Uses of Package
org.biojava.utils
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Packages that use org.biojava.utils 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 outputorg.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 ofSequence
andFeature
.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 functionalityorg.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 databasesorg.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 frameworkorg.biojavax.ga.functions GA functionsorg.biojavax.ga.impl Default implementations and abstract classes.org.biojavax.ontology Extensions to the biojava ontology model that represent BioSQL ontology. -
Classes in org.biojava.utils used by org.biojava.bio Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.alignment Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.annodb Class Description CommitFailure ParserException Exception thrown when an error occurs in document parsing. -
Classes in org.biojava.utils used by org.biojava.bio.dist Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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 Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.gui.sequence Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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 Class 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. -
Classes in org.biojava.utils used by org.biojava.bio.program.gff Class Description ParserException Exception thrown when an error occurs in document parsing. -
Classes in org.biojava.utils used by org.biojava.bio.program.gff3 Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.hmmer Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.homologene Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.program.indexdb Class Description CommitFailure ParserException Exception thrown when an error occurs in document parsing. -
Classes in org.biojava.utils used by org.biojava.bio.program.phred Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.program.tagvalue Class Description ParserException Exception thrown when an error occurs in document parsing. -
Classes in org.biojava.utils used by org.biojava.bio.program.unigene Class 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. -
Classes in org.biojava.utils used by org.biojava.bio.program.xff Class Description 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 Class Description 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 Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.seq Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.seq.db Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.seq.db.biofetch Class 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. -
Classes in org.biojava.utils used by org.biojava.bio.seq.db.biosql Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.seq.db.flat Class 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. -
Classes in org.biojava.utils used by org.biojava.bio.seq.distributed Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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 Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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 Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.seq.io Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.seq.projection Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.bio.symbol Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.taxa Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.ontology Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojava.utils Class 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 ofCommitable
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 byProcessTools
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. -
Classes in org.biojava.utils used by org.biojava.utils.cache Class Description ChangeType Class for all constants which are used to indicate change types. -
Classes in org.biojava.utils used by org.biojava.utils.process Class Description 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.biojavax Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.biojavax.bio Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojavax.bio.db Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojavax.bio.db.biosql Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.biojavax.bio.db.ncbi Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.biojavax.bio.seq Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojavax.bio.taxa Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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. -
Classes in org.biojava.utils used by org.biojavax.ga Class 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. -
Classes in org.biojava.utils used by org.biojavax.ga.functions Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.biojavax.ga.impl Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.biojavax.ontology Class Description AbstractChangeable Useful base-class for objects implementing ChangeableChangeable 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.