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 Implementation of the Alignment interface. 
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.gff GFF manipulation. 
org.biojava.bio.program.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
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.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.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 into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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.utils.math Mathematical utility classes. 
 

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.
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.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.
Annotatable.AnnotationForwarder
          A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
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
Annotatable.AnnotationForwarder
          A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
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.gff
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.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.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
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.search
Annotatable
          Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder
          A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
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.
Annotatable.AnnotationForwarder
          A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
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.
 

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
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 Map.
 

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.
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.ragbag
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.symbol
Annotatable
          Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder
          A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
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.utils.math
BioException
          A nestable biological exception.