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.