Package net.sf.basedb.util

package net.sf.basedb.util

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.

Class	Description
AnnotationUtil	Utility class for working with annotations.
AnnotationUtil.AnnotatableWrapper	This wrapper class is needed because we need to keep track of extracts linked with raw bioassays and derived bioassays until we have loaded the Extracts of a Physical Bioassay.
AnnotationUtil.Cache
AnyToAnyLinkStatistics	Class for holding statisics about any-to-any links between items.
AnyToAnyLinkStatistics.Options	Options to specify how the statistics should be generated.
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.
DynamicFilter	This interface is used together with the BioAssaySetFilterUtil class to help a plugin filter the data of a bioassay set.
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.
GeoLocation	Utility class for geographic location.
GeoLocation.ResponseFilter	We only accept "200" status response, "application/json" content type and not more than 1K bytes (should be a lot less under normal operations).
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.
InputStreamTracker.CurvedScaleFactor	Apply a curved scale factor that has a max upper limit.
InputStreamTracker.IdentityScaleFactor	Do not scale number of bytes.
InputStreamTracker.LinearScaleFactor	Apply a linear scale factor so that when we have read N actual bytes the getNumRead() method return N*scale bytes.
InputStreamTracker.ScaleFactor	A scale factor can be used to match number of read bytes to something that better resembles actual progress.
IntensityCalculator	This interface is used together with the IntensityCalculatorUtil class to help a plugin calculate intensities from raw data spots.
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.JarClassLoaderProxy	A proxy class loader is typically needed when one extension depends on another extension.
JarClassLoader.JarInfo
ListUtil
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
PriorityComparator<T>	A comparator implemenation that sorts a given set of objects before all other object.
ProgressInputStream	Input stream wrapper that calls a progress reporter at regular intervals.
QueryParameters	Utiltity class for parsing string values in the form of HTTP request query parameters:
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.
StaticCache.State	Inner class for performing the actual release of locks and closing of streams (in/out).
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.
TransferRateProgressReporter	A progress reporter implementation that has a "side-effect" that limits the transfer rate.
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.
XmlUtil2	This class contains some useful methods for handling XML documents using JDOM2.
XmlUtil2.Validator	This class is used to handle callbacks from the XML parser.