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See:
Description
Interface Summary | |
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ActivityListener | Interface for object which monitor long-running activities. |
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. |
ChangeHub | Interface implemented by ChangeHubs, i.e. |
ChangeListener | Interface for objects which listen to ChangeEvents. |
Commitable | Implementations of Commitable support atomic changes
from one known state to another via commit/rollback semantics. |
ListTools.Mapper | Maps one object to another. |
ParseErrorListener | Listener for a ParseErrorEvent. |
ParseErrorSource | Source for a ParseErrorEvent. |
ThreadPool | ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava. |
Class Summary | |
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AbstractChangeable | Useful base-class for objects implementing Changeable |
BeanAsMap | |
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. |
ChangeForwarder.Retyper | A ChangeForwarder that systematically uses a given type and wraps the old event. |
ChangeListener.AlwaysVetoListener | An implementation that always vetoes everything. |
ChangeListener.ChangeEventRecorder | A listener that remembers the ChangeEvent of the last change. |
ChangeListener.LoggingListener | A listener that writes information about the event stream to a PrintStream. |
ChangeSupport | A utility class to provide management for informing ChangeListeners of ChangeEvents. |
ChangeType | Class for all constants which are used to indicate change types. |
ClassTools | Utility methods for manipulating class objects and resources. |
Constants | Some usefull constants for working with binary files. |
ExecRunner | Makes running external executables easier, optionally under a watched thread. |
FileAsList | FileAsList creates a writable List
implementation backed by a random access file. |
IndexedChangeHub | implements Changeable support with a ChangeHub that stores ChangeListener by key. |
JDBCConnectionPool | Really simple connection pool for JDBC databases. |
JDBCPooledDataSource | Returns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages. |
ListTools | |
ListTools.Doublet | |
ListTools.SeriesList | A list that represents a series of values. |
ListTools.Triplet | |
MergingIterator | |
MergingSet | |
ObjectUtil | utility methods for implementing the equals() and hashCode() methods of Objects. |
OverlayMap | Overlap one map onto another. |
ParseErrorEvent | Event which signals a bad line when parsing a record. |
ProcessTools | Deprecated. preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package. |
RepeatedCharSequence | |
Services | Utility methods for handling META-INF/services files |
SimpleThreadPool | SimpleThreadPool is a basic implementation of
ThreadPool for use where we don't wish to introduce a
dependency on a 3rd-party pool. |
SingletonList | |
SmallMap | Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability. |
SmallSet | Lightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability. |
StaticMemberPlaceHolder | |
TriState | Class that represents the tristate values possible in a logical operation: true, false and indeterminate. |
TypedProperties | a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of type XXX. |
Unchangeable | This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners. |
Exception Summary | |
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ChangeVetoException | Exception which is thrown when a ChangeListener does not wish a change to take place. |
CommitFailure | |
ParserException | Exception thrown when an error occurs in document parsing. |
ProcessTimeoutException | Exception which is thrown if a child process managed by ProcessTools
exceeds a specified time limit. |
Error Summary | |
---|---|
AssertionFailure | An unchecked exception representing an Assertion failure. |
Miscellaneous utility classes used by other BioJava components.
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