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.
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Interface Summary Interface Description DynamicFilter This interface is used together with theBioAssaySetFilterUtil
class to help a plugin filter the data of a bioassay set.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 theIntensityCalculatorUtil
class to help a plugin calculate intensities from raw data spots. -
Class Summary 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 theIterator
interface for an array of objects.AutoDetectFileFormat This class has methods for autodetecting file formats.AutoDetectFileFormat.IsImportableFilter Filter implementation that filters a collection ofContextUtil.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 forBioAssaySet
.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 JDKThreadLocal
class, but stores one object per class instead of one object per thread.ClassUtil Utility class forClass
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 theInteractivePlugin.isInContext(GuiContext, Object)
method.ContextUtil.IsInContextFilter Filter implementation that works on collections ofContextUtil.ContextResult
:s and return only those that return true fromContextUtil.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 theExportOutputStream
class which directs the output to aFile
in BASE.FileImportInputStream An extension to theImportInputStream
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.IntensityCalculatorUtil This is a utility class for plugins that calculate intensities from raw spot data.IntensityCalculatorUtil.JepIntensityCalculatorImpl An implementation of theIntensityCalculator
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 theComparator
interface which uses the name ofNameable
items to compare the objects.NestedIterator<E> This class implements theIterator
interface for iterating multiple collections as if it was one big collection.NumberFormatUtil Utility class for working withNumberFormat
object.OlderThanFileFilter An implementation of theFileFilter
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 theFileFilter
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 theComparator
interface which uses the result of thetoString
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.