Search results for "dist:FAST ROOT"
lib/FAST/Bio/Root/Root.pm
This is a hashref-based implementation of the FAST::Bio::Root::RootI interface. Most Bioperl objects should inherit from this. See the documentation for FAST::Bio::Root::RootI for most of the methods implemented by this module. Only overridden method...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
lib/FAST/Bio/Root/RootI.pm
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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
lib/FAST/Bio/Root/IO.pm
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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
lib/FAST/Bio/Root/Exception.pm
Exceptions defined in FAST::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 ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
lib/FAST/Bio/Root/Version.pm
This module provides a mechanism by which all other BioPerl modules can share the same $VERSION, without manually synchronizing each file. FAST::Bio::Root::RootI itself uses this module, so any module that directly (or indirectly) uses FAST::Bio::Roo...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::FAST::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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::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 FAST::Bio::Species. This new implementation allows representation of the intermediate nodes not just the ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO - Handler for SeqIO Formats
FAST::Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, FAST::Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The FAST::Bio::SeqIO system can be thought of lik...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::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 FAST::Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For peopl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tree::Tree - An Implementation of TreeI interface.
This object holds handles to Nodes which make up a tree....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::OntologyIO - Parser factory for Ontology formats
This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to FAST::Bio::SeqIO, but the difference is that the chunk of data returned as an object is an entire ontology....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::PullParserI - A base module for fast 'pull' parsing
If you are writing a module to parse some new format, you may wish to use a 'pull' approach whereby you only do work (reading file data, parsing it, turning the parsed data in an object) when absolutely necessary. PullParserI provides a system for do...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
This object holds a pointer to the Root of a Tree which is a FAST::Bio::Tree::NodeI....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in FAST::Bio::Root::Root
This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!)....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points)
This implementation handles locations which span more than one start/end location, or and/or lie on different sequences, and can work with split locations that depend on the specific order of the sublocations ('join') or don't have a specific order b...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium
Needs Graph.pm from CPAN....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AnalysisParserI - Generic analysis output parser interface
AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis being parsed, only that zero or more result sets can be obtained from the input source. This module was derive...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::SeqPattern - represent a sequence pattern or motif
FAST::Bio::Tools::SeqPattern module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"). FAST::Bio::Tools::SeqPattern is a concrete class that inherits from F...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Factory::ObjectFactory - Instantiates a new FAST::Bio::Root::RootI (or derived class) through a factory
This object will build FAST::Bio::Root::RootI objects generically....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC