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)
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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)