Search results for "dist:FAST HEIKKI"
FAST::Bio::Range - Pure perl RangeI implementation
This provides a pure perl implementation of the BioPerl range interface. Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points >= start and <= end are within the range. End is always greater-than or equal-to...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::RangeI - Range interface
This provides a standard BioPerl range interface that should be implemented by any object that wants to be treated as a range. This serves purely as an abstract base class for implementers and can not be instantiated. Ranges are modeled as having (st...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::WebAgent - A base class for Web (any protocol) access
This abstract superclass is a subclass of LWP::UserAgent which allows protocol independent access of remote locations over the Net. It takes care of error handling, proxies and various net protocols. BioPerl classes accessing the net should inherit f...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqUtils - Additional methods for PrimarySeq objects
This class is a holder of methods that work on FAST::Bio::PrimarySeqI- compliant sequence objects, e.g. FAST::Bio::PrimarySeq and FAST::Bio::Seq. These methods are not part of the FAST::Bio::PrimarySeqI interface and should in general not be essentia...
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::SeqIO::scf - .scf file input/output stream
This object can transform .scf files to and from FAST::Bio::Seq::SequenceTrace objects. Mechanisms are present to retrieve trace data from scf files....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information
This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, seq...
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::Seq::Quality - Implementation of sequence with residue quality and trace values
This object stores base quality values together with the sequence string. It is a reimplementation of Chad Matsalla's FAST::Bio::Seq::SeqWithQuality module using FAST::Bio::Seq::MetaI. The implementation is based on FAST::Bio::Seq::Meta::Array. qual(...
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::LargeSeqI - Interface class for sequences that cache their residues in a temporary file
The interface class defines a group of sequence classes that do not keep their sequence information in memory but store it in a file. This makes it possible to work with very large files even with limited RAM. The most important consequence of file c...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::nexus - NEXUS format sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::genbank - GenBank sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. Optional functions _show_dna() (output only) shows the dna or not...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
This object can transform FAST::Bio::SimpleAlign objects to and from PHYLIP format. By default it works with the interleaved format. By specifying the flag -interleaved => 0 in the initialization the module can read or write data in sequential format...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::gbdriver - GenBank handler-based push parser
This object can transform FAST::Bio::Seq objects to and from GenBank flat file databases. The key difference between this parser and the tried-and-true FAST::Bio::SeqIO::genbank parser is this version separates the parsing and data manipulation into ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::SeqStats - Object holding statistics for one particular sequence
FAST::Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create t...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::metafasta - metafasta sequence input/output stream
This object can transform FAST::Bio::Seq::Meta objects to and from metafasta flat file databases. For sequence part the code is an exact copy of FAST::Bio::SeqIO::fasta module. The only added bits deal with meta data IO. The format of a metafasta fil...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Location::Simple - Implementation of a Simple Location on a Sequence
This is an implementation of FAST::Bio::LocationI to manage exact location information on a Sequence: '22' or '12..15' or '16^17'. You can test the type of the location using length() function () or directly location_type() which can one of two value...
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::Tools::CodonTable - Codon table object
Codon tables are also called translation tables or genetic codes since that is what they represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page. CodonT...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC