Miscellaneous utility classes used by other BioJava components.
Interface Summary Interface Description ActivityListenerInterface for object which monitor long-running activities. ChangeableThis 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. ChangeHubInterface implemented by ChangeHubs, i.e. ChangeListenerInterface for objects which listen to ChangeEvents. CommitableImplementations of
Commitablesupport atomic changes from one known state to another via commit/rollback semantics.
ListTools.MapperMaps one object to another. ParseErrorListenerListener for a ParseErrorEvent. ParseErrorSourceSource for a ParseErrorEvent. ThreadPool
ThreadPoolspecifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
Class Summary Class Description AbstractChangeableUseful base-class for objects implementing Changeable BeanAsMap ChangeAdapterThis is a ChangeListener that ignores everything. ChangeEventEvent which encapsulates a change in any mutable BioJava object. ChangeForwarderThis 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.RetyperA ChangeForwarder that systematically uses a given type and wraps the old event. ChangeListener.AlwaysVetoListenerAn implementation that always vetoes everything. ChangeListener.ChangeEventRecorderA listener that remembers the ChangeEvent of the last change. ChangeListener.LoggingListenerA listener that writes information about the event stream to a PrintStream. ChangeSupportA utility class to provide management for informing ChangeListeners of ChangeEvents. ChangeTypeClass for all constants which are used to indicate change types. ClassToolsUtility methods for manipulating class objects and resources. ConstantsSome usefull constants for working with binary files. ExecRunnerMakes running external executables easier, optionally under a watched thread. FileAsList
FileAsListcreates a writable
Listimplementation backed by a random access file.
IndexedChangeHubimplements Changeable support with a ChangeHub that stores ChangeListener by key. JDBCConnectionPoolReally simple connection pool for JDBC databases. JDBCPooledDataSourceReturns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages. ListTools ListTools.Doublet ListTools.SeriesListA list that represents a series of values. ListTools.Triplet MergingIterator MergingSet ObjectUtilutility methods for implementing the equals() and hashCode() methods of Objects. OverlayMapOverlap one map onto another. ParseErrorEventEvent 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 ServicesUtility methods for handling META-INF/services files SimpleThreadPool
SimpleThreadPoolis a basic implementation of
ThreadPoolfor use where we don't wish to introduce a dependency on a 3rd-party pool.
SingletonList SmallMapLightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability. SmallSetLightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability. StaticMemberPlaceHolder TriStateClass that represents the tristate values possible in a logical operation: true, false and indeterminate. TypedPropertiesa 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. UnchangeableThis is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
Exception Summary Exception Description ChangeVetoExceptionException which is thrown when a ChangeListener does not wish a change to take place. CommitFailure ParserExceptionException thrown when an error occurs in document parsing. ProcessTimeoutExceptionException which is thrown if a child process managed by
ProcessToolsexceeds a specified time limit.
Error Summary Error Description AssertionFailureAn unchecked exception representing an Assertion failure.