go::model::evidence(3pm) [debian man page]

GO::Model::Evidence(3pm)				User Contributed Perl Documentation				  GO::Model::Evidence(3pm)

NAME

	 GO::Model::Evidence - evidence for an association

SYNOPSIS

	 my $ev_l = $association->evidence_list;
	 foreach my $ev (@$ev_l) {
	   print "Evidence for association %s : %s
",
	     $association->gene_product->symbol,
	     $ev->code;
	 }

DESCRIPTION

       evidence for an association

       see http://www.geneontology.org/GO.evidence.html for a list of evidence codes

   code
	 Usage	 - $ev->code("IEA");
	 Returns -
	 Args	 -

       gets/sets the evidence code

       see http://www.geneontology.org/GO.evidence.html

   seq_acc
	 Usage	 -
	 Returns -
	 Args	 -

       gets/sets the sequence accesion GO::Model::Xref

       ALPHA CODE  - API may change

       used to set the GO::Model::Xref list from a text string. eg

	 $ev->seq_acc("SGD:RRP41; SGDID:L0003550");

       will actually add two GO::Model::Xref objects

       This method doesnt really belong in the GO::Model::* hierarchy as it contains parsing code. Its a minor hack mainly due to the fact that
       this data is still denormalized in the database.

   add_seq_xref
	 Usage	 -
	 Returns -
	 Args	 -

       equivalent to WITH column in gene_association files, and evidence_dbxref tables in db

   add_pub_xref
	 Usage	 -
	 Returns -
	 Args	 -

   xref
	 Usage	 -
	 Returns -
	 Args	 -

       gets/sets the literature or sequence reference GO::Model::Xref

       NOTE: at some point we may want to deprecate this method and persuade API client code to call

	 $ev->literature_xref

       instead, to make explicit the fact that this is a literature reference as opposed to a sequence reference

   xref_list
	 Usage	 -
	 Returns - GO::Model::Xref listref
	 Args	 -

       returns all (sequence and literature) references

   xref
	 Usage	 -
	 Returns -
	 Args	 -

       deprected - sets first pub_xref_list

   valid_codes
	 Usage	 - print join("; ", GO::Model::Evidence->valid_codes);
	 Returns - string array
	 Args	 -

       list of valid evidence codes

perl v5.14.2							    2013-02-07						  GO::Model::Evidence(3pm)

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

NAME

       Bio::Structure::Chain - Bioperl structure Object, describes a chain

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::Chain->new(
				  -id  => 'human_id',
				  -accession_number => 'AL000012',
						  );

	Function: Returns a new Bio::Structure::Chain object from basic
		       constructors. Usually called from Bio::Structure::IO.
	Returns : a new Bio::Structure::Chain object

   residue()
	Title	: residue
	Usage	:
	Function:  nothing useful until I get symbolic references to do what I want
	Returns :
	Args	:

   add_residue()
	Title	: add_residue
	Usage	:
	Function: nothing useful until I get symbolic references to do what I want
	Returns :
	Args	:

   model()
	Title	: model
	Usage	:
	Function: nothing useful until I get symbolic references to do what I want
	Returns :
	Args	:

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

   _remove_residues()
	Title	: _remove_residues
	Usage	:
	Function:
	Returns :
	Args	:

   _remove_model()
	Title	: _remove_model
	Usage	:
	Function: Removes the Model this Chain is atttached to.
	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::Chain(3pm)