Package org.biojava.utils
package org.biojava.utils
Miscellaneous utility classes used by other BioJava components.
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ClassDescriptionUseful base-class for objects implementing ChangeableInterface for object which monitor long-running activities.An unchecked exception representing an Assertion failure.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.This is a ChangeListener that ignores everything.Event which encapsulates a change in any mutable BioJava object.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.A ChangeForwarder that systematically uses a given type and wraps the old event.Interface implemented by ChangeHubs, i.e.Interface for objects which listen to ChangeEvents.An implementation that always vetoes everything.A listener that remembers the ChangeEvent of the last change.A listener that writes information about the event stream to a PrintStream.A utility class to provide management for informing ChangeListeners of ChangeEvents.Class for all constants which are used to indicate change types.Exception which is thrown when a ChangeListener does not wish a change to take place.Utility methods for manipulating class objects and resources.Implementations of
Commitablesupport atomic changes from one known state to another via commit/rollback semantics.Some usefull constants for working with binary files.Makes running external executables easier, optionally under a watched thread.FileAsListcreates a writableListimplementation backed by a random access file.implements Changeable support with a ChangeHub that stores ChangeListener by key.Really simple connection pool for JDBC databases.Returns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages.Maps one object to another.A list that represents a series of values.utility methods for implementing the equals() and hashCode() methods of Objects.Overlap one map onto another.Event which signals a bad line when parsing a record.Listener for a ParseErrorEvent.Source for a ParseErrorEvent.Exception thrown when an error occurs in document parsing.Exception which is thrown if a child process managed byProcessToolsexceeds a specified time limit.Deprecated.preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.Utility methods for handling META-INF/services filesSimpleThreadPoolis a basic implementation ofThreadPoolfor use where we don't wish to introduce a dependency on a 3rd-party pool.Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.Lightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability.ThreadPoolspecifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.Class that represents the tristate values possible in a logical operation: true, false and indeterminate.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.This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.