|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
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.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 | |
---|---|
Sequence
A biological sequence. |
|
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.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. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |