Package org.biojava.utils

Miscellaneous utility classes used by other BioJava components.

See:
          Description

Interface Summary
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
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
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.
 

Package org.biojava.utils Description

Miscellaneous utility classes used by other BioJava components.