Bio::MAGETAB(3)

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).