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Man Pages
Bio::MAGETAB(3) User Contributed Perl Documentation Bio::MAGETAB(3)

Bio::MAGETAB - A data model and utility API for the MAGE-TAB format.

 # 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();

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.

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.

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.

Bio::MAGETAB::Util::Reader Bio::MAGETAB::Util::Writer Bio::MAGETAB::BaseClass

Tim F. Rayner <tfrayner@gmail.com>

This library is released under version 2 of the GNU General Public License (GPL).
2014-04-11 perl v5.32.1

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