The GO::AnnotatedGene package allows creation of objects that contains the details of a gene as determined from a gene_associations file. Typically these objects will contain the following information:
Column Cardinality Contents ------ ----------- ------------------------------------------------------------- 1 1 Database identifier of the annotated gene 2 1 Standard name of the annotated gene 9 0,1 Name of the product of the annotated gene 10 0,n Alias(es) of the annotated gene 11 1 type of the annotated gene (one of gene, transcript, protein)
Further details can be found at:
It is expected that AnnotatedGene objects will typically be created by concrete subclasses of AnnotationProvider
This is the constructor for a GO::AnnotatedGene object
It expects to receive the following named arguments:
databaseId : The databaseId of the annotated gene standardName : The standardName of the annotated gene type : The type of the annotated gene (one of gene, transcript, protein)
In addition, the following optional arguments may also be provided:
productName : The name of the product of the annotated gene aliases : A reference to an array of aliases
my $annotatedGene = GO::AnnotatedGene->new(databaseId => $databaseId, standardName => $standardName, type => $type, productName => $productName, aliases => $aliases);
This public instance method returns the databaseId.
my $databaseId = $annotatedGene->databaseId;
This public instance method returns the standardName.
my $standardName = $annotatedGene->standardName;
This public instance method returns the type of the annotated gene.
my $type = $annotatedGene->type;
This public instance method returns the product name of the annotated gene, if one exists. Otherwise it returns undef.
my $productName = $annotatedGene->productName;
This public instance method returns an array of aliases for the annotated gene. If no aliases exist, then an empty array will be returned.
my @aliases = $annotatedGene->aliases;
This protected method simply provides a simple way for concrete subclasses to deal with missing arguments from method calls. It will die with an appropriate error message.
Gavin Sherlock, firstname.lastname@example.org