Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
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);
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.
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
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:
http://bugzilla.open-bio.org/
Chris Fields
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none
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
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
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)
Title : value Usage : $obj->value($newval) Function: Get/set the value for this annotation. Returns : value of value Args : newvalue (optional)
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'
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
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().
Title : element Usage : Function: Returns the element name (key name) for this node Example : Returns : scalar Args : none
Title : data Usage : Function: Returns the data structure (array ref) for this node Example : Returns : array ref Args : none
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
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
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
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
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
Title : findval Usage : Function: Example : Returns : returns array of nodes or values Args : none
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
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
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
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
Title : free Usage : $struct->free Function: removes all data from the current node Returns : Args :
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
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
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
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
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
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)
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.