Search results for "distribution:FAST Bio::Tree::Tree"
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::Tree::Node - A Simple Tree Node
Makes a Tree Node suitable for building a Tree....
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::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::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
This interface provides a set of implementated Tree functions which only use the defined methods in the TreeI or NodeI interface....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
This takes tagged data values and stores them in a hierarchal structured element-value hierarchy (complements of Chris Mungall's Data::Stag module). Data can then be represented as text using a variety of output formats (indention, itext, xml, spxr)....
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::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Species - Generic species object.
NOTE: This class is planned for deprecation in favor of the simpler FAST::Bio::Taxon. Please use that class instead. Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of node...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::DB::Taxonomy - Access to a taxonomy database
This is a front end module for access to a taxonomy database....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::bsml - BSML sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from BSML (XML) flatfiles. NOTE: 2/1/02 - I have changed the API to more closely match argument passing used by other BioPerl methods ( -tag => value ). Internal methods are using the same API, ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::swiss - Swissprot sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from Swiss-Pprot flat file databases. There is a lot of flexibility here about how to dump things which needs to be documented. GN (Gene name) line management details A Uniprot/Swiss-Prot entry ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AnnotationI - Annotation interface
Interface all annotations must support. There are two things that each annotation has to support. $annotation->as_text() Annotations have to support an "as_text" method. This should be a single text string, without newlines representing the annotatio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::FeatureHolderI - the base interface an object with features must implement
This is the base interface that all feature-holding objects must implement. Popular feature-holders are for instance FAST::Bio::Seq objects. Since FAST::Bio::SeqFeatureI defines a sub_SeqFeature() method, most FAST::Bio::SeqFeatureI implementations l...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::asciitree - asciitree sequence input/output stream
This is a WRITE-ONLY SeqIO module. It writes a FAST::Bio::SeqI object containing nested SeqFeature objects in such a way that the SeqFeature containment hierarchy is visible as a tree structure...
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
FAST::Bio::SeqIO::game::gameSubs - a base class for game-XML parsing
A bag of tricks for game-XML parsing. The PerlSAX handler methods were stolen from Chris Mungall's XML base class, which he stole from Ken MacLeod's XML::Handler::Subs...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Cluster::SequenceFamily - Sequence Family object
This is a simple Family object that may hold any group of object. For more specific families, one should derive from FamilyI....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI
Bioperl implementation for FAST::Bio::AnnotationCollectionI...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-gtprimary_tag
Class to map $seq_feature->primary_tag...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC