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BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::TreeIO::phyloxml

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
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
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
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