Package net.sf.basedb.util

This package contains some useful utility classes and methods.

See:
Description

Interface Summary

DynamicFilter	This interface is used together with the BioAssaySetFilterUtil class to help a plugin filter the data of a bioassay set.
IntensityCalculator	This interface is used together with the IntensityCalculatorUtil class to help a plugin calculate intensities from raw data spots.

Class Summary

AnnotationUtil	Utility class for working with annotations.
AnnotationUtil.AnnotatableWrapper	This wrapper class is needed because we need to keep track of the RawBioAssay.getArrayNum() property until we have loaded the Labeled Extracts of a Hybridization.
ArrayIterator<E>	This class implements the Iterator interface for an array of objects.
AutoDetectFileFormat	This class has methods for autodetecting file formats.
AutoDetectFileFormat.IsImportableFilter	Filter implementation that filters a collection of ContextUtil.ContextResult:s by checking each plug-ins ability to import a given file.
BioAssaySetFilterUtil	This is a utility class for plugins that filters bioassay set data.
BioAssaySetUtil	This is a utility class for BioAssaySet.
ChainedProgressReporter	An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.
ClassLocal<E>	This class is a similar to the JDK ThreadLocal class, but stores one object per class instead of one object per thread.
ClassUtil	Utility class for Class objects.
ColorGenerator	This class is used to generate colors for numerical values.
ComparableComparator<T extends Comparable<T>>	A comparator implemenation for any Comparable objects.
ConsoleProgressReporter	An implementation of the ProgressReporter interface that writes all messages to the standard console.
ContextUtil	A class with utility methods for plug-ins.
ContextUtil.ContextResult	Class for holding the result of a call to the InteractivePlugin.isInContext(GuiContext, Object) method.
ContextUtil.IsInContextFilter	Filter implementation that works on collections of ContextUtil.ContextResult:s and return only those that return true from ContextUtil.ContextResult.isInContext().
Coordinate	Util class for coordinate transformations in base.
Diff3	This class is helpful when a client application needs to implement long-running transactions and still be able to update items with as few clashes as possible.
EmailUtil	Utility class for email sending.
Enumeration<K,V>
Enumeration.Entry<K,V>
EqualsHelper	Helper class for implementing equals and hash code calculations in classes.
FileCopyRunnable	Runnable implementation that copies data from an input stream to an output stream when executed.
FileExportOutputStream	An extension to the ExportOutputStream class which directs the output to a File in BASE.
FileImportInputStream	An extension to the ImportInputStream class which reads from a file on the BASE file system.
FileUtil	This class collects some useful methods for file and stream handling.
HttpUtil	Useful methods related to HTTP stuff in general and Apache HTTP components in particular.
IncludeExcludeFilter
InputStreamCombiner	An input stream implementation that reads one or more input streams sequentially.
InputStreamSplitter	This class can be used to split an input stream into one or more additional output streams.
InputStreamTracker	This class is used to keep track of the number of bytes read from the underlying input stream.
IntensityCalculatorUtil	This is a utility class for plugins that calculate intensities from raw spot data.
IntensityCalculatorUtil.JepIntensityCalculatorImpl	An implementation of the IntensityCalculator interface using JEP expressions.
JarClassLoader	A class loader implementation that loads classes from JAR files.
JarClassLoader.JarInfo
MD5	This class calculates the MD5 hash of a string and returns it represented as a hexadecimal string.
NameableComparator<T extends Nameable>	An implementation of the Comparator interface which uses the name of Nameable items to compare the objects.
NestedIterator<E>	This class implements the Iterator interface for iterating multiple collections as if it was one big collection.
NumberFormatUtil	Utility class for working with NumberFormat object.
OlderThanFileFilter	An implementation of the FileFilter interface that filter files based on their age.
OwnableUtil
PluginConfigInfo	This class should be used to keep information about a plugin configuration that is loaded from an XML-file.
PluginInfo	A PluginInfo object is used to keep information about external plugin located in a jar file.
PriorityComparator<T>	A comparator implemenation that sorts a given set of objects before all other object.
QueryParameters	Utiltity class for parsing string values in the form of HTTP request query parameters: key1=value1&key2=value2...
RegexpFileFilter	An implementation of the FileFilter interface that filter files and directories based on regular expressions.
RemovableUtil
ShareableUtil
SocketUtil	This class contains some useful methods when working with sockets.
StaticCache	A cache for storing data to files on the file system.
StaticCache.CleanupTask	A timer task that clean up the cache when it is executed.
StaticCache.LockEntry	Keeps track of a locked cached entry.
StaticCache.LockSafeInputStream	A lock-safe input stream that releases the associated read lock when the stream is closed.
StaticCache.LockSafeOutputStream	A lock-safe output stream that releases the associated write lock when the stream is closed.
StreamCacher	Caches the contents of a stream to a local temporary file.
StringLengthComparator	A comparator implementation for strings that sorts them according to their length.
ToStringComparator<T>	An implementation of the Comparator interface which uses the result of the toString method to compare the objects.
Tree<E>
Tree.Entry<E>	Represents an entry for a node in the tree.
Values	This class contains a set of static methods that may be useful for handling strings, ints and other values.
XMLUtil	This class contains some useful methods for handling XML documents.
XMLUtil.Validator	This class is used to handle callbacks from the XML parser.

Package net.sf.basedb.util Description

This package contains some useful utility classes and methods. They are used by the core but can also be used by other client programs, since they do not depend on the core.