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.\" ========================================================================
.\"
.IX Title "Bio::NexmlIO 3pm"
.TH Bio::NexmlIO 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::NexmlIO \- stream handler for NeXML documents
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    #Instantiate a Bio::Nexml object and link it to a file
\&    my $in_nexml = Bio::Nexml\->new(\-file => \*(Aqnexml_doc.xml\*(Aq, \-format => \*(AqNexml\*(Aq);
\&
\&        #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 => \*(Aq>new_nexml_doc.xml\*(Aq, \-format => \*(AqNexml\*(Aq);
\&        $out_nexml\->to_xml();
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
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.
.PP
For more information on the NeXML format, see <http://www.nexml.org>.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Chase Miller"
.IX Header "AUTHOR - Chase Miller"
Email chmille4@gmail.com
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Mark A. Jensen, maj \-at\- fortinbras \-dot\- com
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SH "CONSTRUCTOR"
.IX Header "CONSTRUCTOR"
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $in_nexmlIO = Bio::NexmlIO\->new(\-file => \*(Aqdata.nexml.xml\*(Aq);
\& 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>
.Ve
.SS "doc"
.IX Subsection "doc"
.Vb 5
\& 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
.Ve
.SH "ITERATORS"
.IX Header "ITERATORS"
.SS "next_tree"
.IX Subsection "next_tree"
.Vb 5
\& 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
.Ve
.PP
See Bio::Root::IO, Bio::Tree::Tree
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& 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
.Ve
.PP
See Bio::Root::IO, Bio::Seq
.SS "next_aln"
.IX Subsection "next_aln"
.Vb 5
\& 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
.Ve
.PP
See Bio::Root::IO, Bio::SimpleAlign
.SS "rewind_seq"
.IX Subsection "rewind_seq"
.Vb 5
\& Title   : rewind_seq
\& Usage   : $stream\->rewind_seq
\& Function: Resets the stream for seqs
\& Returns : none
\& Args    : none
.Ve
.PP
See Bio::Root::IO, Bio::Seq
.SS "rewind_aln"
.IX Subsection "rewind_aln"
.Vb 5
\& Title   : rewind_aln
\& Usage   : $stream\->rewind_aln
\& Function: Resets the stream for alns
\& Returns : none
\& Args    : none
.Ve
.PP
See Bio::Root::IO, Bio::Simple::Align
.SS "rewind_tree"
.IX Subsection "rewind_tree"
.Vb 5
\& Title   : rewind_tree
\& Usage   : $stream\->rewind_tree
\& Function: Resets the stream for trees
\& Returns : none
\& Args    : none
.Ve
.PP
See Bio::Root::IO, Bio::tree::tree
.SS "write"
.IX Subsection "write"
.Vb 9
\& 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    : \e@L<Bio::Seq>, \e@L<Bio::SimpleAlign>, \e@L<Bio::Tree::Tree>
.Ve
.PP
See Bio::Root::IO, Bio::tree::tree, Bio::Seq, Bio::SimpleAlign
.SS "extract_seqs"
.IX Subsection "extract_seqs"
.Vb 7
\& 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
.Ve
.PP
See Bio::Seq, Bio::SeqIO
.SS "extract_alns"
.IX Subsection "extract_alns"
.Vb 7
\& 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
.Ve
.PP
See Bio::SimpleAlign, Bio::AlignIO
.SS "extract_trees"
.IX Subsection "extract_trees"
.Vb 7
\& 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
.Ve
.PP
See Bio::Tree::Tree, Bio::TreeIO