See: Description
Interface | Description |
---|---|
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 | 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 | |
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 java.lang.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 | |
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.
|
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. |
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.
|
XMLUtil |
This class contains some useful methods for handling
XML documents.
|
XMLUtil.Validator |
This class is used to handle callbacks from the XML parser.
|