Package | Description |
---|---|
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.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.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.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 and systematically altering their
properties.
|
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.ontology |
A general-purpose API for ontologies.
|
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.process |
Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
|
org.biojavax |
The Biojava extensions packages, classes that extend the core biojava
functionality
The biojavax packages contain a number of extensions to the core biojava
interfaces.
|
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.taxa |
Objects that model the NCBI taxonomy schema as described in the BioSQL
schema.
|
org.biojavax.ga |
Classes to provide a genetic algorithm framework
|
org.biojavax.ga.functions |
GA functions
A genetic algorithm requires a number of functions.
|
org.biojavax.ga.impl |
Default implementations and abstract classes.
|
org.biojavax.ontology |
Extensions to the biojava ontology model that represent BioSQL ontology.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
CommitFailure |
ParserException
Exception thrown when an error occurs in document parsing.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
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.
|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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. |
Class and Description |
---|
ParserException
Exception thrown when an error occurs in document parsing.
|
Class and Description |
---|
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.
|
ParserException
Exception thrown when an error occurs in document parsing.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
CommitFailure |
ParserException
Exception thrown when an error occurs in document parsing.
|
Class and Description |
---|
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.
|
ParseErrorEvent
Event which signals a bad line when parsing a record.
|
ParseErrorListener
Listener for a ParseErrorEvent.
|
ParseErrorSource
Source for a ParseErrorEvent.
|
Class and Description |
---|
ParserException
Exception thrown when an error occurs in document parsing.
|
Class and Description |
---|
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.
|
Class and Description |
---|
ChangeVetoException
Exception which is thrown when a ChangeListener does not
wish a change to take place.
|
Class and Description |
---|
ChangeVetoException
Exception which is thrown when a ChangeListener does not
wish a change to take place.
|
Class and Description |
---|
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.
|
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.
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of
ChangeEvents.
|
ChangeType
Class for all constants which are used to indicate change
types.
|
TriState
Class that represents the tristate values possible in
a logical operation: true, false and indeterminate.
|
Class and Description |
---|
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.
|
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.
|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
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.
|
Class and Description |
---|
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.
|
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.
|
Class and Description |
---|
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.
|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Unchangeable
This is a utility implementation of Changeable that doesn't fire any events
or keep references to any listeners.
|
Class and Description |
---|
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.
|
ChangeAdapter
This is a ChangeListener that ignores everything.
|
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. |
CommitFailure |
IndexedChangeHub.ListenerMemento |
ListTools.Mapper
Maps one object to another.
|
ListTools.SeriesList
A list that represents a series of values.
|
MergingSet |
ParseErrorEvent
Event which signals a bad line when parsing a record.
|
ParseErrorListener
Listener for a ParseErrorEvent.
|
ProcessTimeoutException
Exception which is thrown if a child process managed by
ProcessTools
exceeds a specified time limit. |
ThreadPool
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava. |
TriState
Class that represents the tristate values possible in
a logical operation: true, false and indeterminate.
|
Class and Description |
---|
ChangeType
Class for all constants which are used to indicate change
types.
|
Class and Description |
---|
ThreadPool
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava. |
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
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.
|
Class and Description |
---|
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.
|
Class and Description |
---|
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.
|
Copyright © 2014 BioJava. All rights reserved.