GO::AnnotatedGene(3) User Contributed Perl Documentation GO::AnnotatedGene(3)NAME - will provide an object to hold info about a gene with GO annotation
GO::AnnotatedGeneDESCRIPTION
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:
http://www.geneontology.org/doc/GO.annotation.html#file
It is expected that AnnotatedGene objects will typically be created by
concrete subclasses of AnnotationProvider
TODO
A lot....
Constructor
new
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
Usage:
my $annotatedGene = GO::AnnotatedGene->new(databaseId => $databaseId,
standardName => $standardName,
type => $type,
productName => $productName,
aliases => $aliases);
Public Instance Methods
databaseId
This public instance method returns the databaseId.
Usage :
my $databaseId = $annotatedGene->databaseId;
standardName
This public instance method returns the standardName.
Usage:
my $standardName = $annotatedGene->standardName;
type
This public instance method returns the type of the annotated gene.
Usage:
my $type = $annotatedGene->type;
productName
This public instance method returns the product name of the annotated
gene, if one exists. Otherwise it returns undef.
Usage:
my $productName = $annotatedGene->productName;
aliases
This public instance method returns an array of aliases for the
annotated gene. If no aliases exist, then an empty array will be
returned.
Usage:
my @aliases = $annotatedGene->aliases;
Protected Methods
_handleMissingArgument
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.
Usage:
$self->_handleMissingArgument(argument=>'blah');
AUTHOR
Gavin Sherlock, sherlock@genome.stanford.edu
perl v5.14.1 2003-11-26 GO::AnnotatedGene(3)
