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.
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Classes in org.biojava.utils used by org.biojava.bioClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.alignmentClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.annodbClassDescriptionException thrown when an error occurs in document parsing.
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Classes in org.biojava.utils used by org.biojava.bio.distClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.dpClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.gui.sequenceClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.molbioClassDescriptionThis 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. -
Classes in org.biojava.utils used by org.biojava.bio.program.gff
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Classes in org.biojava.utils used by org.biojava.bio.program.gff3ClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.program.hmmerClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.program.homologeneClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.program.indexdbClassDescriptionException thrown when an error occurs in document parsing.
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Classes in org.biojava.utils used by org.biojava.bio.program.phredClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.program.tagvalue
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Classes in org.biojava.utils used by org.biojava.bio.program.unigeneClassDescriptionThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.program.xffClassDescriptionException which is thrown when a ChangeListener does not wish a change to take place.
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Classes in org.biojava.utils used by org.biojava.bio.proteomicsClassDescriptionException which is thrown when a ChangeListener does not wish a change to take place.
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Classes in org.biojava.utils used by org.biojava.bio.searchClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seqClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.dbClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.db.biofetchClassDescriptionThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.db.biosqlClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.db.flatClassDescriptionThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.distributedClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.homolClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.implClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.ioClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.seq.projectionClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.symbolClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.bio.taxaClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.ontologyClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojava.utilsClassDescriptionThis 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 byProcessTools
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. -
Classes in org.biojava.utils used by org.biojava.utils.cache
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Classes in org.biojava.utils used by org.biojava.utils.processClassDescription
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.biojavaxClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.bioClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.bio.dbClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.bio.db.biosqlClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.bio.db.ncbiClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.bio.seqClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.bio.taxaClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.gaClassDescriptionThis 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.
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Classes in org.biojava.utils used by org.biojavax.ga.functionsClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.ga.implClassDescriptionUseful base-class for objects implementing ChangeableThis 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.
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Classes in org.biojava.utils used by org.biojavax.ontologyClassDescriptionUseful base-class for objects implementing ChangeableThis 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.