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.
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ClassDescriptionUtility class for working with annotations.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.Class for holding statisics about any-to-any links between items.Options to specify how the statistics should be generated.This class implements the
Iterator
interface for an array of objects.This class has methods for autodetecting file formats.Filter implementation that filters a collection ofContextUtil.ContextResult
:s by checking each plug-ins ability to import a given file.This is a utility class for plugins that filters bioassay set data.This is a utility class forBioAssaySet
.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.Utility class forClass
objects.This class is used to generate colors for numerical values.ComparableComparator<T extends Comparable<T>>A comparator implemenation for any Comparable objects.An implementation of the ProgressReporter interface that writes all messages to the standard console.A class with utility methods for plug-ins.Class for holding the result of a call to theInteractivePlugin.isInContext(GuiContext, Object)
method.Filter implementation that works on collections ofContextUtil.ContextResult
:s and return only those that return true fromContextUtil.ContextResult.isInContext()
.Util class for coordinate transformations in base.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.This interface is used together with theBioAssaySetFilterUtil
class to help a plugin filter the data of a bioassay set.Utility class for email sending.Enumeration<K,V> Enumeration.Entry<K,V> Helper class for implementing equals and hash code calculations in classes.Runnable implementation that copies data from an input stream to an output stream when executed.An extension to theExportOutputStream
class which directs the output to aFile
in BASE.An extension to theImportInputStream
class which reads from a file on the BASE file system.This class collects some useful methods for file and stream handling.Utility class for geographic location.We only accept "200" status response, "application/json" content type and not more than 1K bytes (should be a lot less under normal operations).Useful methods related to HTTP stuff in general and Apache HTTP components in particular.An input stream implementation that reads one or more input streams sequentially.This class can be used to split an input stream into one or more additional output streams.This class is used to keep track of the number of bytes read from the underlying input stream.Apply a curved scale factor that has a max upper limit.Do not scale number of bytes.Apply a linear scale factor so that when we have read N actual bytes the getNumRead() method return N*scale bytes.A scale factor can be used to match number of read bytes to something that better resembles actual progress.This interface is used together with theIntensityCalculatorUtil
class to help a plugin calculate intensities from raw data spots.This is a utility class for plugins that calculate intensities from raw spot data.An implementation of theIntensityCalculator
interface using JEP expressions.A class loader implementation that loads classes from JAR files.A proxy class loader is typically needed when one extension depends on another extension.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.This class implements theIterator
interface for iterating multiple collections as if it was one big collection.Utility class for working withNumberFormat
object.An implementation of theFileFilter
interface that filter files based on their age.A comparator implemenation that sorts a given set of objects before all other object.Input stream wrapper that calls a progress reporter at regular intervals.Utiltity class for parsing string values in the form of HTTP request query parameters:An implementation of theFileFilter
interface that filter files and directories based on regular expressions.This class contains some useful methods when working with sockets.A cache for storing data to files on the file system.A timer task that clean up the cache when it is executed.Keeps track of a locked cached entry.A lock-safe input stream that releases the associated read lock when the stream is closed.A lock-safe output stream that releases the associated write lock when the stream is closed.Inner class for performing the actual release of locks and closing of streams (in/out).Caches the contents of a stream to a local temporary file.A comparator implementation for strings that sorts them according to their length.An implementation of theComparator
interface which uses the result of thetoString
method to compare the objects.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.This class contains a set of static methods that may be useful for handling strings, ints and other values.This class contains some useful methods for handling XML documents using JDOM2.This class is used to handle callbacks from the XML parser.