Section 3

Section 3 of the manual describes all library functions excluding the library functions (system call wrappers) described in Section 2, which implement system calls.

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BeagleResource: Description of a hardware resource.
BeagleResourceList: List of hardware resources.
Beep: cdk_misc - Curses Development Kit Miscellaneous Routines
Benchmark: benchmark running times of Perl code
BerkeleyDB: Perl extension for Berkeley DB version 2, 3, 4, 5 or 6
Biber: main module for biber, a bibtex replacement for users of biblatex
Biber::Annotation: Biber::Entry::Annotation - Biber::Annotation objects
Biber::Config: Configuration items which need to be saved across the lifetime of a Biber object
Biber::Constants: global constants for biber
Biber::DataList: Biber::DataLists objects
Biber::DataLists: Biber::DataLists objects
Biber::DataModel: Biber::DataModel objects
Biber::Date::Format: Biber::Date::Format objects
Biber::Entries: Biber::Entries objects
Biber::Entry: Biber::Entry objects
Biber::Entry::Name: Biber::Entry::Name objects
Biber::Entry::Names: Biber::Entry::Names objects
Biber::Input::file::biblatexml: Main data extraction routine. Accepts a data source identifier (filename in this case), preprocesses the file and then looks for the passed keys, creating entries when it finds them and passes out an array of keys it didn't find
Biber::Input::file::bibtex: Invalidate the T::B object cache. Used only in tests when e.g. we change the encoding settings and therefore must force a re-read of the data
Biber::Internals: Internal methods for processing the bibliographic data
Biber::LaTeX::Recode: Encode/Decode chars to/from UTF-8/lacros in LaTeX
Biber::LangTag: Biber::LangTag objects
Biber::LangTags: Biber::LangTags objects
Biber::Output::base: base class for Biber output modules
Biber::Output::bbl: class for Biber output of .bbl
Biber::Output::bblxml: class for Biber output of .bbl in XML format
Biber::Output::biblatexml: class for biblatexml output of tool mode
Biber::Output::bibtex: class for bibtex output
Biber::Output::dot: class for Biber output of GraphViz .dot files
Biber::Section: Biber::Section objects
Biber::Sections: Biber::Sections objects
Biber::UCollate: Biber::UCollate objects
Biber::Utils: Various utility subs used in Biber
Bigarray: Large, multi-dimensional, numerical arrays
Bigarray.Array0: Zero-dimensional arrays
Bigarray.Array1: One-dimensional arrays
Bigarray.Array2: Two-dimensional arrays
Bigarray.Array3: Three-dimensional arrays
Bigarray.Genarray: no description
Binutils: no description
Bio::Align::AlignI: An interface for describing sequence alignments
Bio::Align::DNAStatistics: Calculate some statistics for a DNA alignment
Bio::Align::PairwiseStatistics: Base statistic object for Pairwise Alignments
Bio::Align::ProteinStatistics: Calculate Protein Alignment statistics (mostly distances)
Bio::Align::StatisticsI: Calculate some statistics for an alignment
Bio::Align::Utilities: A collection of utilities regarding converting and manipulating alignment objects
Bio::AlignIO: Handler for AlignIO Formats
Bio::AlignIO::Handler::GenericAlignHandler: Bio::HandlerI-based generic data handler class for alignment-based data
Bio::AlignIO::arp: ARP MSA Sequence input/output stream
Bio::AlignIO::bl2seq: bl2seq sequence input/output stream
Bio::AlignIO::clustalw: clustalw sequence input/output stream
Bio::AlignIO::emboss: Parse EMBOSS alignment output (from applications water and needle)
Bio::AlignIO::fasta: fasta MSA Sequence input/output stream
Bio::AlignIO::largemultifasta: Largemultifasta MSA Sequence input/output stream
Bio::AlignIO::maf: Multiple Alignment Format sequence input stream
Bio::AlignIO::mase: mase sequence input/output stream
Bio::AlignIO::mega: Parse and Create MEGA format data files
Bio::AlignIO::meme: meme sequence input/output stream
Bio::AlignIO::metafasta: Metafasta MSA Sequence input/output stream
Bio::AlignIO::msf: msf sequence input/output stream
Bio::AlignIO::nexus: NEXUS format sequence input/output stream
Bio::AlignIO::pfam: pfam sequence input/output stream
Bio::AlignIO::phylip: PHYLIP format sequence input/output stream
Bio::AlignIO::po: po MSA Sequence input/output stream
Bio::AlignIO::proda: proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)
Bio::AlignIO::prodom: prodom sequence input/output stream
Bio::AlignIO::psi: Read/Write PSI-BLAST profile alignment files
Bio::AlignIO::selex: selex sequence input/output stream
Bio::AlignIO::xmfa: XMFA MSA Sequence input/output stream
Bio::AnalysisI: An interface to any (local or remote) analysis tool
Bio::AnalysisParserI: Generic analysis output parser interface
Bio::AnalysisResultI: Interface for analysis result objects
Bio::AnnotatableI: the base interface an annotatable object must implement
Bio::Annotation::AnnotationFactory: Instantiates a new Bio::AnnotationI (or derived class) through a factory
Bio::Annotation::Collection: Default Perl implementation of AnnotationCollectionI
Bio::Annotation::Comment: A comment object, holding text
Bio::Annotation::DBLink: untyped links between databases
Bio::Annotation::OntologyTerm: An ontology term adapted to AnnotationI
Bio::Annotation::Reference: Specialised DBLink object for Literature References
Bio::Annotation::Relation: Relationship (pairwise) with other objects SeqI and NodeI;
Bio::Annotation::SimpleValue: A simple scalar
Bio::Annotation::StructuredValue: A scalar with embedded structured information
Bio::Annotation::TagTree: AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text
Bio::Annotation::Target: Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Bio::Annotation::Tree: Provide a tree as an annotation to a Bio::AnnotatableI object
Bio::Annotation::TypeManager: Manages types for annotation collections
Bio::AnnotationCollectionI: Interface for annotation collections
Bio::AnnotationI: Annotation interface
Bio::CodonUsage::IO: for reading and writing codon usage tables to file
Bio::CodonUsage::Table: for access to the Codon usage Database at http://www.kazusa.or.jp/codon
Bio::DB::Bam::AlignWrapper: - Add high-level methods to Bio::DB::Bam::Alignment
Bio::DB::Bam::Alignment: - The SAM/BAM alignment object
Bio::DB::Bam::Pileup: - Object passed to pileup() callback
Bio::DB::Bam::PileupWrapper: - Add high-level methods to Bio::DB::Bam::Pileup
Bio::DB::Bam::Query: - Object representing the query portion of a BAM/SAM alignment
Bio::DB::Bam::Target: - Object representing the query portion of a BAM/SAM alignment in NATIVE alignment
Bio::DB::DBFetch: Database object for retrieving using the dbfetch script
Bio::DB::ESoap: Client for the NCBI Entrez EUtilities SOAP server
Bio::DB::ESoap::WSDL: WSDL parsing for Entrez SOAP EUtilities
Bio::DB::Failover: A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs