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.