Module:Bio::TreeIO::phyloxml

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Bio::TreeIO::phyloxml
PDoc Bio::TreeIO::phyloxml
CPAN Bio::TreeIO::phyloxml
metaCPAN Bio::TreeIO::phyloxml



this is a temporary document, it will be gone once the PDoc link is in work.

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
 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
 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
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