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AbstractApplicationLogger - Class in info.bioinfweb.commons.log
Implements basic functionality (especially method delegation) of a application logger.
AbstractApplicationLogger() - Constructor for class info.bioinfweb.commons.log.AbstractApplicationLogger
 
AbstractDocumentEdit - Class in info.bioinfweb.commons.swing
Implements basic functionality for edits on a document that takes track of changes.
AbstractDocumentEdit() - Constructor for class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
AbstractProgressMonitor - Class in info.bioinfweb.commons.progress
Basic implementation of the ProgressMonitor interface.
AbstractProgressMonitor() - Constructor for class info.bioinfweb.commons.progress.AbstractProgressMonitor
 
AbstractSaver - Class in info.bioinfweb.commons.io
 
AbstractSaver() - Constructor for class info.bioinfweb.commons.io.AbstractSaver
 
AbstractSwingComponent - Class in info.bioinfweb.commons.tic.toolkit
The Swing component displaying a PaintableArea.
AbstractSwingComponent(TICComponent) - Constructor for class info.bioinfweb.commons.tic.toolkit.AbstractSwingComponent
 
AbstractSWTWidget - Class in info.bioinfweb.commons.tic.toolkit
The SWT widget displaying a PaintableArea.
AbstractSWTWidget(Composite, int, TICComponent) - Constructor for class info.bioinfweb.commons.tic.toolkit.AbstractSWTWidget
 
AbstractUndoActionManagement - Class in info.bioinfweb.commons.swing
Implements basic functionality for applications using an AccessibleUndoManager to display undoable (and redoable) edits in swing submenus.
AbstractUndoActionManagement() - Constructor for class info.bioinfweb.commons.swing.AbstractUndoActionManagement
 
ACCEPT_LANG_PATTERN_ALL - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
 
ACCEPT_LANG_PATTERN_NO_COUNTRY - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
 
ACCEPT_LANG_PATTERN_NO_QUALITY - Static variable in class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
 
AcceptLanguageEntry - Class in info.bioinfweb.commons.servlet.acceptlanguage
Represents one entry in the list of accepted languages in the Accept-Language HTTP header.
AcceptLanguageEntry() - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
AcceptLanguageEntry(String, String, double) - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
AcceptLanguageEntry(String, String) - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageEntry
 
AcceptLanguageParser - Class in info.bioinfweb.commons.servlet.acceptlanguage
Class that parses the accept-language HTTP header including its quality scores.
AcceptLanguageParser() - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageParser
 
AcceptLanguageRedirectServlet - Class in info.bioinfweb.commons.servlet.acceptlanguage
This servlet redirects the client to the URL associated with its accepted language.
AcceptLanguageRedirectServlet() - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
 
AcceptLanguageRedirectServlet(String) - Constructor for class info.bioinfweb.commons.servlet.acceptlanguage.AcceptLanguageRedirectServlet
 
AccessibleUndoManager - Class in info.bioinfweb.commons.swing
An extension of UndoManager that allows to access all edit objects contained in the underlying list.
AccessibleUndoManager() - Constructor for class info.bioinfweb.commons.swing.AccessibleUndoManager
 
ActionMap - Class in info.bioinfweb.commons.swing
This class allows to store various Action objects in a Map and access them with a unique String.
ActionMap() - Constructor for class info.bioinfweb.commons.swing.ActionMap
 
add(SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
 
add(int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
 
add(int, int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
 
add(long, long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Adds the specified element to this list and moves other elements to the right if necessary.
add(long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Adds the specified element to the end of this list.
add(E) - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
 
add(int, E) - Method in class info.bioinfweb.commons.collections.PackedObjectArrayList
 
add(int, E) - Method in class info.bioinfweb.commons.collections.PackedPrimitiveWrapperArrayList
 
add(E) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
add(E) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
 
add(IOProgressListener) - Method in class info.bioinfweb.commons.io.IOProgressListenerVector
 
addAll(NonOverlappingIntervalList, int, int, boolean) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
Adds all or a part of the intervals contained in another list to this list.
addAll(NonOverlappingIntervalList) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
Adds all of the intervals contained in another list to this list.
addAll(Collection<? extends E>) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
addEdit(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
addError(String, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addError(String) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addError(String) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs an error message to the user.
addError(String, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs an error message to the user.
addError(Throwable, boolean) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs an error message to the user.
addError(Throwable, boolean, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs an error message to the user.
addError(String) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addError(String, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addError(String) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addError(String, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addError(Throwable, boolean) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addError(Throwable, boolean, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addFileChooser(JFileChooser) - Method in class info.bioinfweb.commons.swing.FileChooserDirModel
 
addFileExtension(String) - Method in class info.bioinfweb.commons.io.AbstractSaver
 
addFileExtension(String) - Method in interface info.bioinfweb.commons.io.Savable
Adds an file extension to the list of the allowed file extensions which can be entered by the user in the save as dialog.
addKeyListener(TICKeyListener) - Method in class info.bioinfweb.commons.tic.TICComponent
 
addLeadingKeyword(String, String) - Static method in class info.bioinfweb.commons.sql.SQLUtils
 
addMessage(String, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addMessage(String) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addMessage(ApplicationLoggerMessage) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs a usual message to the user.
addMessage(String) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs a usual message to the user.
addMessage(String, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs a usual message to the user.
addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.JTextAreaApplicationLogger
 
addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addMessage(String) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addMessage(String, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.SwingDocumentApplicationLogger
 
addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.TextFileApplicationLogger
 
addMessage(ApplicationLoggerMessage) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addMessage(String) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addMessage(String, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addMoreButtons(JPanel) - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
 
addMoreButtons(JPanel) - Method in class info.bioinfweb.commons.swing.OkCancelApplyHelpDialog
 
addMouseListener(TICMouseListener) - Method in class info.bioinfweb.commons.tic.TICComponent
 
addName(String) - Method in class info.bioinfweb.commons.text.UniqueNameMap
Adds an original name as the key and its processed version as the values to the map.
addNames(Collection<String>) - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
addTo(Container) - Method in class info.bioinfweb.commons.changemonitor.PropertyChangeMonitor
 
addToColorChannels(Color, int) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
Adds a constant value to all color channels of the specified color.
addToProgressValue(double) - Method in class info.bioinfweb.commons.progress.AbstractProgressMonitor
 
addToProgressValue(double) - Method in interface info.bioinfweb.commons.progress.ProgressMonitor
 
addTrailingKeyword(String, String) - Static method in class info.bioinfweb.commons.sql.SQLUtils
 
addWarning(String, int) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addWarning(String) - Method in class info.bioinfweb.commons.log.AbstractApplicationLogger
 
addWarning(String) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs a warning message to the user.
addWarning(String, int) - Method in interface info.bioinfweb.commons.log.ApplicationLogger
Outputs a warning message to the user.
addWarning(String) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addWarning(String, int) - Method in class info.bioinfweb.commons.log.MultipleApplicationLoggersAdapter
 
addWarning(String) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
addWarning(String, int) - Method in class info.bioinfweb.commons.log.VoidApplicationLogger
 
ALPHA_STRING - Static variable in enum info.bioinfweb.commons.appversion.ApplicationType
 
AlphaImageAssembler - Class in info.bioinfweb.commons.graphics
 
AlphaImageAssembler() - Constructor for class info.bioinfweb.commons.graphics.AlphaImageAssembler
 
ApplicationLogger - Interface in info.bioinfweb.commons.log
Provides a simple logging API that can be used by applications to output log messages to the user.
ApplicationLoggerMessage - Class in info.bioinfweb.commons.log
Represents a message send to an ApplicationLogger.
ApplicationLoggerMessage(ApplicationLoggerMessageType, String) - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
ApplicationLoggerMessage(ApplicationLoggerMessageType, String, int) - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerMessage
 
ApplicationLoggerMessageType - Enum in info.bioinfweb.commons.log
Enumerates the different types of messages which can be send to an ApplicationLogger.
ApplicationLoggerParameterMap - Class in info.bioinfweb.commons.log
 
ApplicationLoggerParameterMap() - Constructor for class info.bioinfweb.commons.log.ApplicationLoggerParameterMap
 
ApplicationType - Enum in info.bioinfweb.commons.appversion
Enumerates the possible types of releases of an application versioned with ApplicationVersion.
ApplicationVersion - Class in info.bioinfweb.commons.appversion
Stores the version of an application.
ApplicationVersion() - Constructor for class info.bioinfweb.commons.appversion.ApplicationVersion
Creates a new instance of this class with the default values 0.0.0.0 (stable).
ApplicationVersion(int, int, int, long, ApplicationType) - Constructor for class info.bioinfweb.commons.appversion.ApplicationVersion
Creates a new instance of this class using the specified values.
apply() - Method in class info.bioinfweb.commons.swing.DecimalInputDialog
 
apply() - Method in class info.bioinfweb.commons.swing.OkCancelApplyDialog
This method is called if the user clicks OK or Apply.
AppVersionXMLConstants - Class in info.bioinfweb.commons.appversion
Constants used for the XML representation of an instance of ApplicationVersion as they are used by AppVersionXMLReadWrite.
AppVersionXMLConstants() - Constructor for class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
AppVersionXMLReadWrite - Class in info.bioinfweb.commons.appversion
Reads or writes an XML tag describing an ApplicationVersion object.
AppVersionXMLReadWrite() - Constructor for class info.bioinfweb.commons.appversion.AppVersionXMLReadWrite
 
argCount() - Method in class info.bioinfweb.commons.CommandLineReader
 
array - Variable in class info.bioinfweb.commons.collections.PackedIntegerArrayList
The array containing the bits used to store values contained in this list.
askToSave() - Method in class info.bioinfweb.commons.io.AbstractSaver
 
askToSave() - Method in interface info.bioinfweb.commons.io.Savable
Promts the user wheather to save changed data and calls save() if necessary.
askToSave(Component) - Method in interface info.bioinfweb.commons.swing.SwingSavable
 
askToSave() - Method in class info.bioinfweb.commons.swing.SwingSaver
 
askToSave(Component) - Method in class info.bioinfweb.commons.swing.SwingSaver
 
assemble(BufferedImage, BufferedImage) - Static method in class info.bioinfweb.commons.graphics.AlphaImageAssembler
 
assignSize() - Method in class info.bioinfweb.commons.tic.TICComponent
Adopts the current component size to the underlying GUI toolkit, if a toolkit specific component has already been created.
ATTR_APP_TYPE - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
ATTR_BUILD_NO - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
ATTR_MAJOR_APP_VERSION - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
ATTR_MINOR_APP_VERSION - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
ATTR_PATCH_LEVEL - Static variable in class info.bioinfweb.commons.appversion.AppVersionXMLConstants
 
ATTR_SCHEMA_LOCATION - Static variable in class info.bioinfweb.commons.io.XMLUtils
 
ATTR_SCHEMA_LOCATION_LOCAL_PART - Static variable in class info.bioinfweb.commons.io.XMLUtils
 
ATTR_XSI_NAMESPACE - Static variable in class info.bioinfweb.commons.io.XMLUtils
 
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