml.org>.

FEEDBACK

   Mailing Lists
       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
       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 Bugs
       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/

AUTHOR - Chase Miller

       Email chmille4@gmail.com

CONTRIBUTORS

       Mark A. Jensen, maj -at- fortinbras -dot- com

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

CONSTRUCTOR

   new
        Title   : new
        Usage   : my $in_nexmlIO = Bio::NexmlIO->new(-file => 'data.nexml.xml');
        Function: Creates a L<Bio::NexmlIO> object linked to a stream
        Returns : a L<Bio::NexmlIO> object
        Args    : file name

        See L<Bio::Root::IO>

   doc
        Title   : doc
        Usage   : my $nexml_doc = $in_nexmlIO->doc();
        Function: returns a L<Bio::Phylo::Project> object that contains all the Bio::Phylo data objects parsed from the stream
        Returns : a L<Bio::Phylo::Project> object
        Args    : none

ITERATORS

   next_tree
        Title   : next_tree
        Usage   : $tree = $stream->next_tree
        Function: Reads the next tree object from the stream and returns it.
        Returns : a L<Bio::Tree::Tree> object
        Args    : none

       See Bio::Root::IO, Bio::Tree::Tree

   next_seq
        Title   : next_seq
        Usage   : $seq = $stream->next_seq
        Function: Reads the next seq object from the stream and returns it.
        Returns : a L<Bio::Seq> object
        Args    : none

       See Bio::Root::IO, Bio::Seq

   next_aln
        Title   : next_aln
        Usage   : $aln = $stream->next_aln
        Function: Reads the next aln object from the stream and returns it.
        Returns : a L<Bio::SimpleAlign> object
        Args    : none

       See Bio::Root::IO, Bio::SimpleAlign

   rewind_seq
        Title   : rewind_seq
        Usage   : $stream->rewind_seq
        Function: Resets the stream for seqs
        Returns : none
        Args    : none

       See Bio::Root::IO, Bio::Seq

   rewind_aln
        Title   : rewind_aln
        Usage   : $stream->rewind_aln
        Function: Resets the stream for alns
        Returns : none
        Args    : none

       See Bio::Root::IO, Bio::Simple::Align

   rewind_tree
        Title   : rewind_tree
        Usage   : $stream->rewind_tree
        Function: Resets the stream for trees
        Returns : none
        Args    : none

       See Bio::Root::IO, Bio::tree::tree

   write
        Title   : write
        Usage   : $stream->write(-alns => $alns,-seqs => $seqs,-trees => $trees)
        Function: converts BioPerl seq, tree, and aln objects into Bio::Phylo
                  seq, tree, and aln objects, constructs a Bio::Phylo::Project
                  object made up of the newly created Bio::Phylo objects, and
                  writes the Bio::Phylo:Project object to the stream as a valid
                  nexml document
        Returns : none
        Args    : \@L<Bio::Seq>, \@L<Bio::SimpleAlign>, \@L<Bio::Tree::Tree>

       See Bio::Root::IO, Bio::tree::tree, Bio::Seq, Bio::SimpleAlign

   extract_seqs
        Title   : extract_seqs
        Usage   : $nexmlIO->extract_seqs(-file => ">$outfile", -format => $format)
        Function: converts BioPerl seqs stored in the NexmlIO object into the provided
                          format and writes it to the provided file. Uses L<Bio::SeqIO> to do
                          the conversion and writing.
        Returns : none
        Args    : file to write to, format to be converted to

       See Bio::Seq, Bio::SeqIO

   extract_alns
        Title   : extract_alns
        Usage   : $nexmlIO->extract_alns(-file => ">$outfile", -format => $format)
        Function: converts BioPerl alns stored in the NexmlIO object into the provided
                          format and writes it to the provided file. Uses L<Bio::AlignIO> to do
                          the conversion and writing.
        Returns : none
        Args    : file to write to, format to be converted to

       See Bio::SimpleAlign, Bio::AlignIO

   extract_trees
        Title   : extract_trees
        Usage   : $nexmlIO->extract_trees(-file => ">$outfile", -format => $format)
        Function: converts BioPerl trees stored in the NexmlIO object into the provided
                          format and writes it to the provided file. Uses L<Bio::TreeIO> to do
                          the conversion and writing.
        Returns : none
        Args    : file to write to, format to be converted to

       See Bio::Tree::Tree, Bio::TreeIO