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.
Interface Summary Interface Description DynamicFilterThis interface is used together with the
BioAssaySetFilterUtilclass to help a plugin filter the data of a bioassay set.
InputStreamTracker.ScaleFactorA scale factor can be used to match number of read bytes to something that better resembles actual progress. IntensityCalculatorThis interface is used together with the
IntensityCalculatorUtilclass to help a plugin calculate intensities from raw data spots.
Class Summary Class Description AnnotationUtilUtility class for working with annotations. AnnotationUtil.AnnotatableWrapperThis 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 AnyToAnyLinkStatisticsClass for holding statisics about any-to-any links between items. AnyToAnyLinkStatistics.OptionsOptions to specify how the statistics should be generated. ArrayIterator<E>This class implements the
Iteratorinterface for an array of objects.
AutoDetectFileFormatThis class has methods for autodetecting file formats. AutoDetectFileFormat.IsImportableFilterFilter implementation that filters a collection of
ContextUtil.ContextResult:s by checking each plug-ins ability to import a given file.
BioAssaySetFilterUtilThis is a utility class for plugins that filters bioassay set data. BioAssaySetUtilThis is a utility class for
ChainedProgressReporterAn 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
ThreadLocalclass, but stores one object per class instead of one object per thread.
ClassUtilUtility class for
ColorGeneratorThis class is used to generate colors for numerical values. ComparableComparator<T extends Comparable<T>>A comparator implemenation for any Comparable objects. ConsoleProgressReporterAn implementation of the ProgressReporter interface that writes all messages to the standard console. ContextUtilA class with utility methods for plug-ins. ContextUtil.ContextResultClass for holding the result of a call to the
ContextUtil.IsInContextFilter CoordinateUtil class for coordinate transformations in base. Diff3This 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. EmailUtilUtility class for email sending. Enumeration<K,V> Enumeration.Entry<K,V> EqualsHelperHelper class for implementing equals and hash code calculations in classes. FileCopyRunnableRunnable implementation that copies data from an input stream to an output stream when executed. FileExportOutputStream FileImportInputStreamAn extension to the
ImportInputStreamclass which reads from a file on the BASE file system.
FileUtilThis class collects some useful methods for file and stream handling. GeoLocationUtility class for geographic location. GeoLocation.ResponseFilterWe only accept "200" status response, "application/json" content type and not more than 1K bytes (should be a lot less under normal operations). HttpUtilUseful methods related to HTTP stuff in general and Apache HTTP components in particular. IncludeExcludeFilter InputStreamCombinerAn input stream implementation that reads one or more input streams sequentially. InputStreamSplitterThis class can be used to split an input stream into one or more additional output streams. InputStreamTrackerThis class is used to keep track of the number of bytes read from the underlying input stream. InputStreamTracker.CurvedScaleFactorApply a curved scale factor that has a max upper limit. InputStreamTracker.IdentityScaleFactorDo not scale number of bytes. InputStreamTracker.LinearScaleFactorApply a linear scale factor so that when we have read N actual bytes the getNumRead() method return N*scale bytes. IntensityCalculatorUtilThis is a utility class for plugins that calculate intensities from raw spot data. IntensityCalculatorUtil.JepIntensityCalculatorImplAn implementation of the
IntensityCalculatorinterface using JEP expressions.
JarClassLoaderA class loader implementation that loads classes from JAR files. JarClassLoader.JarClassLoaderProxyA proxy class loader is typically needed when one extension depends on another extension. JarClassLoader.JarInfo ListUtil MD5This class calculates the MD5 hash of a string and returns it represented as a hexadecimal string. NameableComparator<T extends Nameable>An implementation of the
Comparatorinterface which uses the name of
Nameableitems to compare the objects.
NestedIterator<E>This class implements the
Iteratorinterface for iterating multiple collections as if it was one big collection.
NumberFormatUtilUtility class for working with
OlderThanFileFilterAn implementation of the
FileFilterinterface that filter files based on their age.
OwnableUtil PriorityComparator<T>A comparator implemenation that sorts a given set of objects before all other object. ProgressInputStreamInput stream wrapper that calls a progress reporter at regular intervals. QueryParametersUtiltity class for parsing string values in the form of HTTP request query parameters: RegexpFileFilterAn implementation of the
FileFilterinterface that filter files and directories based on regular expressions.
RemovableUtil ShareableUtil SocketUtilThis class contains some useful methods when working with sockets. StaticCacheA cache for storing data to files on the file system. StaticCache.CleanupTaskA timer task that clean up the cache when it is executed. StaticCache.LockEntryKeeps track of a locked cached entry. StaticCache.LockSafeInputStreamA lock-safe input stream that releases the associated read lock when the stream is closed. StaticCache.LockSafeOutputStreamA lock-safe output stream that releases the associated write lock when the stream is closed. StaticCache.StateInner class for performing the actual release of locks and closing of streams (in/out). StreamCacherCaches the contents of a stream to a local temporary file. StringLengthComparatorA comparator implementation for strings that sorts them according to their length. ToStringComparator<T>An implementation of the
Comparatorinterface which uses the result of the
toStringmethod to compare the objects.
TransferRateProgressReporterA 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. ValuesThis class contains a set of static methods that may be useful for handling strings, ints and other values. XmlUtil2This class contains some useful methods for handling XML documents using JDOM2. XmlUtil2.ValidatorThis class is used to handle callbacks from the XML parser.