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Bio-SeqAlignment-Components-SeqMapping-0.01
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/ Bio::SeqAlignment::Components::SeqMapping::Dataflow

NAME

Bio::SeqAlignment::Components::SeqMapping::Dataflow Components that implement dataflows for sequence mapping

VERSION

version 0.01

SYNOPSIS

use Bio::SeqAlignment::Components::SeqMapping::Dataflow;
use Bio::SeqAlignment::Components::SeqMapping::Dataflow::ComponentName;

DESCRIPTION

This module loads all the components that implement dataflows for mapping query sequences against a database of reference sequences . If you don't want to nuke your namespace with all the components, you can load them as needed by using the specific component name, e.g.:

use Bio::SeqAlignment::Components::SeqMapping::Dataflow::ComponentName;

where ComponentName is the name of the component you need. If you choose violence, you can load all the components at once by using:

use Bio::SeqAlignment::Components::SeqMapping::Dataflow;

COMPONENTS

  • LinearGeneric

    This module provides a Linear Dataflow for use with the Generic Mapper. The Linear Dataflow is a simple linear-linear dataflow that maps a list of query sequences to a reference database of sequences. The module is intended to be applied as a role to the class Bio::SeqAlignment::Components::SeqMapping::Mapper::Generic See the documentation of the Bio::SeqAlignment::Components::SeqMapping::Mapper::Generic module for more information and the EnhancingEdlib for a concrete example.

  • Linear

    This module provides a Linear Dataflow for use with a fully fledged, non-generic mapper. The Linear Dataflow is a simple linear-linear dataflow that maps a list of query sequences to a reference database of sequences. The module is intended to be composed as a role to a class such as a putative Bio::SeqAlignment::Components::SeqMapping::Mapper::AwesomeMapper module. The AwesomeModule is a hypothetical module that implements a mapper that is not generic, but is specific to a particular (pseudo)alignment library, similarity metric, reduction technique, etc. In fact, we suggest you don't use the name AwesomeMapper, but rather something more descriptive of the mapper you are using. This could be something like: AlignmentAlgorithm_Dataflow_SimilarityMetric_ReductionTechnique_Mapper But really it can be anything you want, and it doesn't have to be that long, or even be stored under the Bio::SeqAlignment::Components::SeqMapping::Mapper namespace.

  • LinearLinearGeneric

    This module provides a Linear-Linear Dataflow for use with the Generic Mapper. The Linear-Linear Dataflow is a simple linear-linear dataflow that maps a list of query sequences to a reference database of sequences. The module is intended to be applied as a role to the class Bio::SeqAlignment::Components::SeqMapping::Mapper::Generic See the documentation of the Bio::SeqAlignment::Components::SeqMapping::Mapper::Generic module for more information and the EnhancingEdlib link for a concrete example.

  • LinearLinear

    This module provides a Linear-Linear Dataflow for use with a fully fledged, non-generic mapper. The Linear-Linear Dataflow is a simple linear-linear dataflow that maps a list of query sequences to a reference database of sequences. The module is intended to be composed as a role to a class such as a putative Bio::SeqAlignment::Components::SeqMapping::Mapper::AwesomeMapper module. See under Linear for more information and naming suggestions.

SEE ALSO

AUTHOR

Christos Argyropoulos <chrisarg@cpan.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2024 by Christos Argyropoulos.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.