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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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