GO::AnnotatedGene - GO::AnnotatedGene documentation
Index
Code Index:
NAME - will provide an object to hold info about a gene with GO annotation
DESCRIPTION
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
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
package GO::AnnotatedGene;
# File : AnnotatedGene.pm
# Author : Gavin Sherlock
# Date Begun : March 9th 2003
# $Id: AnnotatedGene.pm,v 1.2 2003/11/26 19:23:52 sherlock Exp $
# License information (the MIT license)
# Copyright (c) 2003 Gavin Sherlock; Stanford University
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
use strict;
use warnings;
use diagnostics;
use vars qw ($PACKAGE $VERSION);
$PACKAGE = "GO::AnnotatedGene";
$VERSION = "0.11";
# CLASS Attributes
#
# These should be considered as constants, and are initialized here
my $kDatabaseId = $PACKAGE.'::__databaseId';
my $kStandardName = $PACKAGE.'::__standardName';
my $kType = $PACKAGE.'::__type';
my $kProductName = $PACKAGE.'::__productName';
my $kAliases = $PACKAGE.'::__aliases';
############################################################################
sub new{
############################################################################
my $self = {};
my $class = shift;
bless $self, $class;
$self->__init(@_);
return $self;
}
############################################################################
sub __init{
############################################################################
# This private method initializes the object, dependent on what arguments
# have been received.
#
my ($self, %args) = @_;
# check required arguments
my $databaseId = $args{'databaseId'} || $self->_handleMissingArgument(argument => 'databaseId');
my $standardName = $args{'standardName'} || $self->_handleMissingArgument(argument => 'standardName');
my $type = $args{'type'} || $self->_handleMissingArgument(argument => 'type');
# store them
$self->{$kDatabaseId} = $databaseId;
$self->{$kStandardName} = $standardName;
$self->{$kType} = $type;
# now check and store optional arguments
if (exists ($args{'productName'}) && defined ($args{'productName'})){
$self->{$kProductName} = $args{'productName'};
}else{
$self->{$kProductName} = undef;
}
if (exists ($args{'aliases'}) && defined ($args{'aliases'})){
$self->{$kAliases} = $args{'aliases'};
}else{
$self->{$kAliases} = []; # default to an empty list
}
}
############################################################################
sub databaseId{
############################################################################
return $_[0]->{$kDatabaseId};
}
############################################################################
sub standardName{
############################################################################
return $_[0]->{$kStandardName};
}
############################################################################
sub type{
############################################################################
return $_[0]->{$kType};
}
############################################################################
sub productName{
############################################################################
return $_[0]->{$kProductName};
}
############################################################################
sub aliases{
############################################################################
return @{$_[0]->{$kAliases}};
}
# need to make this code common to all objects, or to
# start using something like Params-Validate
############################################################################
sub _handleMissingArgument{
############################################################################
##############################################################################
my ($self, %args) = @_;
my $arg = $args{'argument'} || $self->_handleMissingArgument(argument=>'argument');
my $receiver = (caller(1))[3];
my $caller = (caller(2))[3];
die "The method $caller did not provide a value for the '$arg' argument for the $receiver method";
}
1; # to keep Perl happy