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Man Pages


Manual Reference Pages  -  BIO::MAGETAB (3)

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NAME

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

CONTENTS

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).
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