| 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.
|
| Class and 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.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| SequenceAnnotator
An object which adds some additional information to a Sequence.
|
| Class and 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.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and 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. |
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and 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.
|
| Class and Description |
|---|
| StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.
|
| Class and 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.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and 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. |
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.
|
| Class and 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. |
| Class and 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.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and 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.
|
| Class and Description |
|---|
| Sequence
A biological sequence.
|
| Class and Description |
|---|
| FeatureFilter
A filter for accepting or rejecting a feature.
|
| FeatureHolder
The interface for objects that contain features.
|
| Sequence
A biological sequence.
|
| Class and 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.
|
| Class and 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. |
| Class and 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. |
| Class and 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.
|
| Class and 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.
|
| Class and Description |
|---|
| FeatureFilter
A filter for accepting or rejecting a feature.
|
| Class and Description |
|---|
| Feature.Template
Template class for a plain feature.
|
| StrandedFeature.Strand
Class to represent the 'strandedness' of a feature.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and Description |
|---|
| Feature.Template
Template class for a plain feature.
|
| Sequence
A biological sequence.
|
| SequenceIterator
An iterator over a bag of sequences.
|
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