Search results for "distribution:BioPerl Email::Abstract"
Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guaranteed to get for any Bio::SeqI. For most users of the package the documentation (and methods) in this class are not at useful - this is a develo...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::SeqI - Abstract Interface for Sequence databases
Abstract interface for a sequence database...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::LocationI - Abstract interface of a Location on a Sequence
This Interface defines the methods for a Bio::LocationI, an object which encapsulates a location on a biological sequence. Locations need not be attached to actual sequences as they are stand alone objects. LocationI objects are used by Bio::SeqFeatu...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::RangeI - Range interface
This provides a standard BioPerl range interface that should be implemented by any object that wants to be treated as a range. This serves purely as an abstract base class for implementers and can not be instantiated. Ranges are modeled as having (st...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Flat - Interface for indexed flat files
This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the "flat index" and BerkeleyDB indexed flat fil...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::Abstract - Abstract interface for indexing a flat file
This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch). This object is the ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual
This object defines an abstract interface to basic quality information. PrimaryQual is an object just for the quality and its name(s), nothing more. There is a pure perl implementation of this in Bio::Seq::PrimaryQual. If you just want to use Bio::Se...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information
This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, seq...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::LocationI - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::LocationI class defines methods used to retrieve location data from a sequence. This is returned in ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace
This object defines an abstract interface to basic trace information. This information may have come from an ABI- or scf- formatted file or may have been made up....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers-only class which defines what methods have to be implemented b...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::ReferenceI class defines methods used to retrieve reference data from a sequence. This is returned i...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)
This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. This also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the index $inx->make_index($file_...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file
This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the BerkeleyDB-indexed "common" flat file format...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
Supposed to handle a combination of site matrices and/or their corresponding sequence matches (instances). This object inherits from Bio::Matrix::PSM::SiteMatrix, so you can use the respective methods. It may hold also an array of Bio::Matrix::PSM::I...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references
This interface defines the functions one can expect for any object wanting to use database cross-references. This class does not actually provide any implementation, it just provides the definitions of what methods one can call. The database cross-re...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::BlastTable - Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
This object allows one to build an index on a tabular BLAST file (or files) and provide quick access to the blast report for that accession. This also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the index $inx->make_inde...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::AbstractSeq - base class for AbstractSeq
Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and provides a Bio::DB::SeqI interface....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval.
WARNING: Please do NOT spam the web servers with multiple requests. Bio::DB::GenericWebAgent is a generic wrapper around a web agent (LWP::UserAgent), an object which can retain, format, and build parameters for the user agent (Bio::ParameterBaseI), ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files
This module can be used both to index sequence files and also to retrieve sequences from existing sequence files. This object allows indexing of sequence files both by a primary key (say accession) and multiple secondary keys (say ids). This is diffe...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC