Uses of Package
org.biojava.bio.seq

Packages that use org.biojava.bio.seq

org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.das	Development client for the Distributed Annotation System.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.proteomics	Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.filterxml	Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.projection	Code for projecting Feature objects into alternate coordinate systems.
org.biojava.bio.seq.ragbag	The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.

Classes in org.biojava.bio.seq used by org.biojava.bio.dist

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.dp

Sequence
A biological sequence.

SequenceAnnotator
An object which adds some additional information to a Sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.gui.sequence

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.

OptimizableFilter
The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.

Sequence
A biological sequence.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.molbio

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

SequenceAnnotator
An object which adds some additional information to a Sequence.

StrandedFeature
Adds the concept of 'strand' to features.

StrandedFeature.Template
Template class for parameterizing the creation of a new StrandedFeature.

Classes in org.biojava.bio.seq used by org.biojava.bio.program.das

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain feature.

FeatureFilter
A filter for accepting or rejecting a feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

SequenceIterator
An iterator over a bag of sequences.

Classes in org.biojava.bio.seq used by org.biojava.bio.program.gff

FeatureFilter
A filter for accepting or rejecting a feature.

Sequence
A biological sequence.

SequenceAnnotator
An object which adds some additional information to a Sequence.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.program.phred

FeatureHolder
The interface for objects that contain features.

RealizingFeatureHolder
Interface for FeatureHolder objects which know how to instantiate new child Features.

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.program.ssbind

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.program.unigene

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.program.xff

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

StrandedFeature.Template
Template class for parameterizing the creation of a new StrandedFeature.

Classes in org.biojava.bio.seq used by org.biojava.bio.proteomics

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.search

Sequence
A biological sequence.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq

AbstractFeatureHolder
An abstract implementation of FeatureHolder.

Feature
A feature within a sequence, or nested within another feature.

Feature.ByLocationComparator
ByLocationComparator compares Features by the minimum base position of their Location.

Feature.Template
Template class for a plain feature.

FeatureFilter
A filter for accepting or rejecting a feature.

FeatureFilter.ByAnnotationType
A filter that returns all features that have an annotation bundle that is of a given annotation type.

FeatureHolder
The interface for objects that contain features.

FeatureRealizer
Interface for translators which map from Feature.Template instances to real Feature objects.

FeatureTypes.Repository
A named collection of Types.

FeatureTypes.Type
A type of feature.

FilterUtils.FilterTransformer
An object able to transform some FeatureFilter instances sytematically into others.

Frame
Title: Frame.

FramedFeature.ReadingFrame
A singleton to hold the frame information

GappedSequence
Extension of GappedSymbolList which also projects features into the gapped coordinate system.

OptimizableFilter
The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.

RealizingFeatureHolder
Interface for FeatureHolder objects which know how to instantiate new child Features.

RemoteFeature
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.

RemoteFeature.Resolver
The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.

Sequence
A biological sequence.

StrandedFeature
Adds the concept of 'strand' to features.

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.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db

FeatureFilter
A filter for accepting or rejecting a feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

SequenceAnnotator
An object which adds some additional information to a Sequence.

SequenceIterator
An iterator over a bag of sequences.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db.biofetch

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db.biosql

FeatureFilter
A filter for accepting or rejecting a feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

SequenceIterator
An iterator over a bag of sequences.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db.flat

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.distributed

FeatureFilter
A filter for accepting or rejecting a feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.homol

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain feature.

FeatureHolder
The interface for objects that contain features.

StrandedFeature
Adds the concept of 'strand' to features.

StrandedFeature.Template
Template class for parameterizing the creation of a new StrandedFeature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.impl

ComponentFeature
Feature which represents a component in an assembly (contig).

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain 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.

Frame
Title: Frame.

FramedFeature
Title: FramedFeature.

FramedFeature.ReadingFrame
A singleton to hold the frame information

FramedFeature.Template

RealizingFeatureHolder
Interface for FeatureHolder objects which know how to instantiate new child Features.

RemoteFeature
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.

RemoteFeature.Resolver
The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.

RemoteFeature.Template

Sequence
A biological sequence.

SequenceFactory
The interface for objects that will manufacture sequences.

SimpleFeatureHolder
A no-frills implementation of FeatureHolder.

StrandedFeature
Adds the concept of 'strand' to features.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

StrandedFeature.Template
Template class for parameterizing the creation of a new StrandedFeature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io

ComponentFeature
Feature which represents a component in an assembly (contig).

ComponentFeature.Template
Template for constructing a new ComponentFeature.

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain feature.

Sequence
A biological sequence.

SequenceIterator
An iterator over a bag of sequences.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io.agave

Feature
A feature within a sequence, or nested within another feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io.filterxml

FeatureFilter
A filter for accepting or rejecting a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io.game

Feature.Template
Template class for a plain feature.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.projection

Feature
A feature within a sequence, or nested within another feature.

Feature.Template
Template class for a plain feature.

FeatureFilter
A filter for accepting or rejecting a feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

StrandedFeature
Adds the concept of 'strand' to features.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.

Classes in org.biojava.bio.seq used by org.biojava.bio.seq.ragbag

ComponentFeature
Feature which represents a component in an assembly (contig).

Feature.Template
Template class for a plain feature.

FeatureHolder
The interface for objects that contain features.

Sequence
A biological sequence.

StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.