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.

AUTHOR

Tim F. Rayner <tfrayner@gmail.com>

LICENSE

This library is released under version 2 of the GNU General Public License (GPL).