--- name: "Bio::TreeIO::phyloxml" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::TreeIO::phyloxml" --- # Bio::TreeIO::phyloxml(3pm) TreeIO implementation for parsing PhyloXML format. ## 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://github.com/bioperl/bioperl-live/issues ``` ## 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'=>'') 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 ```