SYNOPSIS

use Bio::Annotation::TagTree;
use Bio::Annotation::Collection;
my $col = Bio::Annotation::Collection->new();
# data structure can be an array reference with a data structure
# corresponding to that defined by Data::Stag:
my $sv = Bio::Annotation::TagTree->new(-tagname => 'mytag1',
-value => $data_structure);
$col->add_Annotation($sv);
# regular text passed is parsed based on the tagformat().
my $sv2 = Bio::Annotation::TagTree->new(-tagname => 'mytag2',
-tagformat => 'xml',
-value => $xmltext);
$col->add_Annotation($sv2);

DESCRIPTION

This takes tagged data values and stores them in a hierarchal structured element-value hierarchy (complements of Chris Mungall's Data::Stag module). Data can then be represented as text using a variety of output formats (indention, itext, xml, spxr). Furthermore, the data structure can be queried using various means. See Data::Stag for details.

Data passed in using value() or the '-value' parameter upon instantiation can either be:

1) an array reference corresponding to the data structure for Data::Stag;

2) a text string in 'xml', 'itext', 'spxr', or 'indent' format. The default format is 'xml'; this can be changed using tagformat() prior to using value() or by passing in the proper format using '-tagformat' upon instantiation;

3) another Bio::Annotation::TagTree or Data::Stag node instance. In both cases a deep copy (duplicate) of the instance is generated.

Beyond checking for an array reference no format guessing occurs (so, for roundtrip tests ensure that the IO formats correspond). For now, we recommend when using text input to set tagformat() to one of these formats prior to data loading to ensure the proper Data::Stag parser is selected. After data loading, the tagformat() can be changed to change the text string format returned by value(). (this may be rectified in the future)

This Annotation type is fully BioSQL compatible and could be considered a temporary replacement for nested Bio::Annotation::Collections, at least until BioSQL and bioperl-db can support nested annotation collections.

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via or the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

Chris Fields

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $sv = Bio::Annotation::TagTree->new();
 Function: Instantiate a new TagTree object
 Returns : Bio::Annotation::TagTree object
 Args    : -value => $value to initialize the object data field [optional]
           -tagname => $tag to initialize the tagname [optional]
           -tagformat => format for output [optional]
                      (types 'xml', 'itext', 'sxpr', 'indent', default = 'itext')
           -node => Data::Stag node or Bio::Annotation::TagTree instance

AnnotationI implementing functions

as_text

 Title   : as_text
 Usage   : my $text = $obj->as_text
 Function: return the string "Value: $v" where $v is the value
 Returns : string
 Args    : none

display_text

 Title   : display_text
 Usage   : my $str = $ann->display_text();
 Function: returns a string. Unlike as_text(), this method returns a string
           formatted as would be expected for the specific implementation.
           One can pass a callback as an argument which allows custom text
           generation; the callback is passed the current instance and any text
           returned
 Example :
 Returns : a string
 Args    : [optional] callback

hash_tree

 Title   : hash_tree
 Usage   : my $hashtree = $value->hash_tree
 Function: For supporting the AnnotationI interface just returns the value
           as a hashref with the key 'value' pointing to the value
           Maybe reimplement using Data::Stag::hash()?
 Returns : hashrf
 Args    : none

tagname

 Title   : tagname
 Usage   : $obj->tagname($newval)
 Function: Get/set the tagname for this annotation value.
           Setting this is optional. If set, it obviates the need to provide
           a tag to AnnotationCollection when adding this object.
 Example :
 Returns : value of tagname (a scalar)
 Args    : new value (a scalar, optional)

Specific accessors for TagTree

value

 Title   : value
 Usage   : $obj->value($newval)
 Function: Get/set the value for this annotation.
 Returns : value of value
 Args    : newvalue (optional)

tagformat

 Title   : tagformat
 Usage   : $obj->tagformat($newval)
 Function: Get/set the output tag format for this annotation.
 Returns : value of tagformat
 Args    : newvalue (optional) - format for the data passed into value
           must be of values 'xml', 'indent', 'sxpr', 'itext', 'perl'

node

 Title   : node
 Usage   : $obj->node()
 Function: Get/set the topmost Data::Stag node used for this annotation.  
 Returns : Data::Stag node implementation
           (default is Data::Stag::StagImpl)
 Args    : (optional) Data::Stag node implementation
           (optional)'copy' => flag to create a copy of the node

Data::Stag convenience methods

Because Data::Stag uses blessed arrays and the core Bioperl class uses blessed hashes, TagTree uses an internal instance of a Data::Stag node for data storage. Therefore the following methods actually delegate to the Data:::Stag internal instance.

For consistency (since one could recursively check child nodes), methods retain the same names as Data::Stag. Also, no 'magic' (AUTOLOAD'ed) methods are employed, simply b/c full-fledged Data::Stag functionality can be attained by grabbing the Data::Stag instance using node().

element

 Title   : element
 Usage   :
 Function: Returns the element name (key name) for this node
 Example :
 Returns : scalar
 Args    : none

data

 Title   : data
 Usage   :
 Function: Returns the data structure (array ref) for this node
 Example :
 Returns : array ref
 Args    : none

children

 Title   : children
 Usage   :
 Function: Get the top-level array of Data::Stag nodes or (if the top level is
           a terminal node) a scalar value.
           This is similar to StructuredValue's get_values() method, with the
           key difference being instead of array refs and scalars you get either
           Data::Stag nodes or the value for this particular node.
           For consistency (since one could recursively check nodes),
           we use the same method name as Data::Stag children().
 Example :
 Returns : an array
 Args    : none

subnodes

 Title   : subnodes
 Usage   :
 Function: Get the top-level array of Data::Stag nodes.  Unlike children(),
           this only returns an array of nodes (if this is a terminal node,
           no value is returned)
 Example :
 Returns : an array of nodes
 Args    : none

get

 Title   : get
 Usage   : 
 Function: Returns the nodes or value for the named element or path
 Example : 
 Returns : returns array of nodes or a scalar (if node is terminal)
           dependent on wantarray
 Args    : none

find

 Title   : find
 Usage   : 
 Function: Recursively searches for and returns the nodes or values for the
           named element or path
 Example : 
 Returns : returns array of nodes or scalars (for terminal nodes)
 Args    : none

findnode

 Title   : findnode
 Usage   : 
 Function: Recursively searches for and returns a list of nodes
           of the given element path
 Example : 
 Returns : returns array of nodes
 Args    : none

findval

 Title   : findval
 Usage   : 
 Function: 
 Example : 
 Returns : returns array of nodes or values
 Args    : none

addchild

 Title   : addchild
 Usage   : $struct->addchild(['name' => [['foo'=> 'bar1']]]);
 Function: add new child node to the current node.  One can pass in a node, TagTree,
           or data structure; for instance, in the above, this would translate
           to (in XML):
           <name>
             <foo>bar1</foo>
           </name>
 Returns : node
 Args    : first arg = element name
           all other args are added as tag-value pairs

add

 Title   : add
 Usage   : $struct->add('foo', 'bar1', 'bar2', 'bar3');
 Function: add tag-value nodes to the current node.  In the above, this would
           translate to (in XML):
           <foo>bar1</foo>
           <foo>bar2</foo>
           <foo>bar3</foo>
 Returns : 
 Args    : first arg = element name
           all other args are added as tag-value pairs

set

 Title   : set
 Usage   : $struct->set('foo','bar');
 Function: sets a single tag-value pair in the current node.  Note this
           differs from add() in that this replaces any data already present
 Returns : node
 Args    : first arg = element name
           all other args are added as tag-value pairs

unset

 Title   : unset
 Usage   : $struct->unset('foo');
 Function: unsets all key-value pairs of the passed element from the
           current node
 Returns : node
 Args    : element name

free

 Title   : free
 Usage   : $struct->free
 Function: removes all data from the current node
 Returns : 
 Args    :

hash

 Title   : hash
 Usage   : $struct->hash;
 Function: turns the tag-value tree into a hash, all data values are array refs
 Returns : hash
 Args    : first arg = element name
           all other args are added as tag-value pairs

pairs

 Title   : pairs
 Usage   : $struct->pairs;
 Function: turns the tag-value tree into a hash, all data values are scalar
 Returns : hash
 Args    : first arg = element name
           all other args are added as tag-value pairs, note that duplicates
           will be lost

qmatch

 Title    : qmatch
 Usage    : @persons = $s->qmatch('person', ('name'=>'fred'));
 Function : returns all elements in the node tree which match the
            element name and the key-value pair
 Returns  : Array of nodes
 Args     : return-element str, match-element str, match-value str

tnodes

 Title    : tnodes
 Usage    : @termini = $s->tnodes;
 Function : returns all terminal nodes below this node
 Returns  : Array of nodes
 Args     : return-element str, match-element str, match-value str

ntnodes

 Title    : ntnodes
 Usage    : @termini = $s->ntnodes;
 Function : returns all nonterminal nodes below this node
 Returns  : Array of nodes
 Args     : return-element str, match-element str, match-value str

StructureValue-like methods

get_all_values

 Title    : get_all_values
 Usage    : @termini = $s->get_all_values;
 Function : returns all terminal node values
 Returns  : Array of values
 Args     : return-element str, match-element str, match-value str

This is meant to emulate the values one would get from StructureValue's get_all_values() method. Note, however, using this method dissociates the tag-value relationship (i.e. you only get the value list, no elements)