Section 3 of the manual describes all library functions excluding the library functions (system call wrappers) described in Section 2, which implement system calls.
Page 17
- Bio::Graphics::Browser2::PluginSet
- - A set of plugins
- Bio::Graphics::Browser2::Realign
- Perl extension for Smith-Waterman alignments
- Bio::Graphics::Browser2::Region
- - Provide method for fetching and manipulating regions
- Bio::Graphics::Browser2::RegionSearch
- - Search through multiple databases for feature matches
- Bio::Graphics::Browser2::RemoteSet
- Bio::Graphics::Browser2::PluginSet -- A set of plugins
- Bio::Graphics::Browser2::Render
- - Provide methods to render regions
- Bio::Graphics::Browser2::Render::Slave::AWS_Balancer
- Lincoln Stein
- Bio::Graphics::Browser2::Render::Slave::Status
- Lincoln D. Stein
- Bio::Graphics::Browser2::RenderPanels
- - Provide methods to render a panel
- Bio::Graphics::Browser2::Util
- - Exported utilities
- Bio::HandlerBaseI
- Interface class for handler methods which interact with any event-driven parsers (drivers)
- Bio::IdCollectionI
- interface for objects with multiple identifiers
- Bio::IdentifiableI
- interface for objects with identifiers
- Bio::Index::Abstract
- Abstract interface for indexing a flat file
- Bio::Index::AbstractSeq
- base class for AbstractSeq
- Bio::Index::Blast
- Indexes Blast reports and supports retrieval based on query accession(s)
- Bio::Index::BlastTable
- Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
- Bio::Index::EMBL
- Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format)
- Bio::Index::Fasta
- Interface for indexing (multiple) fasta files
- Bio::Index::Fastq
- Interface for indexing (multiple) fastq files
- Bio::Index::GenBank
- Interface for indexing one or more GenBank files (i.e. flat file GenBank format)
- Bio::Index::Hmmer
- indexes HMMER reports and supports retreival based on query
- Bio::Index::Qual
- Interface for indexing (multiple) fasta qual files
- Bio::Index::SwissPfam
- Interface for indexing swisspfam files
- Bio::Index::Swissprot
- Interface for indexing one or more Swissprot files
- Bio::LocatableSeq
- A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq
- Bio::Location::Atomic
- Implementation of a Atomic Location on a Sequence
- Bio::Location::AvWithinCoordPolicy
- class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
- Bio::Location::CoordinatePolicyI
- Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
- Bio::Location::Fuzzy
- Implementation of a Location on a Sequence which has unclear start and/or end locations
- Bio::Location::FuzzyLocationI
- Abstract interface of a Location on a Sequence which has unclear start/end location
- Bio::Location::NarrowestCoordPolicy
- class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
- Bio::Location::Simple
- Implementation of a Simple Location on a Sequence
- Bio::Location::Split
- Implementation of a Location on a Sequence which has multiple locations (start/end points)
- Bio::Location::SplitLocationI
- Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
- Bio::Location::WidestCoordPolicy
- class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
- Bio::LocationI
- Abstract interface of a Location on a Sequence
- Bio::Matrix::Generic
- A generic matrix implementation
- Bio::Matrix::IO
- A factory for Matrix parsing
- Bio::Matrix::IO::mlagan
- A parser for the mlagan substitution matrix
- Bio::Matrix::IO::phylip
- A parser for PHYLIP distance matricies
- Bio::Matrix::IO::scoring
- A parser for PAM/BLOSUM matricies
- Bio::Matrix::MatrixI
- An interface for describing a Matrix
- Bio::Matrix::Mlagan
- A generic matrix with mlagan fields
- Bio::Matrix::PSM::IO
- PSM parser
- Bio::Matrix::PSM::IO::mast
- PSM mast parser implementation
- Bio::Matrix::PSM::IO::masta
- motif fasta format parser
- Bio::Matrix::PSM::IO::meme
- PSM meme parser implementation
- Bio::Matrix::PSM::IO::psiblast
- PSM psiblast parser
- Bio::Matrix::PSM::IO::transfac
- PSM transfac parser
- Bio::Matrix::PSM::InstanceSite
- A PSM site occurrence
- Bio::Matrix::PSM::InstanceSiteI
- InstanceSite interface, holds an instance of a PSM
- Bio::Matrix::PSM::ProtMatrix
- SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information
- Bio::Matrix::PSM::ProtPsm
- handle combination of site matricies
- Bio::Matrix::PSM::Psm
- handle combination of site matricies
- Bio::Matrix::PSM::PsmHeader
- PSM mast parser implementation
- Bio::Matrix::PSM::PsmHeaderI
- handles the header data from a PSM file
- Bio::Matrix::PSM::PsmI
- abstract interface to handler of site matricies
- Bio::Matrix::PSM::SiteMatrix
- SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
- Bio::Matrix::PSM::SiteMatrixI
- SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
- Bio::Matrix::PhylipDist
- A Phylip Distance Matrix object
- Bio::Matrix::Scoring
- Object which can hold scoring matrix information
- Bio::Ontology::DocumentRegistry
- Keep track of where to find ontologies. Allows lookups by name
- Bio::Ontology::GOterm
- representation of GO terms
- Bio::Ontology::InterProTerm
- Implementation of InterProI term interface
- Bio::Ontology::OBOEngine
- An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
- Bio::Ontology::OBOterm
- representation of OBO terms
- Bio::Ontology::Ontology
- standard implementation of an Ontology
- Bio::Ontology::OntologyEngineI
- Interface a minimal Ontology implementation should satisfy
- Bio::Ontology::OntologyI
- Interface for an ontology implementation
- Bio::Ontology::OntologyStore
- A repository of ontologies
- Bio::Ontology::Path
- a path for an ontology term graph
- Bio::Ontology::PathI
- Interface for a path between ontology terms
- Bio::Ontology::Relationship
- a relationship for an ontology
- Bio::Ontology::RelationshipFactory
- Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
- Bio::Ontology::RelationshipI
- Interface for a relationship between ontology terms
- Bio::Ontology::RelationshipType
- a relationship type for an ontology
- Bio::Ontology::SimpleGOEngine::GraphAdaptor
- Graph adaptor for Bio::Ontology::SimpleGOEngine
- Bio::Ontology::SimpleOntologyEngine
- Implementation of OntologyEngineI interface
- Bio::Ontology::Term
- implementation of the interface for ontology terms
- Bio::Ontology::TermFactory
- Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
- Bio::Ontology::TermI
- interface for ontology terms
- Bio::OntologyIO
- Parser factory for Ontology formats
- Bio::OntologyIO::Handlers::BaseSAXHandler
- base class for SAX Handlers
- Bio::OntologyIO::Handlers::InterProHandler
- XML handler class for InterProParser
- Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
- parse an InterPro XML file and persist the resulting terms to a Biosql database
- Bio::OntologyIO::InterProParser
- Parser for InterPro xml files
- Bio::OntologyIO::dagflat
- a base class parser for GO flat-file type formats
- Bio::OntologyIO::goflat
- a parser for the Gene Ontology flat-file format
- Bio::OntologyIO::obo
- parser for OBO flat-file format
- Bio::OntologyIO::simplehierarchy
- a base class parser for simple hierarchy-by-indentation type formats
- Bio::OntologyIO::soflat
- a parser for the Sequence Ontology flat-file format
- Bio::ParameterBaseI
- Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends
- Bio::Perl
- Functional access to BioPerl for people who don't know objects
- Bio::PrimarySeq
- Bioperl lightweight sequence object
- Bio::PrimarySeqI
- Interface definition for a Bio::PrimarySeq
- Bio::PrimerDesigner
- Design PCR Primers using primer3 and epcr
- Bio::PrimerDesigner::Remote
- A class for remote access to Bio::PrimerDesigner
- Bio::PrimerDesigner::Result
- a class for handling primer design or validation results
- Bio::PrimerDesigner::Tables
- Bio::PrimerDesigner::Table -- Draw HTML tables for PCR primer display