NAME

Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.

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.

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 the bugs and their resolution. Bug reports can be submitted via or the web:

https://redmine.open-bio.org/projects/bioperl/

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq