## Uses of Package
org.biojava.bio.seq

Packages that use org.biojava.bio.seq
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.das: Development client for the Distributed Annotation System.
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.biojava.bio.structure: Interfaces and classes for protein structure (PDB).
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
SequenceIterator An iterator over a bag of sequences.

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.gui.sequence.tracklayout
Sequence A biological sequence.

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
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
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 `Feature`s 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
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.filter
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
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.
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
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.
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
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
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.biojava.bio.structure
Sequence A biological sequence.

Classes in org.biojava.bio.seq used by org.biojavax.bio.db
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
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
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
Feature.Template Template class for a plain feature.
Sequence A biological sequence.
SequenceIterator An iterator over a bag of sequences.