Search results for "dist:FAST Bio::LocatableSeq"
FAST::Bio::LocatableSeq - A FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
The LocatableSeq sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this. It is, to be honest, not well integrated with the rest ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as files in the tempdir
FAST::Bio::Seq::LargeLocatableSeq - object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. This object, unlike FAST::Bio::LocatableSeq, stores a sequence as a series of files in a temporary di...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::GFF - A FAST::Bio::SeqAnalysisParserI compliant GFF format parser
This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO - Handler for AlignIO Formats
FAST::Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, FAST::Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a FAST::Bio::Align::AlignI-complian...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information
This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are FAST::Bio::LocatableSeq objects with additional methods to store that meta information. See FAST::Bio::LocatableSeq and FAST::B...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::arp - ARP MSA Sequence input/output stream
This object can create FAST::Bio::SimpleAlign objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele se...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::meme - meme sequence input/output stream
This object transforms the "sites sorted by position p-value" sections of a meme (text) output file into a series of FAST::Bio::SimpleAlign objects. Each SimpleAlign object contains FAST::Bio::LocatableSeq objects which represent the individual align...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Align::AlignI - An interface for describing sequence alignments.
This interface describes the basis for alignment objects....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information
This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are FAST::Bio::LocatableSeq objects with additional methods to store that meta information. See FAST::Bio::LocatableSeq and FAST::B...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::PullHSPI - FAST::Bio::Search::HSP::HSPI interface for pull parsers.
PullHSP is for fast implementations that only do parsing work on the hsp data when you actually request information by calling one of the HSPI methods. Many methods of HSPI are implemented in a way suitable for inheriting classes that use FAST::Bio::...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::Handler::GenericAlignHandler - FAST::Bio::HandlerI-based generic data handler class for alignment-based data
This is an experimental implementation of a alignment-based HandlerBaseI parser and may change over time. It is possible that the way handler methods are set up will change over development to allow more flexibility. Standard Developer caveats: Here ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC