Uses of Package
org.biojava.bio.seq

Packages that use org.biojava.bio.seq

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
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.gui.sequence.tracklayout	Classes for the handling of the layout of a WrappedSequencePanel.
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.fastq	FASTQ and variants sequence format I/O.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
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.filter
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 and systematically altering their properties.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

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

Class	Description
GappedSequence	Extension of GappedSymbolList which also projects features into the gapped coordinate system.
Sequence	A biological sequence.
SequenceIterator	An iterator over a bag of sequences.

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

Class	Description
Sequence	A biological sequence.

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

Class	Description
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

Class	Description
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.gui.sequence.tracklayout

Class	Description
Sequence	A biological sequence.

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

Class	Description
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.fastq

Class	Description
Sequence	A biological sequence.

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

Class	Description
Feature	A feature within a sequence, or nested within another feature.
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.gff3

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

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

Class	Description
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

Class	Description
Sequence	A biological sequence.

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

Class	Description
Sequence	A biological sequence.

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

Class	Description
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

Class	Description
Sequence	A biological sequence.

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

Class	Description
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

Class	Description
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.

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

Class	Description
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

Class	Description
Sequence	A biological sequence.

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

Class	Description
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

Class	Description
Sequence	A biological sequence.

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

Class	Description
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.filter

Class	Description
FeatureFilter	A filter for accepting or rejecting a feature.
FeatureFilter.And	A filter that returns all features accepted by both child filter.
FeatureFilter.ByAncestor	Filter by applying a nested FeatureFilter to all ancestor features.
FeatureFilter.ByChild	Filter by applying a nested FeatureFilter to the child features.
FeatureFilter.ByDescendant	Filter by applying a nested FeatureFilter to all descendant features.
FeatureFilter.ByParent	Filter by applying a nested FeatureFilter to the parent feature.
FeatureFilter.Not	A filter that returns all features not accepted by a child filter.
FeatureFilter.OnlyChildren	Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyDescendants	Accepts features where all descendants meet the supplied filter.
FeatureFilter.Or	A filter that returns all features accepted by at least one child filter.

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

Class	Description
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

Class	Description
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.
FilterUtils.FilterTransformer	An object able to transform some FeatureFilter instances sytematically into others.
Frame	Title: Frame.
FramedFeature	Title: FramedFeature.
FramedFeature.ReadingFrame	A singleton to hold the frame information
FramedFeature.Template
GappedSequence	Extension of GappedSymbolList which also projects features into the gapped coordinate system.
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	Deprecated. use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder
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

Class	Description
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

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

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

Class	Description
FeatureFilter	A filter for accepting or rejecting a feature.

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

Class	Description
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

Class	Description
AbstractFeatureHolder	An abstract implementation of FeatureHolder.
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.
FilterUtils.FilterTransformer	An object able to transform some FeatureFilter instances sytematically into others.
Sequence	A biological sequence.
StrandedFeature.Strand	Class to represent the 'strandedness' of a feature.

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

Class	Description
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.biojavax.bio.db.biosql

Class	Description
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.

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

Class	Description
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.
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.biojavax.bio.seq.io

Class	Description
Feature.Template	Template class for a plain feature.
Sequence	A biological sequence.
SequenceIterator	An iterator over a bag of sequences.