Uses of Package
org.biojava.bio

Packages that use org.biojava.bio
org.biojava.bio The core classes that will be used throughout the bio packages. 
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
org.biojava.bio.annodb Databases of generic structured data (annotation) objects. 
org.biojava.bio.chromatogram Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment. 
org.biojava.bio.dist Probability distributions over Alphabets. 
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.dp.onehead   
org.biojava.bio.dp.twohead   
org.biojava.bio.gui Graphical interfaces for biojava objects. 
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.abi ABI Trace Handling. 
org.biojava.bio.program.das Development client for the Distributed Annotation System. 
org.biojava.bio.program.das.dasalignment   
org.biojava.bio.program.formats Experimental parsers using the tagvalue framework. 
org.biojava.bio.program.gff GFF manipulation. 
org.biojava.bio.program.gff3 Support for reading and writing GFF3. 
org.biojava.bio.program.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
org.biojava.bio.program.homologene Support classes for Homologene data. 
org.biojava.bio.program.indexdb A flat-file ascii index of ascii flat files as per the OBDA specification. 
org.biojava.bio.program.phred Parser for Phred output 
org.biojava.bio.program.sax.blastxml Parsers for the XML output from NCBI blast. 
org.biojava.bio.program.ssaha SSAHA sequence searching API. 
org.biojava.bio.program.ssbind Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. 
org.biojava.bio.program.tagvalue Process files as streams of records, each with tags with values. 
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.proteomics.aaindex Classes and interfaces to load Amino Acid Index database files. 
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.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.projection Code for projecting Feature objects and systematically altering their properties. 
org.biojava.bio.structure Interfaces and classes for protein structure (PDB). 
org.biojava.bio.structure.io Input and Output of Structures 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
org.biojava.bio.taxa Taxonomy object for representing species information. 
org.biojava.directory Open Bio Sequence Database Access (OBDA) registry support. 
org.biojava.ontology A general-purpose API for ontologies. 
org.biojava.utils.automata   
org.biojava.utils.math Mathematical utility classes. 
org.biojava.utils.regex This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets. 
org.biojava.utils.walker   
org.biojavax The Biojava extensions packages, classes that extend the core biojava functionality 
org.biojavax.bio Classes to represent biological entities and their relationships. 
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.db.ncbi Interfaces to NCBI data. 
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. 
org.biojavax.ontology Extensions to the biojava ontology model that represent BioSQL ontology. 
 

Classes in org.biojava.bio used by org.biojava.bio
AbstractAnnotation
          A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
Annotation
           Arbitrary annotation associated with one or more objects.
AnnotationType
          A set of constraints on the data contained in an Annotation.
AnnotationType.Abstract
          An abstract base class useful for implementing AnnotationType instances.
CollectionConstraint
          Used by AnnotationType to represent the constraint on the collection of values in a property-slot.
EcNumber
          An ec (enzyme classification) number.
EcNumber.Impl
          A simple implementation of EcNumber.
PropertyConstraint
          PropertyConstraints describes a constraint applied to the members of an annotation bundle.
 

Classes in org.biojava.bio used by org.biojava.bio.alignment
BioError
          A nestable biological error.
BioException
          A nestable biological exception.
BioRuntimeException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.annodb
AnnotationType
          A set of constraints on the data contained in an Annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.chromatogram
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.dist
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.dp
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.dp.onehead
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.dp.twohead
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.gui
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.molbio
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.abi
BioError
          A nestable biological error.
 

Classes in org.biojava.bio used by org.biojava.bio.program.das
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.das.dasalignment
Annotation
           Arbitrary annotation associated with one or more objects.
AnnotationType
          A set of constraints on the data contained in an Annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.formats
AnnotationType
          A set of constraints on the data contained in an Annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.gff
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.gff3
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.hmmer
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
 

Classes in org.biojava.bio used by org.biojava.bio.program.homologene
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.indexdb
Annotation
           Arbitrary annotation associated with one or more objects.
AnnotationType
          A set of constraints on the data contained in an Annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.phred
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.sax.blastxml
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.ssaha
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.ssbind
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.tagvalue
Annotation
           Arbitrary annotation associated with one or more objects.
AnnotationType
          A set of constraints on the data contained in an Annotation.
 

Classes in org.biojava.bio used by org.biojava.bio.program.unigene
Annotatable
          Indicates that an object has an associated annotation.
AnnotationType
          A set of constraints on the data contained in an Annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.program.xff
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.proteomics
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.proteomics.aaindex
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.search
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
AnnotationType
          A set of constraints on the data contained in an Annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.db
BioException
          A nestable biological exception.
BioRuntimeException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.db.biofetch
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.db.biosql
BioException
          A nestable biological exception.
BioRuntimeException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.db.flat
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.distributed
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.homol
Annotatable
          Indicates that an object has an associated annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.impl
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.io
AbstractAnnotation
          A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.io.agave
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
SimpleAnnotation
          A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.io.filterxml
AnnotationType
          A set of constraints on the data contained in an Annotation.
CollectionConstraint
          Used by AnnotationType to represent the constraint on the collection of values in a property-slot.
PropertyConstraint
          PropertyConstraints describes a constraint applied to the members of an annotation bundle.
 

Classes in org.biojava.bio used by org.biojava.bio.seq.projection
Annotatable
          Indicates that an object has an associated annotation.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.structure
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.structure.io
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.symbol
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.bio.taxa
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.directory
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.ontology
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
 

Classes in org.biojava.bio used by org.biojava.utils.automata
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.utils.math
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.utils.regex
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojava.utils.walker
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
 

Classes in org.biojava.bio used by org.biojavax.bio
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax.bio.db
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax.bio.db.biosql
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax.bio.db.ncbi
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax.bio.seq
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax.bio.seq.io
BioException
          A nestable biological exception.
 

Classes in org.biojava.bio used by org.biojavax.ontology
Annotatable
          Indicates that an object has an associated annotation.
Annotation
           Arbitrary annotation associated with one or more objects.