Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bio::treeio::phyloxml(3pm) [debian man page]

Bio::TreeIO::phyloxml(3pm)				User Contributed Perl Documentation				Bio::TreeIO::phyloxml(3pm)

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 perl v5.14.2 2012-03-02 Bio::TreeIO::phyloxml(3pm)
Man Page

Featured Tech Videos