go::objfactory(3pm) [debian man page]

GO::ObjFactory(3pm)					User Contributed Perl Documentation				       GO::ObjFactory(3pm)

NAME

	 GO::ObjFactory     - GO Object Factory

SYNOPSIS

       You should not use this method directly

DESCRIPTION

       You only need to be aware of this class if you are generating new objects. You should not directly create objects like this:

	 $term = GO::Model::Term->new($h);

       Instead you should create them like this:

	 $fac = GO::ObjFactory->new();
	 $term = $fac->create_term_obj($h);

       Usually you do not need to instantiate a factory, as all objects created with a factory carry around a reference to that factory, so you
       can do this:

	 # $graph object was previously created via a factory
	 $term = $graph->create_term_obj($h);

       If you are only using the go-perl module, then factories do not buy you much. However, if you are also using go-db-perl and GO::AppHandle,
       then factories can be useful - all objects generated from the database will be attached to an AppHandle which means that "lazy loading" can
       be used. See GO::AppHandle in go-db-perl for details

   create_term_obj
	 Usage	 - $term = $apph->create_term_obj;
	 Returns - L<GO::Model::Term>
	 Args	 -

   create_relationship_obj
	 Usage	 - $relationship = $apph->create_relationship_obj;
	 Returns - L<GO::Model::Relationship>
	 Args	 -

   create_xref_obj
	 Usage	 - $xref = $apph->create_xref_obj;
	 Returns - L<GO::Model::Xref>
	 Args	 -

   create_evidence_obj
	 Usage	 - $evidence = $apph->create_evidence_obj;
	 Returns - L<GO::Model::Evidence>
	 Args	 -

   create_seq_obj
	 Usage	 - $seq = $apph->create_seq_obj;
	 Returns - L<GO::Model::Seq>
	 Args	 -

   create_db_obj
	 Usage	 - $db = $apph->create_db_obj;
	 Returns - L<GO::Model::DB>
	 Args	 -

   create_association_obj
	 Usage	 - $association = $apph->create_association_obj;
	 Returns - L<GO::Model::Association>
	 Args	 -

   create_gene_product_obj
	 Usage	 - $gene_product = $apph->create_gene_product_obj;
	 Synonym - create_product_obj
	 Returns - L<GO::Model::GeneProduct>
	 Args	 -

   create_species_obj
	 Usage	 - $species = $apph->create_species_obj;
	 Returns - L<GO::Model::Species>
	 Args	 -

   create_graph_obj
	 Usage	 - $graph = $apph->create_graph_obj;
	 Returns - L<GO::Model::Graph>
	 Args	 -

perl v5.14.2							    2010-05-12						       GO::ObjFactory(3pm)

Bio::Structure::Model(3pm)				User Contributed Perl Documentation				Bio::Structure::Model(3pm)

NAME

       Bio::Structure::Model - Bioperl structure Object, describes a Model

SYNOPSIS

	 #add synopsis here

DESCRIPTION

       This object stores a Bio::Structure::Chain

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 the
       web:

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

AUTHOR - Kris Boulez
       Email kris.boulez@algonomics.com

APPENDIX

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

   new()
	Title	: new()
	Usage	: $struc = Bio::Structure::Model->new(
						  -id  => 'human_id',
						  );

	Function: Returns a new Bio::Structure::Model object from basic
	       constructors. Probably most called from Bio::Structure::IO.
	Returns : a new Bio::Structure::Model object

   chain()
	Title	: chain
	Usage	:
	Function: will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   add_chain()
	Title	: add_chain
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   entry()
	Title	: entry
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   id()
	Title	: id
	Usage	: $model->id("model 5")
	Function: Gets/sets the ID for this model
	Returns : the ID
	Args	: the ID

   residue()
	Title	: residue
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   add_residue()
	Title	: add_residue
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   _remove_chains()
	Title	: _remove_chains
	Usage	:
	Function: Removes the chains attached to a Model. Tells the chains they
	       don't belong to this Model any more
	Returns :
	Args	:

   _remove_entry()
	Title	: _remove_entry
	Usage	:
	Function: Removes the Entry this Model is atttached to.
	Returns :
	Args	:

   _create_default_chain()
	Title	: _create_default_chain
	Usage	:
	Function: Creates a default Chain for this Model. Typical situation
	       in an X-ray structure where there is only one chain
	Returns :
	Args	:

   _grandparent()
	Title	: _grandparent
	Usage	:
	Function: get/set a symbolic reference to our grandparent
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						Bio::Structure::Model(3pm)