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.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 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
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.