NAME

       Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format.

SYNOPSIS

         # do not use this module directly
         use Bio::TreeIO;
         my $treeio = Bio::TreeIO->new(-format => 'phyloxml',
                                       -file => 'tree.dnd');
         my $tree = $treeio->next_tree;

DESCRIPTION

       This module handles parsing and writing of phyloXML format.

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted viax the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mira Han

       Email mirhan@indiana.edu

APPENDIX

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

   next_tree
        Title   : next_tree
        Usage   : my $tree = $treeio->next_tree
        Function: Gets the next tree in the stream
        Returns : Bio::Tree::TreeI
        Args    : none

   add_attribute
        Title   : add_phyloXML_annotation
        Usage   : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -attr=>"id_source = \"A\"")
        Function: add attributes to an object
        Returns : the node that we added annotations to
        Args    : -obj   => object that will have the Annotation. (Bio::Tree::AnnotatableNode)
                  -attr  => string in the form "A = B", where A is the attribute name and B is the attribute value

   add_phyloXML_annotation
        Title   : add_phyloXML_annotation
        Usage   : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -xml=>$xmlstring)
                  my $tree = $treeio->add_phyloXML_annotation('-obj'=>$tree, '-xml'=>'<sequence_relation id_ref_0="A" id_ref_1="B" type="orthology"/>')

        Function: add annotations to a node in the phyloXML format string
        Returns : the node that we added annotations to
        Args    : -obj   => object that will have the Annotation. (Bio::Tree::AnnotatableNode)
                  -xml  => string in phyloXML format that describes the annotation for the node

   write_tree
        Title   : write_tree
        Usage   : $treeio->write_tree($tree);
        Function: Write a tree out to data stream in phyloxml format
        Returns : none
        Args    : Bio::Tree::TreeI object

   _write_tree_Helper_annotatableNode
        Title   : _write_tree_Helper_annotatableNode
        Usage   : internal method used by write_tree, not to be used directly
        Function: recursive helper function of write_tree for the annotatableNodes.
                  translates annotations into xml elements.
        Returns : string describing the node
        Args    : Bio::Node::AnnotatableNode object, string

   _write_tree_Helper_generic
        Title   : _write_tree_Helper_generic
        Usage   : internal method used by write_tree, not to be used directly
        Function: recursive helper function of write_tree for generic NodesI.
                  all tags are translated into property elements.
        Returns : string describing the node
        Args    : Bio::Node::NodeI object, string

   _relation_to_string
        Title   : _relation_to_string
        Usage   : internal method used by write_tree, not to be used directly
        Function: internal function used by write_tree to translate Annotation::Relation objects into xml elements.
        Returns : string describing the node
        Args    : Bio::Node::AnnotatableNode (or Bio::SeqI) object that contains the Annotation::Relation,
                  the Annotation::Relation object,
                  the string

   read_annotation
        Title   : read_annotation
        Usage   : $treeio->read_annotation(-obj=>$node, -path=>$path, -attr=>1);
        Function: read text value (or attribute value) of the annotations corresponding to the element path
        Returns : list of text values of the annotations matching the path
        Args    : -obj   => object that contains the Annotation. (Bio::Tree::AnnotatableNode or Bio::SeqI)
                  -path  => path of the nested elements
                  -attr  => Boolean value to indicate whether to get the attribute of the element or the text value.
                           (default is 0, meaning text value is returned)

Methods for parsing the XML document

   processXMLNode
        Title   : processXMLNode
        Usage   : $treeio->processXMLNode
        Function: read the XML node and process according to the node type
        Returns : none
        Args    : none

   processAttribute
        Title   : processAttribute
        Usage   : $treeio->processAttribute(\%hash_for_attribute);
        Function: reads the attributes of the current element into a hash
        Returns : none
        Args    : hash reference where the attributes will be stored.

   element_phylogeny
        Title   : element_phylogeny
        Usage   : $treeio->element_phylogeny
        Function: initialize the parsing of a tree
        Returns : none
        Args    : none

   end_element_phylogeny
        Title   : end_element_phylogeny
        Usage   : $treeio->end_element_phylogeny
        Function: ends the parsing of a tree building a Tree::TreeI object.
        Returns : Tree::TreeI
        Args    : none

   element_clade
        Title   : element_clade
        Usage   : $treeio->element_clade
        Function: initialize the parsing of a node
                  creates a new AnnotatableNode with annotations
        Returns : none
        Args    : none

   end_element_clade
        Title   : end_element_clade
        Usage   : $treeio->end_element_clade
        Function: ends the parsing of a node
        Returns : none
        Args    : none

   element_relation
        Title   : element_relation
        Usage   : $treeio->element_relation
        Function: starts the parsing of clade relation & sequence relation
        Returns : none
        Args    : none

   end_element_relation
        Title   : end_element_relation
        Usage   : $treeio->end_element_relation
        Function: ends the parsing of clade relation & sequence relation
        Returns : none
        Args    : none

   element_default
        Title   : element_default
        Usage   : $treeio->element_default
        Function: starts the parsing of all other elements
        Returns : none
        Args    : none

   end_element_default
        Title   : end_element_default
        Usage   : $treeio->end_element_default
        Function: ends the parsing of all other elements
        Returns : none
        Args    : none

   annotateNode
        Title   : annotateNode
        Usage   : $treeio->annotateNode($element, $ac)
        Function: adds text value and attributes to the AnnotationCollection
                  that has element name as key. If there are nested elements,
                  optional AnnotationCollections are added recursively,
                  with the nested element name as key.
                  The structure of each AnnotationCollection is
                  'element' => AnnotationCollection {
                      '_text' => SimpleValue (text value)
                      '_attr' => AnnotationCollection {
                          attribute1 => SimpleValue (attribute value 1)
                          attribute2 => SimpleValue (attribute value 2)
                          ...
                      }
                      ['nested element' => AnnotationCollection ]
                  }
        Returns : none
        Args    : none

Methods for exploring the document

   current_attr
        Title   : current_attr
        Usage   : $attr_hash = $treeio->current_attr;
        Function: returns the attribute hash for current item
        Returns : reference of the attribute hash
        Args    : none

   prev_attr
        Title   : prev_attr
        Usage   : $hash_ref = $treeio->prev_attr
        Function: returns the attribute hash for previous item
        Returns : reference of the attribute hash
        Args    : none

   current_element
        Title   : current_element
        Usage   : $element = $treeio->current_element
        Function: returns the name of the current element
        Returns : string (element name)
        Args    : none

   prev_element
        Title   : prev_element
        Usage   : $element = $treeio->current_element
        Function: returns the name of the previous element
        Returns : string (element name)
        Args    : none

   treetype
        Title   : treetype
        Usage   : $obj->treetype($newval)
        Function: returns the tree type (default is Bio::Tree::Tree)
        Returns : value of treetype
        Args    : newvalue (optional)

   nodetype
        Title   : nodetype
        Usage   : $obj->nodetype($newval)
        Function: returns the node type (default is Bio::Node::AnnotatableNode)
        Returns : value of nodetype
        Args    : newvalue (optional)

Methods for implementing to_string callback for AnnotatableNode

   node_to_string
        Title   : node_to_string
        Usage   : $annotatablenode->to_string_callback(\&node_to_string)
        Function: set as callback in AnnotatableNode, prints the node information in string
        Returns : string of node information
        Args    : none

   print_annotation
        Title   : print_annotation
        Usage   : $str = $annotatablenode->print_annotation($str, $annotationcollection)
        Function: prints the annotationCollection in a phyloXML format.
        Returns : string of annotation information
        Args    : string to which the Annotation should be concatenated to,
                  annotationCollection that holds the Annotations

   print_attr
        Title   : print_attr
        Usage   : $str = $annotatablenode->print_attr($str, $annotationcollection)
        Function: prints the annotationCollection in a phyloXML format.
        Returns : string of attributes
        Args    : string to which the Annotation should be concatenated to,
                  AnnotationCollection that holds the attributes

   print_sequence_annotation
        Title   : print_sequence_annotation
        Usage   : $str = $node->print_seq_annotation( $str, $seq );
        Function: prints the Bio::Seq object associated with the node
                  in a phyloXML format.
        Returns : string that describes the sequence
        Args    : string to which the Annotation should be concatenated to,
                  Seq object to print in phyloXML