go::model::geneproduct(3pm) [debian man page]
GO::Model::GeneProduct(3pm) User Contributed Perl Documentation GO::Model::GeneProduct(3pm) NAME
GO::Model::GeneProduct - gene product in a particular species DESCRIPTION
represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a gene may have >1 product) acc Usage - Returns - Args - symbol Usage - Returns - Args - type Usage - Returns - Args - full_name Usage - Returns - Args - as_str Usage - Returns - Args - add_synonym synonym_list accessor: gets/set list of synonyms [array reference] speciesdb Usage - Returns - Args - add_seq Usage - Returns - Args - GO::Model::Seq seq_list Usage - Returns - GO::Model::Seq listref Args - seq Usage - Returns - GO::Model::Seq Args - returns representative sequence object for this product properties Usage - Returns - hashref Args - hashref set_property Usage - $sf->set_property("wibble", "on"); Returns - Args - property key, property scalar note: the property is assumed to be multivalued, therefore $sf->set_property($k, $scalar) will add to the array, and $sf->set_property($k, $arrayref) will set the array get_property Usage - Returns - first element of the property Args - property key get_property_list Usage - Returns - the property arrayref Args - property key to_fasta Usage - Returns - Args - returns the longest seq by default perl v5.14.2 2013-02-07 GO::Model::GeneProduct(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)