Package org.biojava.utils

Miscellaneous utility classes used by other BioJava components.

Interface Summary

Interface	Description
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

Class	Description
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

Exception	Description
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

Error	Description
AssertionFailure	An unchecked exception representing an Assertion failure.