Search results for "dist:BioPerl Bio::AnnotationI"
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::swiss - Swissprot sequence input/output stream
This object can transform 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 holds ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object
Provides a Bio::AnnotationI object which contains a Bio::Tree::TreeI, which can be added to a Bio::AnnotationCollectionI, which in turn be attached to a Bio::AnnotatableI (typically a Bio::AlignI object)...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
Ontology term annotation object...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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)....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::AnnotationI, this class also implements Bio::IdentifiableI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;
Scalar value annotation object...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
This object is a specialization of Bio::Search::HSP::ModelHSP and is used for searches which involve a query model, such as a Hidden Markov Model (HMM), covariance model (CM), descriptor, or anything else besides a sequence. Note that results from an...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI
Bioperl implementation for Bio::AnnotationCollectionI...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::SimpleValue - A simple scalar
Scalar value annotation object...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory
This object will build Bio::AnnotationI objects generically....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::StructuredValue - A scalar with embedded structured information
Scalar value annotation object....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation
Bio::SeqFeatureI defines light-weight annotation of features through tag/value pairs. Conversely, Bio::AnnotationCollectionI together with Bio::AnnotationI defines an annotation bag, which is better typed, but more heavy-weight because it contains ev...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC