Uses of Package
org.biojava.utils

Packages that use org.biojava.utils
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
Databases of generic structured data (annotation) objects.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
GFF manipulation.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
Support classes for Homologene data.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Parser for Phred output
Process files as streams of records, each with tags with values.
Objects for representing Unigene clusters.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken from a number of data sources.
The classes and interfaces for defining sequence similarity and honology.
Standard in-memory implementations of Sequence and Feature.
Classes and interfaces for processing and producing flat-file representations of sequences.
Code for projecting Feature objects and systematically altering their properties.
Representation of the Symbols that make up a sequence, and locations within them.
Taxonomy object for representing species information.
A general-purpose API for ontologies.
Miscellaneous utility classes used by other BioJava components.
A simple cache system with pluggable caching behaviours.
Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
The Biojava extensions packages, classes that extend the core biojava functionality
Classes to represent biological entities and their relationships.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Rich implementations of Sequences, Locations and Features.
Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Extensions to the biojava ontology model that represent BioSQL ontology.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which encapsulates a change in any mutable BioJava object.
    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.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
     
    Exception thrown when an error occurs in document parsing.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which encapsulates a change in any mutable BioJava object.
    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.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    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.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which encapsulates a change in any mutable BioJava object.
    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.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    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 specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
  • Class
    Description
    Exception thrown when an error occurs in document parsing.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    Exception thrown when an error occurs in document parsing.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
     
    Exception thrown when an error occurs in document parsing.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which signals a bad line when parsing a record.
    Listener for a ParseErrorEvent.
    Source for a ParseErrorEvent.
  • Class
    Description
    Exception thrown when an error occurs in document parsing.
  • Class
    Description
    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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    Exception thrown when an error occurs in document parsing.
  • Class
    Description
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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.
    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.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Class that represents the tristate values possible in a logical operation: true, false and indeterminate.
  • Class
    Description
    Useful base-class for objects implementing 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.
    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.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which encapsulates a change in any mutable BioJava object.
    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.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    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.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    Event which signals a bad line when parsing a record.
    Listener for a ParseErrorEvent.
    Source for a ParseErrorEvent.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which encapsulates a change in any mutable BioJava object.
    Interface for objects which listen to ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Event which encapsulates a change in any mutable BioJava object.
    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.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    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.
    This is a ChangeListener that ignores everything.
    Event which encapsulates a change in any mutable BioJava object.
    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.
    Interface implemented by ChangeHubs, i.e.
    Interface for objects which listen to ChangeEvents.
    A utility class to provide management for informing ChangeListeners of ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    Implementations of Commitable support atomic changes from one known state to another via commit/rollback semantics.
     
     
    Maps one object to another.
    A list that represents a series of values.
     
    Event which signals a bad line when parsing a record.
    Listener for a ParseErrorEvent.
    Exception which is thrown if a child process managed by ProcessTools exceeds a specified time limit.
    ThreadPool specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
    Class that represents the tristate values possible in a logical operation: true, false and indeterminate.
  • Class
    Description
    Class for all constants which are used to indicate change types.
  • Class
    Description
    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.biojavax
    Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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
    Description
    Useful base-class for objects implementing 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.
    Interface for objects which listen to ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
    This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Interface for objects which listen to ChangeEvents.
    Class for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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.
    Exception which is thrown when a ChangeListener does not wish a change to take place.
  • Class
    Description
    Useful base-class for objects implementing 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 for all constants which are used to indicate change types.
    Exception which is thrown when a ChangeListener does not wish a change to take place.