NAME
Bio::MAGETAB - A data model and utility API for the MAGE-TAB format.
SYNOPSIS
# Use case 1: using Bio::MAGETAB simply to import all of the MAGE-TAB
# classes:
use Bio::MAGETAB;
my $sample = Bio::MAGETAB::Sample->new({ name => "Sample 1" });
# Use case 2: a Bio::MAGETAB object as a container for MAGE-TAB objects:
use Bio::MAGETAB;
# Instantiation automatically installs the new object as the default
# container for objects subsequently instantiated from all classes
# derived from Bio::MAGETAB::BaseClass.
my $container = Bio::MAGETAB->new();
# Create some samples.
for ( 1 .. 4 ) {
Bio::MAGETAB::Sample->new({ name => "Sample $_" });
}
# Retrieve all the Samples created so far.
$container->get_samples();
DESCRIPTION
The Bio::MAGETAB module provides the core set of classes used to support the perl MAGE-TAB API. This module provides a set of data structures and type constraints which help to reliably handle data in MAGE-TAB format. See the Reader, Writer and GraphViz modules for classes which can be used to read, write and visualize MAGE-TAB data respectively.
This top-level Bio::MAGETAB class provides convenience methods for managing MAGE-TAB objects. It can be used to import the class namespaces needed for all the MAGE-TAB classes, but more usefully it can also be used to create container objects which automatically track object creation.
METHODS
Generic methods
- new
-
Instantiate a new container object. This method writes its result to a Bio::MAGETAB::BaseClass class variable such that the new container will automatically receive all subsequently instantiated MAGE-TAB objects.
- add_objects( @objects )
-
Add the passed objects to the Bio::MAGETAB container object. The objects are sorted by class behind the scenes. Note that this method is typically invoked for you upon instantiation of MAGE-TAB objects; it is only needed in cases where you are using multiple Bio::MAGETAB container classes.
- delete_objects( @objects )
-
Delete the passed MAGE-TAB object from the container.
- get_objects( $class )
-
Return all the remaining MAGE-TAB objects of the specified class. Usually you will want one of the class-specific accessors listed below which wrap this method, but
get_objects
can be used as a simple way of dynamically accessing the objects of multiple classes.
Class-specific methods
Each MAGE-TAB class has its own predicate (has_*) and accessor (get_*) method. Note that the has_baseClasses
and get_baseClasses
methods can be used to query all MAGE-TAB objects held by the container.
- has_arrayDesigns
-
Returns true if the container holds any ArrayDesign objects, and false otherwise.
- get_arrayDesigns
-
Returns all the ArrayDesign objects held by the container.
- has_assays
-
Returns true if the container holds any Assay objects, and false otherwise.
- get_assays
-
Returns all the Assay objects held by the container.
- has_baseClasses
-
Returns true if the container holds any BaseClass objects, and false otherwise.
- get_baseClasses
-
Returns all the BaseClass objects held by the container.
- has_comments
-
Returns true if the container holds any Comment objects, and false otherwise.
- get_comments
-
Returns all the Comment objects held by the container.
- has_compositeElements
-
Returns true if the container holds any CompositeElement objects, and false otherwise.
- get_compositeElements
-
Returns all the CompositeElement objects held by the container.
- has_contacts
-
Returns true if the container holds any Contact objects, and false otherwise.
- get_contacts
-
Returns all the Contact objects held by the container.
- has_controlledTerms
-
Returns true if the container holds any ControlledTerm objects, and false otherwise.
- get_controlledTerms
-
Returns all the ControlledTerm objects held by the container.
- has_data
-
Returns true if the container holds any Data objects, and false otherwise.
- get_data
-
Returns all the Data objects held by the container.
- has_dataAcquisitions
-
Returns true if the container holds any DataAcquisition objects, and false otherwise.
- get_dataAcquisitions
-
Returns all the DataAcquisition objects held by the container.
- has_dataFiles
-
Returns true if the container holds any DataFile objects, and false otherwise.
- get_dataFiles
-
Returns all the DataFile objects held by the container.
- has_dataMatrices
-
Returns true if the container holds any DataMatrix objects, and false otherwise.
- get_dataMatrices
-
Returns all the DataMatrix objects held by the container.
- has_databaseEntries
-
Returns true if the container holds any DatabaseEntry objects, and false otherwise.
- get_databaseEntries
-
Returns all the DatabaseEntry objects held by the container.
- has_designElements
-
Returns true if the container holds any DesignElement objects, and false otherwise.
- get_designElements
-
Returns all the DesignElement objects held by the container.
- has_edges
-
Returns true if the container holds any Edge objects, and false otherwise.
- get_edges
-
Returns all the Edge objects held by the container.
- has_events
-
Returns true if the container holds any Event objects, and false otherwise.
- get_events
-
Returns all the Event objects held by the container.
- has_extracts
-
Returns true if the container holds any Extract objects, and false otherwise.
- get_extracts
-
Returns all the Extract objects held by the container.
- has_factors
-
Returns true if the container holds any Factor objects, and false otherwise.
- get_factors
-
Returns all the Factor objects held by the container.
- has_factorValues
-
Returns true if the container holds any FactorValue objects, and false otherwise.
- get_factorValues
-
Returns all the FactorValue objects held by the container.
- has_features
-
Returns true if the container holds any Feature objects, and false otherwise.
- get_features
-
Returns all the Feature objects held by the container.
- has_investigations
-
Returns true if the container holds any Investigation objects, and false otherwise.
- get_investigations
-
Returns all the Investigation objects held by the container.
- has_labeledExtracts
-
Returns true if the container holds any LabeledExtract objects, and false otherwise.
- get_labeledExtracts
-
Returns all the LabeledExtract objects held by the container.
- has_materials
-
Returns true if the container holds any Material objects, and false otherwise.
- get_materials
-
Returns all the Material objects held by the container.
- has_matrixColumns
-
Returns true if the container holds any MatrixColumn objects, and false otherwise.
- get_matrixColumns
-
Returns all the MatrixColumn objects held by the container.
- has_matrixRows
-
Returns true if the container holds any MatrixRow objects, and false otherwise.
- get_matrixRows
-
Returns all the MatrixRow objects held by the container.
- has_measurements
-
Returns true if the container holds any Measurement objects, and false otherwise.
- get_measurements
-
Returns all the Measurement objects held by the container.
- has_nodes
-
Returns true if the container holds any Node objects, and false otherwise.
- get_nodes
-
Returns all the Node objects held by the container.
- has_normalizations
-
Returns true if the container holds any Normalization objects, and false otherwise.
- get_normalizations
-
Returns all the Normalization objects held by the container.
- has_parameterValues
-
Returns true if the container holds any ParameterValue objects, and false otherwise.
- get_parameterValues
-
Returns all the ParameterValue objects held by the container.
- has_protocols
-
Returns true if the container holds any Protocol objects, and false otherwise.
- get_protocols
-
Returns all the Protocol objects held by the container.
- has_protocolApplications
-
Returns true if the container holds any ProtocolApplication objects, and false otherwise.
- get_protocolApplications
-
Returns all the ProtocolApplication objects held by the container.
- has_protocolParameters
-
Returns true if the container holds any ProtocolParameter objects, and false otherwise.
- get_protocolParameters
-
Returns all the ProtocolParameter objects held by the container.
- has_publications
-
Returns true if the container holds any Publication objects, and false otherwise.
- get_publications
-
Returns all the Publication objects held by the container.
- has_reporters
-
Returns true if the container holds any Reporter objects, and false otherwise.
- get_reporters
-
Returns all the Reporter objects held by the container.
- has_sdrfs
-
Returns true if the container holds any SDRF objects, and false otherwise.
- get_sdrfs
-
Returns all the SDRF objects held by the container.
- has_sdrfRows
-
Returns true if the container holds any SDRFRow objects, and false otherwise.
- get_sdrfRows
-
Returns all the SDRFRow objects held by the container.
- has_samples
-
Returns true if the container holds any Sample objects, and false otherwise.
- get_samples
-
Returns all the Sample objects held by the container.
- has_sources
-
Returns true if the container holds any Source objects, and false otherwise.
- get_sources
-
Returns all the Source objects held by the container.
- has_termSources
-
Returns true if the container holds any TermSource objects, and false otherwise.
- get_termSources
-
Returns all the TermSource objects held by the container.
SEE ALSO
Bio::MAGETAB::Util::Reader Bio::MAGETAB::Util::Writer Bio::MAGETAB::BaseClass
AUTHOR
Tim F. Rayner <tfrayner@gmail.com>
LICENSE
This library is released under version 2 of the GNU General Public License (GPL).