Provided by: libbio-perl-perl_1.7.2-2_all 
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'=>'<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