Bio::TreeIO::phyloxml.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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_phyloXML_annotation

  Title   : add_phyloXML_annotation
  Usage   : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -xml=>$xmlstring)
  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