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Packages that use org.biojava.utils | |
org.biojava.bibliography | The data structures and interfaces included in this package define an interoperable framework for bibliographic searches. |
org.biojava.bio | The core classes that will be used throughout the bio packages. |
org.biojava.bio.alignment |
Implementation of the Alignment interface. |
org.biojava.bio.chromatogram | Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment. |
org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.gui.sequence | Graphical displays of biological sequences and associated annotations. |
org.biojava.bio.molbio | The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. |
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.program.gff | GFF manipulation. |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
org.biojava.bio.program.indexdb | A flat-file ascii index of ascii flat files as per the OBDA specification. |
org.biojava.bio.program.phred | Parser for Phred output |
org.biojava.bio.program.ssaha | SSAHA sequence searching API. |
org.biojava.bio.program.tagvalue | Process files as streams of records, each with tags with values. |
org.biojava.bio.program.unigene | Objects for representing Unigene clusters. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
org.biojava.bio.search | Interfaces and classes for representing sequence similarity search results. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.db | Collections of biological sequence data. |
org.biojava.bio.seq.db.biofetch | Client for the OBDA BioFetch protocol. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.db.flat | Support for OBDA flatfile databases. |
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources. |
org.biojava.bio.seq.homol | The classes and interfaces for defining sequence similarity and honology. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.seq.projection | Code for projecting Feature objects into alternate coordinate systems. |
org.biojava.bio.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
org.biojava.bio.taxa | Taxonomy object for representing species information. |
org.biojava.directory | Open Bio Sequence Database Access (OBDA) registry support. |
org.biojava.utils | Miscellaneous utility classes used by other BioJava components. |
org.biojava.utils.cache | A simple cache system with pluggable caching behaviours. |
org.biojava.utils.candy | The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies. |
Classes in org.biojava.utils used by org.biojava.bibliography | |
NestedException
A general perpose Exception that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.bio | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
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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. |
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ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
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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. |
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ChangeListener
Interface for objects which listen to ChangeEvents. |
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ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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NestedError
A general purpose Error that can wrap another Throwable object. |
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NestedException
A general perpose Exception that can wrap another exception. |
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NestedRuntimeException
A general perpose RuntimeException that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.bio.alignment | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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NestedRuntimeException
A general perpose RuntimeException that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.bio.chromatogram | |
NestedException
A general perpose Exception that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.bio.dist | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
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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. |
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ChangeListener
Interface for objects which listen to ChangeEvents. |
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ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.dp | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
|
ChangeForwarder
This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
|
NestedException
A general perpose Exception that can wrap another exception. |
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Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.gui.sequence | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
|
ChangeForwarder
This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.molbio | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
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ThreadPool
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava. |
Classes in org.biojava.utils used by org.biojava.bio.program.das | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
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ActivityListener
Interface for object which monitor long-running activities. |
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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. |
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ChangeListener
Interface for objects which listen to ChangeEvents. |
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ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.program.gff | |
ParserException
Exception thrown when an error occurs in document parsing. |
Classes in org.biojava.utils used by org.biojava.bio.program.hmmer | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.program.indexdb | |
NestedException
A general perpose Exception that can wrap another exception. |
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ParserException
Exception thrown when an error occurs in document parsing. |
Classes in org.biojava.utils used by org.biojava.bio.program.phred | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
Classes in org.biojava.utils used by org.biojava.bio.program.ssaha | |
NestedException
A general perpose Exception that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.bio.program.tagvalue | |
ParserException
Exception thrown when an error occurs in document parsing. |
Classes in org.biojava.utils used by org.biojava.bio.program.unigene | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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ParserException
Exception thrown when an error occurs in document parsing. |
Classes in org.biojava.utils used by org.biojava.bio.program.xff | |
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.proteomics | |
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.search | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
Classes in org.biojava.utils used by org.biojava.bio.seq | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.seq.db | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
|
ChangeForwarder
This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
|
NestedException
A general perpose Exception that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.bio.seq.db.biofetch | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
|
Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.seq.db.biosql | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.seq.db.flat | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
|
Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.seq.distributed | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.seq.homol | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
|
Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.seq.impl | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.seq.io | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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NestedException
A general perpose Exception that can wrap another exception. |
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ParseErrorEvent
Event which signals a bad line when parsing a record. |
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ParseErrorListener
Listener for a ParseErrorEvent. |
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ParseErrorSource
Source for a ParseErrorEvent. |
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Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.seq.projection | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
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ChangeListener
Interface for objects which listen to ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.seq.ragbag | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
Classes in org.biojava.utils used by org.biojava.bio.symbol | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
|
ChangeForwarder
This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source. |
|
ChangeListener
Interface for objects which listen to ChangeEvents. |
|
ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
|
ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
|
NestedException
A general perpose Exception that can wrap another exception. |
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Unchangeable
This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Classes in org.biojava.utils used by org.biojava.bio.taxa | |
AbstractChangeable
Useful base-class for objects implementing Changeable |
|
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
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ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
|
ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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NestedException
A general perpose Exception that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.directory | |
NestedException
A general perpose Exception that can wrap another exception. |
Classes in org.biojava.utils used by org.biojava.utils | |
Changeable
This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents. |
|
ChangeEvent
Event which encapsulates a change in any mutable BioJava object. |
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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. |
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ChangeHub
Interface implemented by ChangeHubs, i.e. |
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ChangeListener
Interface for objects which listen to ChangeEvents. |
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ChangeSupport
A utility class to provide management for informing ChangeListeners of ChangeEvents. |
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ChangeType
Class for all constants which are used to indicate change types. |
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ChangeVetoException
Exception which is thrown when a ChangeListener does not wish a change to take place. |
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Commitable
Implementations of Commitable support atomic changes
from one known state to another via commit/rollback semantics. |
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IndexedChangeHub.ListenerMemento
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NestedException
A general perpose Exception that can wrap another exception. |
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ParseErrorEvent
Event which signals a bad line when parsing a record. |
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ParseErrorListener
Listener for a ParseErrorEvent. |
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ThreadPool
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava. |
Classes in org.biojava.utils used by org.biojava.utils.cache | |
ChangeType
Class for all constants which are used to indicate change types. |
Classes in org.biojava.utils used by org.biojava.utils.candy | |
NestedException
A general perpose Exception that can wrap another exception. |
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