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Bio::MAGETAB(3)	      User Contributed Perl Documentation      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).

perl v5.32.1			  2014-04-11		       Bio::MAGETAB(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | AUTHOR | LICENSE

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