## Uses of Package
org.biojava.utils

Packages that use org.biojava.utils
org.biojava.bibliography: The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
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.gui.sequence: Graphical displays of biological sequences and associated annotations.
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.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.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.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: Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.cache: A simple cache system with pluggable caching behaviours.
org.biojava.utils.candy: The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.

Classes in org.biojava.utils used by org.biojava.bibliography
NestedException A general perpose Exception that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.bio
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedError A general purpose Error that can wrap another Throwable object.
NestedException A general perpose Exception that can wrap another exception.
NestedRuntimeException A general perpose RuntimeException that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.bio.alignment
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedRuntimeException A general perpose RuntimeException that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.bio.chromatogram
NestedException A general perpose Exception that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.bio.dist
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.dp
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedException A general perpose Exception that can wrap another exception.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.gui.sequence
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.molbio
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ThreadPool `ThreadPool` specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.

Classes in org.biojava.utils used by org.biojava.bio.program.das
AbstractChangeable Useful base-class for objects implementing Changeable
ActivityListener Interface for object which monitor long-running activities.
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.program.gff
ParserException Exception thrown when an error occurs in document parsing.

Classes in org.biojava.utils used by org.biojava.bio.program.hmmer
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.program.indexdb
NestedException A general perpose Exception that can wrap another exception.
ParserException Exception thrown when an error occurs in document parsing.

Classes in org.biojava.utils used by org.biojava.bio.program.phred
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.

Classes in org.biojava.utils used by org.biojava.bio.program.ssaha
NestedException A general perpose Exception that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.bio.program.tagvalue
ParserException Exception thrown when an error occurs in document parsing.

Classes in org.biojava.utils used by org.biojava.bio.program.unigene
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
ParserException Exception thrown when an error occurs in document parsing.

Classes in org.biojava.utils used by org.biojava.bio.program.xff
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.proteomics
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.search
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.

Classes in org.biojava.utils used by org.biojava.bio.seq
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.seq.db
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedException A general perpose Exception that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.bio.seq.db.biofetch
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.seq.db.biosql
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.seq.db.flat
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.seq.distributed
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.seq.homol
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.seq.impl
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.seq.io
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedException A general perpose Exception that can wrap another exception.
ParseErrorEvent Event which signals a bad line when parsing a record.
ParseErrorListener Listener for a ParseErrorEvent.
ParseErrorSource Source for a ParseErrorEvent.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.seq.projection
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.seq.ragbag
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.

Classes in org.biojava.utils used by org.biojava.bio.symbol
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedException A general perpose Exception that can wrap another exception.
Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Classes in org.biojava.utils used by org.biojava.bio.taxa
AbstractChangeable Useful base-class for objects implementing Changeable
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
NestedException A general perpose Exception that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.directory
NestedException A general perpose Exception that can wrap another exception.

Classes in org.biojava.utils used by org.biojava.utils
Changeable This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeEvent Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeHub Interface implemented by ChangeHubs, i.e.
ChangeListener Interface for objects which listen to ChangeEvents.
ChangeSupport A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeType Class for all constants which are used to indicate change types.
ChangeVetoException Exception which is thrown when a ChangeListener does not wish a change to take place.
Commitable Implementations of `Commitable` support atomic changes from one known state to another via commit/rollback semantics.
IndexedChangeHub.ListenerMemento
NestedException A general perpose Exception that can wrap another exception.
ParseErrorEvent Event which signals a bad line when parsing a record.
ParseErrorListener Listener for a ParseErrorEvent.
ThreadPool `ThreadPool` specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.

Classes in org.biojava.utils used by org.biojava.utils.cache
ChangeType Class for all constants which are used to indicate change types.

Classes in org.biojava.utils used by org.biojava.utils.candy
NestedException A general perpose Exception that can wrap another exception.