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

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

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)

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)