Search results for "distribution:FAST Bio::AnnotationI"
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::AnnotationCollectionI - Interface for annotation collections
Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an A...
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::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
Ontology term annotation object...
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::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::Annotation::AnnotationFactory - Instantiates a new FAST::Bio::AnnotationI (or derived class) through a factory
This object will build FAST::Bio::AnnotationI objects generically....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Provides an object which represents a target (ie, a similarity hit) from one object to something in another database without prescribing what is in the other database...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser
This is EntrezGene ASN bioperl parser. It is built on top of FAST::Bio::ASN1::EntrezGene, a low level ASN parser built by Mingyi Liu (<http://sourceforge.net/projects/egparser>). The easiest way to use it is shown above. You will get most of the Entr...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Annotation::DBLink - untyped links between databases
Provides an object which represents a link from one object to something in another database without prescribing what is in the other database. Aside from FAST::Bio::AnnotationI, this class also implements FAST::Bio::IdentifiableI....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Annotation::Comment - A comment object, holding text
A holder for comments in annotations, just plain text. This is a very simple object, and justifiably so....
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::Annotation::Reference - Specialised DBLink object for Literature References
Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (i...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Annotation::SimpleValue - A simple scalar
Scalar value annotation object...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC