## Package org.biojava.bio.seq

Classes and Interfaces for defining biological sequences and informatics objects.

See:
Description

Interface Summary
Feature: A feature within a sequence, or nested within another feature.
FeatureFilter: A filter for accepting or rejecting a feature.
FeatureHolder: The interface for objects that contain features.
FeatureRealizer: Interface for translators which map from Feature.Template instances to real Feature objects.
RealizingFeatureHolder: Interface for `FeatureHolder` objects which know how to instantiate new child Features.
Sequence: A sequence.
SequenceAnnotator: An object which adds some additional information to a Sequence.
SequenceFactory: The interface for objects that will manufacture sequences.
SequenceIterator: An iterator over a bag of sequences.
StrandedFeature: Adds the concept of 'strand' to features.

Class Summary
AbstractFeatureHolder: An abstract implementation of FeatureHolder.
DNATools: Usefull functionality for processing DNA sequences.
Feature.Template: Template class for a plain feature.
FeatureFilter.AcceptAllFilter: The class that accepts all features.
FeatureFilter.And: A filter that returns all features accepted by both child filter.
FeatureFilter.BySource: Construct one of these to filter features by source.
FeatureFilter.ByType: Construct one of these to filter features by type.
FeatureFilter.ContainedByLocation: A filter that returns all features contained within a location.
FeatureFilter.Not: A filter that returns all features not accepted by a child filter.
FeatureFilter.Or: A filter that returns all features accepted by at least one child filter.
FeatureFilter.OverlapsLocation: A filter that returns all features overlapping a location.
FeatureHolder.EmptyFeatureHolder
GeneticCode: Constant TranslationTable instances that embody the genetic code.
MergeFeatureHolder: FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
ProteinTools: The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
SimpleFeatureHolder: A no-frills implementation of FeatureHolder.
SimpleFeatureRealizer: FeatureRealizer which uses a lookup table to map template classes to implementations.
SimpleSequence: A basic implementation of the `Sequence` interface.
SimpleSequenceFactory: A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
StrandedFeature.Strand: Class to represent the 'strandedness' of a feature.
StrandedFeature.Template: Template class for parameterizing the creation of a new `StrandedFeature`.
ViewSequence: A view onto another Sequence object.

## Package org.biojava.bio.seq Description

Classes and Interfaces for defining biological sequences and informatics objects.

This package contains the core classes and interfaces for defining sequences and features, sequence database and iterators, and miscelaneous biological inforation. All definitions are interfaces. Where ever possible, at least one pure java implementation of the interface is supplied.

The Sequence interface inherits the SymbolList interface, making it a list of Symbol objects. It also implements Annotatable which allows annotation to be attached to the entire sequence. Lastly, it implements FeatureHolder so that it can contain features. A Sequence instance represents a concrete piece of biological data, rather than a comp-sci abstraction.

Features are regions of a sequence which have location-specific annotation or meaning. The locatin of a feature is a Location object. Features can contain sub-features, as they are FeatureHolder implementors. They are also annotatable. Lastly, they contain a couple of fields aimed at enhancing GFF interoperability.

Also within this package are the classes that implement these interfaces. They are usualy preceeded with 'Simple' to indicate that they are vanilla, pure-java implementations. You should be able to use these object out-of-the-box.

The DNATools and ProteinTools classes provide a central point-of-access to the DNA and Protein alphabets and add on many operators specific to these domains. For example, DNATools has a method 'complement' that will complement a DNA SymbolList.