Search results for "dist:BioPerl ROOT"
Bio::Root::Root - implementation of Bio::Root::RootI interface
This is a hashref-based implementation of the Bio::Root::RootI interface. Most Bioperl objects should inherit from this. See the documentation for Bio::Root::RootI for most of the methods implemented by this module. Only overridden methods are descri...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::IO - BioPerl base IO handling class
This module provides methods that will usually be needed for any sort of file- or stream-related input/output, e.g., keeping track of a file handle, transient printing and reading from the file handle, a close method, automatically closing the handle...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::Test - common base for all BioPerl test scripts
This provides a common base for all BioPerl test scripts. It safely handles the loading of Test::Most, itself a simple wrapper around several highly used test modules: Test::More, Test::Exception, Test::Warn, Test::Deep, and Test::Diff. It also prese...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::RootI - base interface for all BioPerl classes
This is just a set of methods which do not assume anything about the object they are on. The methods provide the ability to throw exceptions with nice stack traces. This is what should be inherited by all Bioperl compliant interfaces, even if they ar...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::Version - don't use, get version from each module
This module provides a mechanism by which all other BioPerl modules can share the same $VERSION, without manually synchronizing each file. Bio::Root::RootI itself uses this module, so any module that directly (or indirectly) uses Bio::Root::RootI wil...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::HTTPget - module for fallback HTTP get operations when LWP:: is unavailable
This is basically an last-chance module for doing network HTTP get requests in situations where more advanced external CPAN modules such as LWP:: are not installed. The particular reason this module was developed was so that the Open Bio Database Acc...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::Storable - Safely store/retrieve objects from disk
Generic module that allows objects to be safely stored/retrieved from disk. Can be inhereted by any BioPerl object. As it will not usually be the first class in the inheretence list, _initialise_storable() should be called during object instantiation...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::Utilities - general-purpose utilities
Provides general-purpose utilities of potential interest to any Perl script. The ":obj" tag is a convenience that imports a $Util symbol into your namespace representing a Bio::Root::Utilities object. This saves you from creating your own Bio::Root::...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::Exception - BioPerl exceptions
Exceptions defined in Bio::Root::Exception These are generic exceptions for typical problem situations that could arise in any module or script. Using defined exception classes like these is a good idea because it indicates the basic nature of what w...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Root::TestObject - An implementation of TestInterface
This module attempts to provide an implementation of TestInterface and is used for illustrating exception throwing using Graham Barr's Error.pm object....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
BioPerl - Perl modules for biology
BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documen...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO - Handler for SeqIO Formats
Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Taxon - A node in a represented taxonomy
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the specie...
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::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqUtils - Additional methods for PrimarySeq objects
This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be essential to the primary functio...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::Tree - An implementation of the TreeI interface.
This object holds handles to Nodes which make up a tree....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Seg - parse seg output
"seg" identifies low-complexity regions on a protein sequence. It is usually part of the "WU-BLAST" and "InterProScan" packages. The Bio::Tools::Seg module will only parse the "fasta" output modes of "seg", i.e. "seg -l" (low complexity regions only)...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::OntologyIO - Parser factory for Ontology formats
This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to Bio::SeqIO, but the difference is that the chunk of data returned as an object is an entire ontology....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::NodeI - Interface describing a Tree Node
A NodeI is capable of the basic structure of building a tree and storing the branch length between nodes. The branch length is the length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid bran...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC