Tim Rayner > Bio-MAGETAB > Bio::MAGETAB

Download:
Bio-MAGETAB-1.31.tar.gz

Dependencies

Annotate this POD

CPAN RT

Open  0
View/Report Bugs
Module Version: 1.31   Source  

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).

syntax highlighting: