A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

AboutDialog - Class in databionics.esom.gui
Window with the About information
AboutDialog() - Constructor for class databionics.esom.gui.AboutDialog
Default Constructor Creates a window with the About information
AbstractCallback - Interface in databionics.esom.tool
 
AbstractFileParameter - Class in databionics.modules
Parameter with filename argument.
AbstractFileParameter() - Constructor for class databionics.modules.AbstractFileParameter
 
AbstractGuiComponent - Interface in databionics.esom.gui
 
AbstractLoadAction - Class in databionics.esom.tool
 
AbstractLoadAction(FileType, AbstractTool) - Constructor for class databionics.esom.tool.AbstractLoadAction
 
AbstractSaveAction - Class in databionics.esom.tool
 
AbstractSaveAction(FileType, AbstractTool) - Constructor for class databionics.esom.tool.AbstractSaveAction
 
AbstractStringParameter - Class in databionics.modules
Base class for all string parameters
AbstractStringParameter() - Constructor for class databionics.modules.AbstractStringParameter
 
AbstractTool - Class in databionics.esom.tool
Superclass for all of Somana's GUI-Tools.
AbstractTool(boolean, Application) - Constructor for class databionics.esom.tool.AbstractTool
Standard Constructor.
AbstractToolRenderer - Class in databionics.esom.tool
 
AbstractToolRenderer(AbstractTool) - Constructor for class databionics.esom.tool.AbstractToolRenderer
Standard Constructor.
AbstractToolTable - Class in databionics.esom.tool
 
AbstractToolTable(AbstractTool) - Constructor for class databionics.esom.tool.AbstractToolTable
 
accept(File) - Method in class databionics.io.FileExtensionFilter
Return true if this file should be shown in the directory pane, false if it shouldn't.
accept(File, String) - Method in class databionics.util.FileExtensionFilter
 
accept(File) - Method in class databionics.util.FolderFilter
 
actionPerformed(ActionEvent) - Method in class databionics.esom.gui.MainMenu
 
actionPerformed(ActionEvent) - Method in class databionics.esom.gui.util.ClassNameDialog
 
actionPerformed(ActionEvent) - Method in class databionics.esom.gui.util.ColorEditor
 
actionPerformed(ActionEvent) - Method in class databionics.esom.gui.util.MessagePanel
handles action
actionPerformed(ActionEvent) - Method in class databionics.esom.gui.util.RunDialog
Handle clicks on the four buttons
actionPerformed(ActionEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
Event handling for background GUI elements.
actionPerformed(ActionEvent) - Method in class databionics.esom.renderer.foreground.ForegroundTool
GUI event handling
actionPerformed(ActionEvent) - Method in class databionics.esom.renderer.RendererTool
 
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.AbstractTool
If the big ControlButton is pressed, select this Tool also the draw/undrawbutton is handled here.
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTool
If the big ControlButton is pressed, select this Tool
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.component.ComponentTable
handles performed actions
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.component.ComponentTool
 
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.data.DataTool
controls the popUp-Menues
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.dataclass.DataclassTool
handles the performed action
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.island.IslandTool
 
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.island.SaveImxFileAction
handles performed action
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.projection.ClassifyAction
handle the performed action, start projection and manage ending
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.projection.ProjectAction
handle the performed action, start projection and manage ending
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.slideshow.PngPrefixQuestion
handles performed actions
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.slideshow.PrefixAction
calls the dialog for choosing prefix
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.slideshow.SlideShowAction
This method is called, when the slide show is called in the main menu Prepares slide show and opens a window for it
actionPerformed(ActionEvent) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
actionPerformed(ActionEvent) - Method in class databionics.esom.train.TrainAction
Opens a window for Training
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.ExitAction
handle the performed action
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.LoadFileAction
Ask for a filename by dialog
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.PrefixAction
 
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.ResetAction
handle performed action, reset renderer and somana gui
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.SaveFileAction
Ask for a filename by dialog
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.ShowAboutAction
This method is called, when showAbout is called in MainMenu Opens a window for about information
actionPerformed(ActionEvent) - Method in class databionics.esom.util.actions.ShowHelpAction
Evokes runProgram with the specific help documentation
actionPerformed(ActionEvent) - Method in class databionics.gui.LogPanel.ClearAction
 
actionPerformed(ActionEvent) - Method in class databionics.gui.RunDialog
Handle clicks on the four buttons
actPoly - Variable in class databionics.esom.tool.ProtoPanel
 
add(String, String, boolean, boolean, String) - Method in class databionics.cli.PropertyOptions
Adds a new option with the specified values
add(String, String, boolean, boolean, String, String) - Method in class databionics.cli.PropertyOptions
Adds a new option with the specified values
add(double, double, int, int) - Method in class databionics.esom.gui.util.DoublePolygon
Add a new point to the polygon
add - Variable in class databionics.esom.tool.ProtoPanel
 
add(DoubleMatrix1D, int) - Method in class databionics.esom.train.BestMatchHit
add a vector to the running sum
add(DoubleMatrix1D) - Method in class databionics.esom.train.BestMatchHit
add a vector to the running sum
add(int, int) - Method in class databionics.io.ClassmaskFile
Add an index - class number pair
add(int, int) - Method in class databionics.io.ClsFile
Add an index - class number pair
add(int, int) - Method in class databionics.io.DiagnosisFile
Add an index - class number pair
add(int, String) - Method in class databionics.io.DiagnosisFile
Add an index - class number pair
add(DataItem) - Method in class databionics.io.MapFile
Add item to list and map.
add(String) - Method in class databionics.text.StringCounter
 
add2bold(int) - Method in class databionics.io.ClsFile
add an single class to boldclass
addAll(StringList) - Method in class databionics.text.StringList
Add another StringList
addAll(StringList, String) - Method in class databionics.text.StringList
Add another StringList with a prefix in front of each item
addBmListener(BmChangeListener) - Method in class databionics.esom.renderer.Renderer
 
addBoundary(Rectangle2D) - Method in class databionics.esom.renderer.foreground.BoundaryList
 
addChangeListener(ChangeListener) - Method in class databionics.project.Project
Adds a class to the list of changeListeners
addChoice(MultipleChoiceElement) - Method in class databionics.modules.MultipleChoiceParameter
Add a value to the list of allowed values
addClass(int) - Method in class databionics.io.ClassmaskFile
Add a data class if it's not in the list
addClass(int, String) - Method in class databionics.io.ClsFile
Add a data class if it's not in the list
addClass(int) - Method in class databionics.io.ClsFile
Add a data class if it's not in the list
addCursor - Variable in class databionics.esom.gui.RenderPanel
 
addEntry(int, double) - Method in class databionics.io.ColorStatistics
 
addExtension(String) - Method in class databionics.io.FileExtensionFilter
Adds a filetype "dot" extension to filter against.
addFile(FileType, BaseFile, String) - Method in class databionics.project.Project
Add fileslot for file object and try to load file
addForeground(ForegroundRenderer) - Method in class databionics.esom.renderer.foreground.ForegroundList
Adds a foregroundRenderer to thid list at the right position, depending on its RndLayer.
addForeground(AbstractToolRenderer) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Add an AbstractToolRenderer.
addForeground(ForegroundRenderer) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Add a foreground.
addLrnListener(LrnChangeListener) - Method in class databionics.esom.renderer.Renderer
 
addPoint() - Method in class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
addPoint() - Method in class databionics.esom.tool.data.SelectionPanel
 
addPoint() - Method in class databionics.esom.tool.ProtoPanel
 
addToClassification(int, int) - Method in class databionics.esom.tool.dataclass.DataclassCreatorPanel
 
addTool(AbstractTool) - Method in interface databionics.esom.gui.AbstractGuiComponent
 
addTool(AbstractTool) - Method in class databionics.esom.gui.BottomBar
adds the given tool
addTool(AbstractTool) - Method in class databionics.esom.gui.MainFrame
 
addTool(AbstractTool) - Method in class databionics.esom.gui.RenderPanel
 
addTool(AbstractTool) - Method in class databionics.esom.gui.ToolLoader
 
addWtsListener(WtsChangeListener) - Method in class databionics.esom.renderer.Renderer
 
afterEpoch() - Method in class databionics.esom.train.Batch2SOM
Now, the neurons are updated.
afterEpoch() - Method in class databionics.esom.train.BatchSOM
Now, the neurons are updated.
afterEpoch() - Method in class databionics.esom.train.HybridBatchSOM
Now, the neurons are updated.
afterEpoch() - Method in class databionics.esom.train.KBatchSOM
Now, the neurons are updated.
afterEpoch() - Method in class databionics.esom.train.SlowBatchSOM
Now, the neurons are updated.
afterEpoch() - Method in class databionics.esom.train.SOM
Things to be done after each epoch.
afterUpdate(int, int) - Method in class databionics.esom.train.BatchSOM
Store the data vector projected on this bestmatch in a BestMatchHit object.
afterUpdate(int, int) - Method in class databionics.esom.train.HybridBatchSOM
Store the data vector projected on this bestmatch in a BestMatchHit object.
afterUpdate(int, int) - Method in class databionics.esom.train.KBatchSOM
Store the data vector projected on this bestmatch in a BestMatchHit object.
afterUpdate(int, int) - Method in class databionics.esom.train.SOM
Things to be done after updating a weight vector.
alignRight(String, int) - Static method in class databionics.text.StringUtils
Right align a string by adding spaces on the left up to specified length.
alignRight(int, int) - Static method in class databionics.text.StringUtils
Right align a number by adding spaces on the left up to specified length.
allClasses - Variable in class databionics.io.DiagnosisFile
Column with class numbers
allowEmptyLines - Variable in class databionics.io.BaseFile
Flag whether to allow empty lines, usually false, except rules files
alpha - Variable in class databionics.esom.tool.classmask.ClassmaskRenderer
 
alphaSpinner - Variable in class databionics.esom.tool.classmask.ClassmaskTool
 
Analyze - Class in databionics.esom
GUI tool for ESOM training, clustering, visualization, and analysis.
Analyze() - Constructor for class databionics.esom.Analyze
standard constructor.
app - Static variable in class databionics.esom.Cluster
the application
app - Static variable in class databionics.esom.Project
the application
app - Static variable in class databionics.esom.Render
interface to log4j system
app - Static variable in class databionics.esom.SlideShow
the application
app - Static variable in class databionics.esom.Train
application
app - Variable in class databionics.esom.util.actions.ExitAction
 
app - Variable in class databionics.modules.Job
corresponding application
app - Static variable in class databionics.runner.MatlabRunner
interface to log4j system
app - Static variable in class databionics.runner.Runner
interface to log4j system
append(String) - Method in class databionics.gui.LogPanel
Parse the text for progress or add text to the panel
appender - Variable in class databionics.gui.LogPanel
appender to add to logger
Application - Class in databionics
Base class for applications.
Application() - Constructor for class databionics.Application
Standard constructor.
Application(boolean) - Constructor for class databionics.Application
Constructor with flag for standalone mode.
application - Variable in class databionics.esom.gui.BottomBar
 
application - Variable in class databionics.esom.gui.MainFrame
 
application - Variable in class databionics.esom.gui.RenderPanel
 
application - Variable in class databionics.esom.gui.ToolLoader
link back to main Application
application - Variable in class databionics.esom.tool.AbstractTool
Reference to the running application.
ArffFile - Class in databionics.io
File that stores multivariate data sets in a 2D array in WEKA format.
ArffFile() - Constructor for class databionics.io.ArffFile
Standard constructor
ArffFile(String) - Constructor for class databionics.io.ArffFile
Constructor with a filename
ArffFile(int, int) - Constructor for class databionics.io.ArffFile
Constructor with size for an empty array.
ArffFile(ArffFile) - Constructor for class databionics.io.ArffFile
Clone constructor
ArffFile(LrnFile) - Constructor for class databionics.io.ArffFile
Clone constructor
args - Variable in class databionics.runner.MatlabRunner
unparsed arguments
Array2DFile - Class in databionics.io
Base class for all filetypes with 2D data arrays.
Array2DFile() - Constructor for class databionics.io.Array2DFile
Standard constructor
Array2DFile(String) - Constructor for class databionics.io.Array2DFile
Constructor with a filename
Array2DFile(int, int) - Constructor for class databionics.io.Array2DFile
Constructor with size for an empty array.
Array3DFile - Class in databionics.io
Base class for all filetypes with 3D data arrays actually stored in 3D array.
Array3DFile() - Constructor for class databionics.io.Array3DFile
Standard constructor
Array3DFile(String) - Constructor for class databionics.io.Array3DFile
Constructor with a filename
Array3DFile(int, int, int) - Constructor for class databionics.io.Array3DFile
Constructor with size for an empty array.
autoClassify(RectangularGrid, ClassmaskFile, BMFile) - Method in class databionics.esom.tool.projection.ProjectionTool
 
autoClust(int, int, boolean, boolean) - Method in class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
autoFlood - Variable in class databionics.esom.tool.classmask.ClassmaskTool
Automated floodfill or not.
autoload - Variable in class databionics.project.FileSlot
automatically load file when name is set
autoRender - Variable in class databionics.esom.renderer.Renderer
Flag whether render() is called after properties are changed

B

background - Variable in class databionics.esom.renderer.Renderer
The renderer for the background
backgroundBox - Variable in class databionics.esom.renderer.background.BackgroundTool
Drop down list to choose backgrounds
backgroundList - Variable in class databionics.esom.renderer.background.BackgroundTool
A list containing the backgrounds.
backgroundNames - Variable in class databionics.esom.renderer.background.BackgroundTool
A list containing the names oft the backgrounds.
BackgroundRenderer - Class in databionics.esom.renderer.background
Base class for all background renderers.
BackgroundRenderer() - Constructor for class databionics.esom.renderer.background.BackgroundRenderer
Standard constructor.
backgroundTool - Variable in class databionics.esom.gui.ToolLoader
 
BackgroundTool - Class in databionics.esom.renderer.background
GUI-interface to manage the various backgrounds.
BackgroundTool(boolean, Application) - Constructor for class databionics.esom.renderer.background.BackgroundTool
Standard Constructor.
backgroundTool - Variable in class databionics.esom.renderer.Renderer
 
backward - Variable in class databionics.esom.tool.slideshow.SlideShow
 
balance(String) - Static method in class databionics.text.StringUtils
Balance parentethese, braces and brackets Could be much more sophisticated! later...
balanceOne(String, String, String) - Static method in class databionics.text.StringUtils
Balance open and closing strings
banner - Variable in class databionics.Application
long program name with version
BaseFile - Class in databionics.io
Base class for all filetypes.
BaseFile() - Constructor for class databionics.io.BaseFile
Standard constructor
BaseFile(String) - Constructor for class databionics.io.BaseFile
Constructor with a filename
BaseMainFrame - Class in databionics.gui
Base class for all main windows.
BaseMainFrame() - Constructor for class databionics.gui.BaseMainFrame
standard constructor
Batch2SOM - Class in databionics.esom.train
batch version of SOM Training, without counting more hits, just update everything after whole epoche
Batch2SOM() - Constructor for class databionics.esom.train.Batch2SOM
Standard constructor
BatchSOM - Class in databionics.esom.train
Implementation of the batch SOM training.
BatchSOM() - Constructor for class databionics.esom.train.BatchSOM
Standard constructor
beforeEpoch() - Method in class databionics.esom.train.SOM
Things to be done before each epoch.
beforeSearch(int) - Method in class databionics.esom.train.SOM
Things to be done before searching for a best match.
beforeUpdate(int) - Method in class databionics.esom.train.SOM
Things to be done before updating a weight vector Empty by default.
Bestmatch - Class in databionics.io
Represent a best match of a data point on an ESOM.
Bestmatch() - Constructor for class databionics.io.Bestmatch
Standard constructor
Bestmatch(int) - Constructor for class databionics.io.Bestmatch
Constructor with index
Bestmatch(int, int, int) - Constructor for class databionics.io.Bestmatch
Constructor with index and coordinates
bestmatches - Variable in class databionics.esom.renderer.Renderer
List with best match positions
bestmatches - Variable in class databionics.esom.tool.legend.LegendRenderer
 
bestmatches - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
bestmatches - Variable in class databionics.esom.train.SOM
indices of best matching neurons for data points
BestMatchHit - Class in databionics.esom.train
Represent the projection of one ore more data vectors on a best match.
BestMatchHit() - Constructor for class databionics.esom.train.BestMatchHit
standard constructor
BestMatchHit(DoubleMatrix1D) - Constructor for class databionics.esom.train.BestMatchHit
constructor for first hit
BestMatchHit(DoubleMatrix1D, int) - Constructor for class databionics.esom.train.BestMatchHit
constructor for first hit
BestmatchRenderer - Class in databionics.esom.renderer.foreground
Best match foreground renderer.
BestmatchRenderer() - Constructor for class databionics.esom.renderer.foreground.BestmatchRenderer
Standard constructor
bgImage - Variable in class databionics.esom.renderer.Renderer
The background image in 1:1 size
bm - Variable in class databionics.esom.util.actions.LoadUmxFileAction
flag for loading other fileType
bm - Variable in class databionics.esom.util.actions.LoadWtsFileAction
flag for loading other fileType
bmChanged - Variable in class databionics.esom.renderer.background.BackgroundRenderer
flag wether Bestmatches changed.
bmChanged() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Called when the bestmatches changed.
bmChanged() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
bmChanged() - Method in interface databionics.esom.util.BmChangeListener
Called when the bestmatches have changed.
BmChangeListener - Interface in databionics.esom.util
Listener for changes of bestmatches.
bmFile - Variable in class databionics.esom.SlideShow
 
BMFile - Class in databionics.io
File that stores a list of best matches.
BMFile() - Constructor for class databionics.io.BMFile
Standard constructor
BMFile(String) - Constructor for class databionics.io.BMFile
Constructor with a filename
bmFilename - Variable in class databionics.esom.renderer.Renderer
 
BMInfoPanel - Class in databionics.esom.tool.bminfo
panel for activating single bms
BMInfoPanel(AbstractTool) - Constructor for class databionics.esom.tool.bminfo.BMInfoPanel
standard constructor
bmInfoTool - Variable in class databionics.esom.gui.ToolLoader
 
BMInfoTool - Class in databionics.esom.tool.bminfo
activates non-polygone selected bms on the map
BMInfoTool(boolean, Application) - Constructor for class databionics.esom.tool.bminfo.BMInfoTool
 
BMInfoTool(boolean, Application, ToolLoader) - Constructor for class databionics.esom.tool.bminfo.BMInfoTool
 
bmListeners - Variable in class databionics.esom.renderer.Renderer
 
bmRenderer - Variable in class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
 
BmSearch - Class in databionics.esom.train.search
abstract class for all search methods
BmSearch() - Constructor for class databionics.esom.train.search.BmSearch
 
bmSearch - Variable in class databionics.esom.train.SOM
the search system
BmSearchStat - Class in databionics.esom.train.search
stats for hiting correct bms
BmSearchStat() - Constructor for class databionics.esom.train.search.BmSearchStat
 
bmSize - Variable in class databionics.esom.renderer.foreground.BestmatchRenderer
size of bestmatch
bmSize - Variable in class databionics.esom.renderer.foreground.ForegroundList
Size in grid-neurons for the smallest bm.
bmSize - Variable in class databionics.esom.renderer.Renderer
int for size of bm
bmStat - Variable in class databionics.esom.train.SOM
the bm search statistic
bmStatNeeded - Variable in class databionics.esom.train.SOM
 
boldClasses - Variable in class databionics.io.ClsFile
Class indices to be highlighted in some display
BottomBar - Class in databionics.esom.gui
TabbedPane where the informational tabs where added
BottomBar() - Constructor for class databionics.esom.gui.BottomBar
standard constructor
bottomBar - Variable in class databionics.esom.gui.MainFrame
the bottom bar holding the informational tabs
bottomBar - Variable in class databionics.esom.gui.ToolLoader
link to the BottomBar
bottomBar - Variable in class databionics.esom.tool.AbstractTool
Somana's main BottomPanel
bottomTab - Variable in class databionics.esom.tool.AbstractTool
BottomTab to be inserted into BottomBar.
BottomTab - Class in databionics.esom.tool
 
BottomTab(AbstractTool) - Constructor for class databionics.esom.tool.BottomTab
 
boundaries - Variable in class databionics.esom.renderer.foreground.BoundaryList
 
BoundaryList - Class in databionics.esom.renderer.foreground
List of rectangles with test for intersection.
BoundaryList() - Constructor for class databionics.esom.renderer.foreground.BoundaryList
 
btnBrowse - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
btnClear - Variable in class databionics.esom.tool.AbstractTool
Standard clear-button for the Toolbar.
btnColor - Variable in class databionics.esom.tool.data.DataTool
 
btnCreateShow - Variable in class databionics.esom.tool.slideshow.SlideshowTool
newSlideShowItem, which has to switch betwenn enabled and disabled
btnLoad - Variable in class databionics.esom.tool.AbstractTool
Standard load-button for the Toolbar.
btnPaint - Variable in class databionics.esom.tool.AbstractTool
Button to switch foreground-rendering on/off.
btnReset - Variable in class databionics.esom.tool.info.InfoTool
 
btnRobZTrans - Variable in class databionics.esom.tool.data.DataTool
 
btnSave - Variable in class databionics.esom.tool.AbstractTool
Standard save-button for the Toolbar.
btnStartShow - Variable in class databionics.esom.tool.slideshow.SlideshowTool
slideShowItem, which has to switch betwenn enabled and disabled
btnUpdate - Variable in class databionics.esom.tool.component.ComponentTool
 
btnZeroOne - Variable in class databionics.esom.tool.data.DataTool
 
btnZTrans - Variable in class databionics.esom.tool.data.DataTool
 
BubbleNeighborhood - Class in databionics.esom.neighborhood
Very simple neighborhood kernel with a constant weight of 1.
BubbleNeighborhood() - Constructor for class databionics.esom.neighborhood.BubbleNeighborhood
Create a new neighborhood object
BubbleNeighborhood(int, double) - Constructor for class databionics.esom.neighborhood.BubbleNeighborhood
Create a new neighborhood object
buildHeader() - Method in class databionics.io.ArffFile
Generate header.
buildHeader() - Method in class databionics.io.Array2DFile
Generate header.
buildHeader() - Method in class databionics.io.Array3DFile
Generate header.
buildHeader() - Method in class databionics.io.BaseFile
Generate a fresh header based on the data structure for saving.
buildHeader() - Method in class databionics.io.BMFile
Generate header.
buildHeader() - Method in class databionics.io.ClassmaskFile
Generate header.
buildHeader() - Method in class databionics.io.ClsFile
Generate header.
buildHeader() - Method in class databionics.io.CsvFile
Generate header.
buildHeader() - Method in class databionics.io.ExplFile
Generate header.
buildHeader() - Method in class databionics.io.LrnFile
Generate header.
buildHeader() - Method in class databionics.io.NamesFile
Generate header.
buildHeader() - Method in class databionics.io.PicturesFile
Generate header.
buildHeader() - Method in class databionics.io.UmxFile
Generate header.
buildLine(int) - Method in class databionics.io.ArffFile
Construct a line for saving.
buildLine(int) - Method in class databionics.io.Array2DFile
Construct a line for saving.
buildLine(int) - Method in class databionics.io.BaseFile
Construct a line in subclasses for saving the data to a file.
buildLine(int) - Method in class databionics.io.ClassmaskFile
Construct a line for saving.
buildLine(int) - Method in class databionics.io.ClsFile
Construct a line for saving.
buildLine(int) - Method in class databionics.io.ColorTable
Get line for file.
buildLine(int) - Method in class databionics.io.DiagnosisFile
Construct a line for saving.
buildLine(int) - Method in class databionics.io.ListFile
Construct a line for saving.
buildLine(int) - Method in class databionics.io.LrnFile
Construct a line for saving.
buttons - Variable in class databionics.esom.gui.util.MessagePanel
 

C

cache - Variable in class databionics.esom.cooling.CachedCooling
cache with precalculated values of the parameter
CachedCooling - Class in databionics.esom.cooling
Abstract base class for cooling of a parameter with a cache of precalculated values.
CachedCooling() - Constructor for class databionics.esom.cooling.CachedCooling
Create a new cooling object with default parameters start = 1.0,steps = 100,end = 0.0, size = 100
CachedCooling(double, int, double) - Constructor for class databionics.esom.cooling.CachedCooling
Create a new cooling object with cache size equals to steps.
CachedCooling(double, int, double, int) - Constructor for class databionics.esom.cooling.CachedCooling
Create a new cooling object
CachedNeighborhood - Class in databionics.esom.neighborhood
Abstract base class for neighborhood kernels with a cache of precalculated values.
CachedNeighborhood() - Constructor for class databionics.esom.neighborhood.CachedNeighborhood
Create a new neighborhood object
CachedNeighborhood(int, double) - Constructor for class databionics.esom.neighborhood.CachedNeighborhood
Create a new neighborhood object
cacheMatrix - Variable in class databionics.esom.renderer.background.BackgroundRenderer
Store the rendered Matrix to avoid rerendering
calcQerror() - Method in class databionics.esom.train.SOM
 
calculate(int) - Method in class databionics.esom.cooling.CenterCooling
Calculate the parameter value for this step.
calculate(int) - Method in class databionics.esom.cooling.Cooling
Calculate the parameter value for this step.
calculate(int) - Method in class databionics.esom.cooling.ExponentialCooling
Calculate the parameter value for this step: value(step) = start * exp(step*ln(end/start)/steps)
calculate(int) - Method in class databionics.esom.cooling.LinearCooling
Calculate the parameter value for this step.
calculate(int) - Method in class databionics.esom.cooling.NoCooling
Calculate the parameter value for this step.
calculate(int) - Method in class databionics.esom.neighborhood.BubbleNeighborhood
Calculate the weight value for this distance.
calculate(int) - Method in class databionics.esom.neighborhood.ConeNeighborhood
Calculate the weight value for this distance.
calculate(int) - Method in class databionics.esom.neighborhood.EpanechicovNeighborhood
Calculate the weight value for this distance.
calculate(int) - Method in class databionics.esom.neighborhood.GaussNeighborhood
Calculate the weight value for this distance.
calculate(int) - Method in class databionics.esom.neighborhood.MexicanHatNeighborhood
Calculate the weight value for this distance.
calculate(int) - Method in class databionics.esom.neighborhood.Neighborhood
Calculate the weight value for this distance.
calculateBestmatches() - Method in class databionics.esom.tool.dataclass.DataclassCreatorPanel
 
calculateDensities() - Method in class databionics.math.ParetoDensity
Calculate the densities for a given radius The result is stored in the densities field.
calculateDistances() - Method in class databionics.math.Distances
 
calculateDistances() - Method in class databionics.math.ParetoDensity
calculate pairwise distances and fill percentile vector
calculateMapSpace() - Method in class databionics.esom.tool.dataclass.DataclassTool
calcuate the map space of each class
calendar - Variable in class databionics.io.CsvFile
calendar for date calculations.
callback - Variable in class databionics.esom.Cluster
callback if called from gui
callback - Variable in class databionics.esom.gui.util.RunDialog
 
callback - Variable in class databionics.esom.Project
callback if called from gui
callback - Variable in class databionics.esom.SlideShow
 
callback() - Method in interface databionics.esom.tool.AbstractCallback
 
callback(Object) - Method in class databionics.esom.tool.AbstractTool
If this tool has registered a callback anywhere this function will be called.
callback() - Method in class databionics.esom.tool.bminfo.BMInfoPanel
 
callback(Object) - Method in class databionics.esom.tool.bminfo.BMInfoTool
mostly for musicminer atm.
callback - Variable in class databionics.esom.tool.projection.ClassifyAction
 
callback - Variable in class databionics.esom.tool.projection.ProjectAction
 
CallBack - Interface in databionics.gui
Callback for actions using the RunDialog
callback - Variable in class databionics.gui.RunDialog
Callback for actions when job is done
cancelCreation() - Method in class databionics.esom.tool.ProtoPanel
Stops the actual creation process
caseKey - Variable in class databionics.io.DiffCondition
The name of the key column of the cases.
caseKey - Variable in class databionics.io.Rule
The name of the key column of the cases.
caseName - Variable in class databionics.io.Rule
The (file)name of the cases used to generate the rule
cbxDrawOverlap - Variable in class databionics.esom.tool.island.IslandTool
 
cbxDrawTransparent - Variable in class databionics.esom.tool.island.IslandTool
 
center - Variable in class databionics.esom.train.SOM
flag for centering the map
CenterCooling - Class in databionics.esom.cooling
Linear cooling of a parameter centered between constant non cooling periods in the first and last 1/5th of the steps
CenterCooling(double, int, double) - Constructor for class databionics.esom.cooling.CenterCooling
Create a new linear cooling object
centerMap() - Method in class databionics.esom.train.SOM
center map at neuron with highest density
centerPanel - Variable in class databionics.esom.tool.slideshow.SlideShow
 
centers - Variable in class databionics.math.ParetoDensity
the sphere centers
changeIndex(int, int) - Method in class databionics.io.ClassmaskFile
Change Index of class.
changeIndex(int, int) - Method in class databionics.io.ClsFile
Change Index of class.
changeListeners - Variable in class databionics.project.Project
List with all classes, which are informed when the files in this project have changed
CharRule - Class in databionics.io
Characterization rule
CharRule() - Constructor for class databionics.io.CharRule
Standard constructor
CharRule(String, String, String, String, String) - Constructor for class databionics.io.CharRule
Constructor with all important fields.
checkHeader() - Method in class databionics.io.ArffFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.BaseFile
Check consistency of header information with data structure in subclasses.
checkHeader() - Method in class databionics.io.BMFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.ClassmaskFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.ClsFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.CsvFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.DiagnosisFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.LrnFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.NamesFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.PicturesFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.RuleFile
Check consistency of header information.
checkHeader() - Method in class databionics.io.UmxFile
Check consistency of header information.
checkHeaderAgainstSize(int) - Method in class databionics.io.BaseFile
Check consistency of header line with size information.
chkAutoFlood - Variable in class databionics.esom.tool.classmask.ClassmaskTool
Chechbox for automated floodfill
chkCascade - Variable in class databionics.esom.gui.MainMenu
 
chkCascade - Variable in class databionics.esom.tool.options.OptionsTool
 
chkDrawCircular - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
chkFloodFill - Variable in class databionics.esom.tool.classmask.ClassmaskTool
Checkbox wether to use floodfill
chkLetters - Variable in class databionics.esom.tool.dataclass.DataclassTool
Button controls wether the ClassBestmatchRenderer draws b/w Letters instead of coloured squares
choices - Variable in class databionics.modules.MultipleChoiceParameter
list of allowed values
circle - Variable in class databionics.esom.renderer.foreground.BestmatchRenderer
draw circles instead of rectangles
CircularGrid1D - Class in databionics.esom.grid
One dimensional circle of neurons
CircularGrid1D() - Constructor for class databionics.esom.grid.CircularGrid1D
Standard constructor
CircularGrid1D(int, int) - Constructor for class databionics.esom.grid.CircularGrid1D
Constructor with sizes
ClassBestmatchRenderer - Class in databionics.esom.tool.dataclass
Best match foreground renderer.
ClassBestmatchRenderer() - Constructor for class databionics.esom.tool.dataclass.ClassBestmatchRenderer
Standard constructor
ClassBestmatchRenderer(ClsFile) - Constructor for class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
classColors - Variable in class databionics.io.ClassmaskFile
Default color table
classColors - Variable in class databionics.io.ClsFile
Default color table
classColumnIndex - Variable in class databionics.io.LrnFile
Index of class column.
classColumnName - Variable in class databionics.io.LrnFile
Name of class column.
ClassComboBox - Class in databionics.esom.gui.util
Combobox to select a class to perform a task
ClassComboBox(String, String, String, String) - Constructor for class databionics.esom.gui.util.ClassComboBox
Constructor with info which classes to display
classes - Variable in class databionics.esom.renderer.Renderer
list with class numbers of lrn File
classes - Variable in class databionics.esom.train.SOM
 
classes - Variable in class databionics.io.ClassmaskFile
Column with class numbers
classes - Variable in class databionics.io.ClsFile
Column with class numbers
classes - Variable in class databionics.io.LrnFile
Column with class numbers, not stored in the main array.
classification - Variable in class databionics.esom.renderer.foreground.NamesRenderer
Bestmatch classification
classification - Variable in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
classify(boolean[][], boolean, boolean) - Method in class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
classify(boolean, boolean) - Method in class databionics.esom.tool.dataclass.DataclassCreatorPanel
Called by the ClassDialog to set all selected bestmatches to be in the selected class
ClassifyAction - Class in databionics.esom.tool.projection
 
ClassifyAction(ToolLoader) - Constructor for class databionics.esom.tool.projection.ClassifyAction
standard constructor
ClassifyCallback - Class in databionics.esom.tool.projection
callback for classify bestmatches
ClassifyCallback(ToolLoader) - Constructor for class databionics.esom.tool.projection.ClassifyCallback
constructor
classList - Variable in class databionics.esom.train.BestMatchHit
 
classmask - Variable in class databionics.esom.SlideShow
 
classmask - Variable in class databionics.esom.tool.classmask.ClassmaskRenderer
 
ClassmaskCreatorPanel - Class in databionics.esom.tool.classmask
 
ClassmaskCreatorPanel(AbstractTool) - Constructor for class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
ClassmaskFile - Class in databionics.io
 
ClassmaskFile() - Constructor for class databionics.io.ClassmaskFile
Standard constructor
ClassmaskFile(int) - Constructor for class databionics.io.ClassmaskFile
 
ClassmaskFile(String) - Constructor for class databionics.io.ClassmaskFile
Constructor with a filename
classmaskLoad - Variable in class databionics.esom.tool.projection.ClassifyAction
 
ClassmaskLoadAction - Class in databionics.esom.tool.classmask
 
ClassmaskLoadAction(AbstractTool) - Constructor for class databionics.esom.tool.classmask.ClassmaskLoadAction
 
ClassmaskRenderer - Class in databionics.esom.tool.classmask
 
ClassmaskRenderer() - Constructor for class databionics.esom.tool.classmask.ClassmaskRenderer
 
ClassmaskSaveAction - Class in databionics.esom.tool.classmask
 
ClassmaskSaveAction(AbstractTool) - Constructor for class databionics.esom.tool.classmask.ClassmaskSaveAction
 
ClassmaskTable - Class in databionics.esom.tool.classmask
 
ClassmaskTable(AbstractTool) - Constructor for class databionics.esom.tool.classmask.ClassmaskTable
 
ClassmaskTableModel - Class in databionics.esom.tool.classmask
 
ClassmaskTableModel(AbstractTool) - Constructor for class databionics.esom.tool.classmask.ClassmaskTableModel
Basic constructor.
classmaskTool - Variable in class databionics.esom.gui.ToolLoader
 
ClassmaskTool - Class in databionics.esom.tool.classmask
 
ClassmaskTool(boolean, Application) - Constructor for class databionics.esom.tool.classmask.ClassmaskTool
 
ClassmaskToolRenderer - Class in databionics.esom.tool.classmask
 
ClassmaskToolRenderer(AbstractTool) - Constructor for class databionics.esom.tool.classmask.ClassmaskToolRenderer
 
className - Variable in class databionics.io.DiffCondition
The name of the class described by the rule.
className - Variable in class databionics.io.Rule
The name of the class described by the rule.
ClassNameDialog - Class in databionics.esom.gui.util
 
clean - Variable in class databionics.project.Project
flag for a new project - to ask for a name when saving
clear() - Method in class databionics.esom.renderer.foreground.BoundaryList
 
clear() - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
clears the classmask
clear() - Method in class databionics.gui.LogPanel
Clear contents
clear() - Method in class databionics.io.ClassmaskFile
Clear class list, set all class numbers to 0
clear() - Method in class databionics.io.ClsFile
Clear class list, set all class numbers to 0
clear() - Method in class databionics.io.FileExtensionFilter
Clears list of file filters and descriptions
clear(String) - Static method in class databionics.project.DataManager
 
clearAll() - Static method in class databionics.project.DataManager
 
clearItm - Variable in class databionics.esom.tool.AbstractTool
 
clickMode - Variable in class databionics.esom.tool.AbstractTool
Booleans for different selection modes
clip - Variable in class databionics.esom.renderer.Renderer
The clip factor for clipped heights
clipMatrix(boolean, double, DoubleMatrix2D, DoubleMatrix2D) - Static method in class databionics.esom.renderer.RendererTools
Clip a Height matrix
clipping - Variable in class databionics.esom.renderer.Renderer
Flag if clipping is active
clone() - Method in class databionics.io.ClassmaskFile
Deprecated. might not work correct
clone() - Method in class databionics.io.ClsFile
Deprecated. deprecated because incomplete. TODO: make complete
clone() - Method in class databionics.io.DataClass
 
clone() - Method in class databionics.modules.FileParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.FloatParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.FolderParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.InputFileParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.IntParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.MultipleChoiceParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.OutputFileParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.Parameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.StringParameter
Creates and returns a copy of this object.
clone() - Method in class databionics.modules.SwitchParameter
Creates and returns a copy of this object.
cloneBgImage() - Method in class databionics.esom.renderer.Renderer
Copy zoomed image to current image.
clonedBgImage - Variable in class databionics.esom.renderer.Renderer
 
cloneImage() - Method in class databionics.esom.renderer.Renderer
Copy zoomed image to current image.
close() - Method in class databionics.gui.LogPanelWriter
Ignore call to close
closeButton - Variable in class databionics.esom.gui.util.RunDialog
 
closeButton - Variable in class databionics.gui.RunDialog
 
clrFourtimes - Variable in class databionics.esom.tool.island.IslandRenderer
 
clrFourtimes - Variable in class databionics.esom.tool.island.IslandTool
 
clrThreetimes - Variable in class databionics.esom.tool.island.IslandRenderer
 
clrThreetimes - Variable in class databionics.esom.tool.island.IslandTool
 
clrTwice - Variable in class databionics.esom.tool.island.IslandRenderer
 
clrTwice - Variable in class databionics.esom.tool.island.IslandTool
 
clrWater - Variable in class databionics.esom.tool.island.IslandRenderer
 
clrWater - Variable in class databionics.esom.tool.island.IslandTool
 
clrZeros - Variable in class databionics.esom.tool.island.IslandRenderer
 
clrZeros - Variable in class databionics.esom.tool.island.IslandTool
 
cls - Variable in class databionics.esom.util.actions.LoadUmxFileAction
flag for loading other fileType
cls - Variable in class databionics.esom.util.actions.LoadWtsFileAction
flag for loading other fileType
CLS_COLUMN - Static variable in class databionics.io.LrnFile
 
clsFile - Variable in class databionics.esom.SlideShow
 
ClsFile - Class in databionics.io
File that stores classification of data points or best matches.
ClsFile() - Constructor for class databionics.io.ClsFile
Standard constructor
ClsFile(String) - Constructor for class databionics.io.ClsFile
Constructor with a filename
ClsFile(BMFile) - Constructor for class databionics.io.ClsFile
 
clsrnd - Variable in class databionics.esom.Render
foreground for bestmatches with class colors
Cluster - Class in databionics.esom
Command line tool to cluster neurons of an ESOM and thus create a class mask.
Cluster() - Constructor for class databionics.esom.Cluster
standard constructor.
clusters - Variable in class databionics.math.ParetoDensity
the current number of expected clusters
cmd - Variable in class databionics.Application
interface to command line
color - Variable in class databionics.io.DataClass
Color of class
ColorEditor - Class in databionics.esom.gui.util
stolen from java tutorial
ColorEditor() - Constructor for class databionics.esom.gui.util.ColorEditor
 
colorify - Variable in class databionics.esom.renderer.Renderer
factor for colorification
colorifying - Variable in class databionics.esom.renderer.Renderer
flag wether to colorify or not
colorizeAreasOnImage(float, int, int, int, ClsFile, BufferedImage) - Static method in class databionics.esom.renderer.RendererTools
 
colorizeBackground() - Method in class databionics.esom.renderer.Renderer
 
colorizeImageWithMatrix2(float, int, BufferedImage, DoubleMatrix2D) - Static method in class databionics.esom.renderer.RendererTools
 
ColorizeRenderer - Class in databionics.esom.renderer.foreground
TODO: move colorize code from Renderer here
ColorizeRenderer() - Constructor for class databionics.esom.renderer.foreground.ColorizeRenderer
 
ColorLegend - Class in databionics.esom.tool.legend
Legend with used colors and their heights- or densities values More the 20 colors are never shown
ColorLegend() - Constructor for class databionics.esom.tool.legend.ColorLegend
standard constructor, needed for Instance
ColorLegend(Renderer) - Constructor for class databionics.esom.tool.legend.ColorLegend
Constructor with renderer
colorMap - Variable in class databionics.esom.renderer.Renderer
Colors really used to render background dependend on colors&colorSteps
ColorMapping - Class in databionics.io
Mapping of a ColorTable to a given number of color steps.
ColorMapping(ColorTable, int) - Constructor for class databionics.io.ColorMapping
Constructor initialises colorTable and stepList.
ColorRenderer - Class in databionics.esom.gui.util
 
ColorRenderer(boolean) - Constructor for class databionics.esom.gui.util.ColorRenderer
 
colors - Variable in class databionics.esom.renderer.Renderer
Colors used to render the background
colorStat - Variable in class databionics.esom.tool.legend.LegendRenderer
 
ColorStatistics - Class in databionics.io
Statistics about colors used in rendering ESOM.
ColorStatistics(int) - Constructor for class databionics.io.ColorStatistics
 
colorStats - Variable in class databionics.io.ColorMapping
 
colorSteps - Variable in class databionics.esom.renderer.Renderer
Number of steps in Colortable to be used
colorSteps - Variable in class databionics.esom.tool.legend.LegendRenderer
 
colorTable - Variable in class databionics.esom.tool.classmask.ClassmaskTool
 
colorTable - Variable in class databionics.esom.tool.dataclass.DataclassTool
 
colorTable - Variable in class databionics.io.ColorMapping
 
ColorTable - Class in databionics.io
File that stores a color table from *.rgb files.
ColorTable() - Constructor for class databionics.io.ColorTable
Standard constructor
ColorTable(String) - Constructor for class databionics.io.ColorTable
Constructor with a filename
colorTables - Variable in class databionics.esom.gui.util.GradientComboBox
list with all color tables
cols - Variable in class databionics.io.Array3DFile
Number of columns of 3D array.
cols - Variable in class databionics.io.BMFile
Number of columns from header.
column - Variable in class databionics.io.Bestmatch
Column of data point's best match.
columns - Variable in class databionics.esom.grid.RectangularGrid
columns of rectangle
command - Variable in class databionics.modules.Tool
command to run this tool
comment - Variable in class databionics.io.BaseFile
Comment of file.
commentPrefix - Variable in class databionics.io.BaseFile
Comment prefix.
completeCreation(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
Called when the creation is finished and updates the umx-data
component - Variable in class databionics.esom.renderer.background.ComponentRenderer
the dimension to use for rendering
componentHidden(ComponentEvent) - Method in class databionics.esom.gui.MainFrame
handle event
componentHidden(ComponentEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
componentHidden(ComponentEvent) - Method in class databionics.esom.tool.ProtoPanel
 
componentHidden(ComponentEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
componentMoved(ComponentEvent) - Method in class databionics.esom.gui.MainFrame
handle event
componentMoved(ComponentEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
componentMoved(ComponentEvent) - Method in class databionics.esom.tool.ProtoPanel
 
componentMoved(ComponentEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
ComponentRenderer - Class in databionics.esom.renderer.background
Component plane background renderer.
ComponentRenderer() - Constructor for class databionics.esom.renderer.background.ComponentRenderer
Standard constructor
componentResized(ComponentEvent) - Method in class databionics.esom.gui.MainFrame
handle resizing of components
componentResized(ComponentEvent) - Method in class databionics.esom.gui.RenderPanel
Change the boundaries all the displayed panels, when the component is resized
componentResized(ComponentEvent) - Method in class databionics.esom.tool.ProtoPanel
Update Polygon when the component is resized
componentResized(ComponentEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
components - Variable in class databionics.esom.gui.util.RunDialog
Job created to run the tool
components - Variable in class databionics.esom.renderer.Renderer
List with weight components to use
components - Variable in class databionics.gui.RunDialog
Job created to run the tool
componentShown(ComponentEvent) - Method in class databionics.esom.gui.MainFrame
handle event
componentShown(ComponentEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
componentShown(ComponentEvent) - Method in class databionics.esom.tool.ProtoPanel
 
componentShown(ComponentEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
ComponentTable - Class in databionics.esom.tool.component
 
ComponentTable(AbstractTool) - Constructor for class databionics.esom.tool.component.ComponentTable
constructor with given renderer
ComponentTableModel - Class in databionics.esom.tool.component
Table model for components = subset of dimensions.
ComponentTableModel(AbstractTool) - Constructor for class databionics.esom.tool.component.ComponentTableModel
constructor
componentTool - Variable in class databionics.esom.gui.ToolLoader
 
ComponentTool - Class in databionics.esom.tool.component
 
ComponentTool(boolean, Application) - Constructor for class databionics.esom.tool.component.ComponentTool
 
compos - Variable in class databionics.esom.gui.RenderPanel
are Components shown rather than a single map?
Condition - Class in databionics.io
Abstract base class for rule conditions.
Condition() - Constructor for class databionics.io.Condition
Standard constructor
Condition(String, Float, Float, Float) - Constructor for class databionics.io.Condition
Constructor with all fields.
conditions - Variable in class databionics.io.Rule
The rule conditions.
ConeNeighborhood - Class in databionics.esom.neighborhood
Simple but fast and effective neighborhood kernel with linear decay.
ConeNeighborhood() - Constructor for class databionics.esom.neighborhood.ConeNeighborhood
Create a new neighborhood object
ConeNeighborhood(int, double) - Constructor for class databionics.esom.neighborhood.ConeNeighborhood
Create a new neighborhood object
conf - Variable in class databionics.Application
name of config file
Constant - Class in databionics.esom.train.search
searchs in constant range
Constant() - Constructor for class databionics.esom.train.search.Constant
 
constant - Variable in class databionics.modules.Parameter
flag whether this parameter should be constant or changeable
contains(String, String) - Static method in class databionics.project.DataManager
 
contains(String) - Static method in class databionics.project.DataManager
 
contours - Variable in class databionics.esom.renderer.Renderer
Flag for countour lines
controlButton - Variable in class databionics.esom.tool.AbstractTool
the Main Button switching the Tool on for the ControlPanel.
convert(RectangularGrid, LrnFile) - Method in class databionics.esom.tool.projection.ProjectionTool
 
cool() - Method in class databionics.esom.train.SOM
Cool down the parameters
Cooling - Class in databionics.esom.cooling
Abstract base class for cooling of a parameter.
Cooling() - Constructor for class databionics.esom.cooling.Cooling
Create a new cooling object with default parameters start = 1.0,steps = 100,end = 0.0
Cooling(double, int, double) - Constructor for class databionics.esom.cooling.Cooling
Create a new cooling object
coordinates2index(int, int, int) - Static method in class databionics.esom.grid.RectangularGrid
Convert row/column coordinates on grid to unique index
coordinates2index(int, int) - Method in class databionics.esom.grid.RectangularGrid
Convert row/column coordinates on grid to unique index
coordinates2index(int, int) - Method in class databionics.esom.grid.ToroidRectangularGrid
Convert row/column coordinates on grid to unique index Coordinates outside of the grid are wrapped around.
coordinates2index(int, int, int) - Static method in class databionics.esom.renderer.RendererTools
Convert row/column coordinates on grid to unique index
copyFile(File, File) - Static method in class databionics.util.Utils
Copy a file and display progress.
correctSpelling(String) - Static method in class databionics.text.StringUtils
Correct spelling in a string as typically found int song titles.
count - Variable in class databionics.esom.train.SOM
 
countSimilarExtTrigramMetric(StringList) - Method in class databionics.text.SimilarString
Count how many Strings in this list are similar to this String based on the trigram metric and a threshhold of 0.5.
cov - Variable in class databionics.esom.train.Descriptives
matrix of covariances
createFileType(String) - Static method in class databionics.io.FileType
Generic filetype
createImage() - Method in class databionics.esom.gui.RenderPanel
creating the image
createInputComponents() - Method in class databionics.esom.gui.util.RunDialog
Set up input fields for the tool
createInputComponents() - Method in class databionics.gui.RunDialog
Set up input fields for the tool
createIslandOverlapMatrix(DoubleMatrix2D) - Static method in class databionics.esom.renderer.RendererTools
 
createIslandOverlapMatrix() - Method in class databionics.esom.tool.island.IslandTool
 
createIslandOverlapMatrix(DoubleMatrix2D) - Method in class databionics.esom.tool.island.IslandTool
 
createLayout() - Method in class databionics.esom.gui.util.RunDialog
Set up dialog layout
createLayout() - Method in class databionics.gui.RunDialog
Set up dialog layout
createReaderByFilename(String) - Static method in class databionics.util.Utils
Create a possibly compressed reader based on the filename if the filename ends with ".zip" a ZipInputStream ist used if the filename ends with ".gz" a GZIPInputStream ist used if the filename ends with ".bz2" a CBZip2InputStream ist used otherwise a plain FileInputStream is used
createReaderByFilename(File) - Static method in class databionics.util.Utils
Create a possibly compressed reader based on the filename if the filename ends with ".zip" a ZipInputStream ist used if the filename ends with ".gz" a GZIPInputStream ist used if the filename ends with ".bz2" a CBZip2InputStream ist used otherwise a plain FileInputStream is used
createToroidPolygons(int, int, JPanel) - Method in class databionics.esom.gui.util.DoublePolygon
 
createWriterByFilename(String) - Static method in class databionics.util.Utils
Create a possibly compressed writer based on the filename if the filename ends with ".zip" a ZipOutputStream ist used if the filename ends with ".gz" a GZIPOutputStream ist used if the filename ends with ".bz2" a CBZip2OutputStream ist used otherwise a plain FileOutputStream is used
createWriterByFilename(File) - Static method in class databionics.util.Utils
Create a possibly compressed writer based on the filename if the filename ends with ".zip" a ZipOutputStream ist used if the filename ends with ".gz" a GZIPOutputStream ist used if the filename ends with ".bz2" a CBZip2OutputStream ist used otherwise a plain FileOutputStream is used
creatorPanel - Variable in class databionics.esom.tool.AbstractTool
CreatorPanel to be linked to renderPanel.
cRenderer - Variable in class databionics.esom.tool.legend.Legend
 
CsvFile - Class in databionics.io
Comma seperated values So far only tested with loading data from finance.yahoo.com.
CsvFile() - Constructor for class databionics.io.CsvFile
Standard constructor
CsvFile(String) - Constructor for class databionics.io.CsvFile
Constructor with a filename
CsvFile(int, int) - Constructor for class databionics.io.CsvFile
Constructor with size for an empty array.
CsvFile(LrnFile) - Constructor for class databionics.io.CsvFile
Clone constructor
currentClass - Variable in class databionics.esom.tool.classmask.ClassmaskTable
 
currentClass - Variable in class databionics.esom.tool.classmask.ClassmaskTool
 
currentClass - Variable in class databionics.esom.tool.dataclass.DataclassCreatorPanel
 
currentClass - Variable in class databionics.esom.tool.dataclass.DataclassTool
 
currentRule - Variable in class databionics.io.RuleFile
Buffer for current rule.

D

DAT_COLUMN - Static variable in class databionics.io.LrnFile
 
data - Variable in class databionics.esom.renderer.Renderer
matrix with training data
data - Variable in class databionics.esom.tool.classmask.ClassmaskTool
 
data - Variable in class databionics.esom.tool.data.SelectedDataTableModel
DoubleMatrix2D with selected rows of lrnFile
data - Variable in class databionics.esom.tool.dataclass.DataclassTool
 
data - Variable in class databionics.esom.tool.island.IslandTool
 
data - Variable in class databionics.esom.tool.legend.LegendRenderer
 
data - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
data - Variable in class databionics.esom.train.Descriptives
matrix with data
data - Variable in class databionics.esom.train.SOM
matrix with training data
data - Variable in class databionics.io.Array2DFile
2D matrix.
data - Variable in class databionics.io.ListFile
List containing the data.
data - Variable in class databionics.math.Distances
 
data2d - Variable in class databionics.math.Distances
 
databionics - package databionics
Base classes for all applications handling command line parsing and configuration file loading.
databionics.cli - package databionics.cli
Extension of commons-cli with loading default values from config file.
databionics.esom - package databionics.esom
The ESOM Tools command line programs and the ESOM Analyzer.
databionics.esom.cooling - package databionics.esom.cooling
Provides strategies for cooling of a parameter, like the learning rate for SOM training.
databionics.esom.grid - package databionics.esom.grid
ESOM grids: A grid holds the prototype vector and defines the map space topology by the function findNeighbors.
databionics.esom.gui - package databionics.esom.gui
The basic GUI components of the ESOM Analyzer.
databionics.esom.gui.util - package databionics.esom.gui.util
Some GUI components of the ESOM Analyzer.
databionics.esom.neighborhood - package databionics.esom.neighborhood
Provides neighborhood kernels for SOM training.
databionics.esom.renderer - package databionics.esom.renderer
Global classes for visualization.
databionics.esom.renderer.background - package databionics.esom.renderer.background
Background visualization methods that all inherit from BackgroundRenderer.
databionics.esom.renderer.foreground - package databionics.esom.renderer.foreground
Foreground visualization methods that all inherit from ForegroundRenderer.
databionics.esom.tool - package databionics.esom.tool
 
databionics.esom.tool.bminfo - package databionics.esom.tool.bminfo
 
databionics.esom.tool.classmask - package databionics.esom.tool.classmask
 
databionics.esom.tool.component - package databionics.esom.tool.component
 
databionics.esom.tool.data - package databionics.esom.tool.data
 
databionics.esom.tool.dataclass - package databionics.esom.tool.dataclass
 
databionics.esom.tool.info - package databionics.esom.tool.info
 
databionics.esom.tool.island - package databionics.esom.tool.island
 
databionics.esom.tool.legend - package databionics.esom.tool.legend
 
databionics.esom.tool.mapview - package databionics.esom.tool.mapview
 
databionics.esom.tool.options - package databionics.esom.tool.options
 
databionics.esom.tool.pointinfo - package databionics.esom.tool.pointinfo
 
databionics.esom.tool.projection - package databionics.esom.tool.projection
 
databionics.esom.tool.similarity - package databionics.esom.tool.similarity
 
databionics.esom.tool.slideshow - package databionics.esom.tool.slideshow
 
databionics.esom.train - package databionics.esom.train
Implementation of training algorithms.
databionics.esom.train.search - package databionics.esom.train.search
 
databionics.esom.util - package databionics.esom.util
Some utility classes mainly for the GUI.
databionics.esom.util.actions - package databionics.esom.util.actions
Event handling mainly for menu of the ESOM Analyzer.
databionics.gui - package databionics.gui
Useful GUI classes like a panel displaying log4j messages and a dialog for running programs based on an XML description of the parameters.
databionics.io - package databionics.io
Loading and saving of all file formats.
databionics.math - package databionics.math
Pairwise distance calculation and Pareto Density Estimation.
databionics.modules - package databionics.modules
Description of program parameters loadable from XML files.
databionics.project - package databionics.project
Managing a collection of file types.
databionics.runner - package databionics.runner
Helper class to run external tools (non-Java).
databionics.text - package databionics.text
Some simple string routines including n-gram similarity.
databionics.util - package databionics.util
Some utilities including searching for classes in a jar and reading an environment variable.
DataClass - Class in databionics.io
The DataClass of a data point or a bestmatch.
DataClass() - Constructor for class databionics.io.DataClass
Standard constructor
DataClass(int) - Constructor for class databionics.io.DataClass
Constructor with index
DataClass(int, String) - Constructor for class databionics.io.DataClass
Constructor with index and name
DataClass(int, String, Color) - Constructor for class databionics.io.DataClass
Constructor with all fields.
DataclassCreatorPanel - Class in databionics.esom.tool.dataclass
 
DataclassCreatorPanel(AbstractTool) - Constructor for class databionics.esom.tool.dataclass.DataclassCreatorPanel
 
DataclassLoadAction - Class in databionics.esom.tool.dataclass
 
DataclassLoadAction(DataclassTool) - Constructor for class databionics.esom.tool.dataclass.DataclassLoadAction
 
DataclassRenderer - Class in databionics.esom.tool.dataclass
 
DataclassRenderer(AbstractTool) - Constructor for class databionics.esom.tool.dataclass.DataclassRenderer
 
DataclassSaveAction - Class in databionics.esom.tool.dataclass
 
DataclassSaveAction(AbstractTool) - Constructor for class databionics.esom.tool.dataclass.DataclassSaveAction
 
DataclassTable - Class in databionics.esom.tool.dataclass
 
DataclassTable(AbstractTool) - Constructor for class databionics.esom.tool.dataclass.DataclassTable
 
DataclassTableModel - Class in databionics.esom.tool.dataclass
 
DataclassTableModel(AbstractTool) - Constructor for class databionics.esom.tool.dataclass.DataclassTableModel
standard constructor.
dataclassTool - Variable in class databionics.esom.gui.ToolLoader
 
dataclassTool - Variable in class databionics.esom.tool.data.DataTableModel
 
dataclassTool - Variable in class databionics.esom.tool.data.SelectedDataTableModel
the renderer
DataclassTool - Class in databionics.esom.tool.dataclass
 
DataclassTool(boolean, Application) - Constructor for class databionics.esom.tool.dataclass.DataclassTool
 
DataItem - Class in databionics.io
Base class for data items with an index.
DataItem() - Constructor for class databionics.io.DataItem
Standard constructor
DataItem(int) - Constructor for class databionics.io.DataItem
Constructor with index
DataManager - Class in databionics.project
DataManager ensures access to globally used Objects, providing unlimited number of flags, specified by unique strings, if recomputation has to be done.
DataManager() - Constructor for class databionics.project.DataManager
 
dataTable - Variable in class databionics.esom.tool.AbstractTool
 
dataTable - Variable in class databionics.esom.tool.BottomTab
 
DataTable - Class in databionics.esom.tool.data
 
DataTable(AbstractTool) - Constructor for class databionics.esom.tool.data.DataTable
Constructor with data model
dataTableModel - Variable in class databionics.esom.tool.AbstractTool
Table model for the dataTable.
DataTableModel - Class in databionics.esom.tool.data
 
DataTableModel(AbstractTool) - Constructor for class databionics.esom.tool.data.DataTableModel
Basic constructor.
dataTool - Variable in class databionics.esom.gui.ToolLoader
 
dataTool - Variable in class databionics.esom.renderer.Renderer
 
DataTool - Class in databionics.esom.tool.data
 
DataTool(boolean, Application) - Constructor for class databionics.esom.tool.data.DataTool
 
DataToolRenderer - Class in databionics.esom.tool.data
 
DataToolRenderer(AbstractTool) - Constructor for class databionics.esom.tool.data.DataToolRenderer
 
def - Variable in class databionics.modules.AbstractStringParameter
default value
def - Variable in class databionics.modules.FloatParameter
default value
def - Variable in class databionics.modules.IntParameter
default value
def - Variable in class databionics.modules.MultipleChoiceParameter
default value
def - Variable in class databionics.modules.SwitchParameter
default value
defines - Variable in class databionics.io.LrnFile
Type of data columns from header.
deleteOutliers(int[]) - Method in class databionics.esom.tool.data.DataTool
delete the selected points
deleteOutliers(IntArrayList) - Method in class databionics.esom.tool.data.DataTool
delete the selected points
delimiter - Variable in class databionics.io.BaseFile
Default saving delimiter character.
delimiters - Variable in class databionics.io.BaseFile
Default parsing delimiter characters.
densities - Variable in class databionics.math.ParetoDensity
the list to hold the density values
densities() - Method in class databionics.math.ParetoDensity
Return densities evaluated at centers.
density - Variable in class databionics.esom.tool.legend.LegendRenderer
 
description - Variable in class databionics.io.FileType
 
description - Variable in class databionics.io.KeyName
Description of key.
description - Variable in class databionics.modules.Module
description of the module
description - Variable in class databionics.modules.MultipleChoiceElement
parameter description
description - Variable in class databionics.modules.Parameter
decription to be displayed in dialogs
description - Variable in class databionics.modules.Tool
description
description - Variable in class databionics.project.Project
description of the project
Descriptives - Class in databionics.esom.train
Computes and stores important characteristics of the data
Descriptives() - Constructor for class databionics.esom.train.Descriptives
standard constructor
Descriptives(DoubleMatrix2D) - Constructor for class databionics.esom.train.Descriptives
constructor who sets data and EigenvalueDecomposition
descriptives - Variable in class databionics.esom.train.SOM
statistics about data
deselectGroup(int, int) - Method in class databionics.esom.tool.data.DataTable
deselects group in all cases including start and end
deselectIndex(int) - Method in class databionics.esom.tool.data.DataTable
deselects index i in all cases
df - Variable in class databionics.esom.renderer.background.BackgroundTool
Number format for parameters for some backgrounds.
df - Variable in class databionics.io.CsvFile
date format.
DiagnosisFile - Class in databionics.io
File that stores possibly multiple classification of data points or best matches.
DiagnosisFile() - Constructor for class databionics.io.DiagnosisFile
Standard constructor
DiagnosisFile(String) - Constructor for class databionics.io.DiagnosisFile
Constructor with a filename
diff - Variable in class databionics.esom.cooling.CenterCooling
difference between succesive y values
diff - Variable in class databionics.esom.cooling.ExponentialCooling
difference between succesive x values
diff - Variable in class databionics.esom.cooling.LinearCooling
difference between succesive y values
DiffCondition - Class in databionics.io
Condition linking to a differentiation rule.
DiffCondition() - Constructor for class databionics.io.DiffCondition
Standard constructor
DiffCondition(String, String, String) - Constructor for class databionics.io.DiffCondition
Constructor with all fields.
DiffRule - Class in databionics.io
Differentiazation rule
DiffRule() - Constructor for class databionics.io.DiffRule
Standard constructor
DiffRule(String, String, String, String, String, String) - Constructor for class databionics.io.DiffRule
Constructor with all important fields.
dim - Variable in class databionics.esom.grid.Grid
number weights per neuron
dim() - Method in class databionics.esom.grid.Grid
Get the value of dim.
dim - Variable in class databionics.esom.gui.RenderPanel
java dimension
dimName - Variable in class databionics.io.Condition
The dimension name.
dimName - Variable in class databionics.io.IntervalCondition
The dimension name.
displayForeground(ForegroundRenderer) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Show a foreground.
displayForeground(String) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Show a foreground by name.
displayPanel - Variable in class databionics.esom.tool.AbstractTool
Can be used to display Data in the BottomTab.
distance - Variable in class databionics.io.WtsFile
Data space distance function name
DistanceFactory - Class in databionics.math
Get a distance function by name.
DistanceFactory() - Constructor for class databionics.math.DistanceFactory
 
distanceFunction - Variable in class databionics.esom.grid.Grid
distance function in data space
distanceFunction - Variable in class databionics.esom.tool.projection.ProjectionTool
distance function in data space
distanceFunction - Variable in class databionics.esom.train.SOM
distance function in data space
distanceFunction - Variable in class databionics.math.Distances
 
distanceFunctionName - Variable in class databionics.esom.grid.Grid
distance function name for debugging
distancePercentiles - Variable in class databionics.math.ParetoDensity
 
distances - Variable in class databionics.esom.train.SOM
current distances between bestmatches and datapoints
Distances - Class in databionics.math
Computes all pairwise distances between row vectors of a DoubleMatrix2D.
Distances() - Constructor for class databionics.math.Distances
 
distances - Variable in class databionics.math.Distances
 
done - Variable in class databionics.Application
flag whether app is done, is set when calling the exit method
doubleActPoly - Variable in class databionics.esom.tool.ProtoPanel
 
DoublePolygon - Class in databionics.esom.gui.util
Class to handle polygons consisting of a bunch of xpoint, ypoints, widths, heights
DoublePolygon() - Constructor for class databionics.esom.gui.util.DoublePolygon
Basic constructor
dragMode - Variable in class databionics.esom.tool.AbstractTool
 
drawBackground() - Method in class databionics.esom.renderer.Renderer
 
drawBestmatch(int, int, int, int, int, Renderer) - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Draws the bestmatch
drawBestmatch(int, int, int, int, int, Renderer) - Method in class databionics.esom.renderer.foreground.LineRenderer
Draws the bestmatch
drawBestmatch(int, int, int, int, int, Renderer) - Method in class databionics.esom.tool.data.HighlightRenderer
draws the bestmatch.
drawBestmatch(int, int, int, int, int, Renderer) - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
Draws the bestmatch
drawEyeland(int, DoubleMatrix2D, BufferedImage) - Static method in class databionics.esom.renderer.RendererTools
 
drawEyelandOverlapMatrix(int, DoubleMatrix2D, BufferedImage) - Static method in class databionics.esom.renderer.RendererTools
 
drawing - Variable in class databionics.esom.tool.AbstractTool
Flag decides if Foreground is rendered.
drawing - Variable in class databionics.esom.tool.AbstractToolRenderer
 

E

EDIT - Static variable in class databionics.esom.gui.util.ColorEditor
 
end - Variable in class databionics.esom.cooling.Cooling
final value of the parameter
end - Variable in class databionics.modules.Job
date and time when running job was ended
env - Variable in class databionics.Application
name of envorinment variable
EpanechicovNeighborhood - Class in databionics.esom.neighborhood
Epanechicovian neighborhood kernel
EpanechicovNeighborhood() - Constructor for class databionics.esom.neighborhood.EpanechicovNeighborhood
Create a new neighborhood object
EpanechicovNeighborhood(int, double) - Constructor for class databionics.esom.neighborhood.EpanechicovNeighborhood
Create a new neighborhood object
epoch - Variable in class databionics.esom.train.SOM
current epoch number 0..epochs-1, only used internally
epochs - Variable in class databionics.esom.train.SOM
number of training epochs
equals(Object) - Method in class databionics.io.FileType
Equals() only depends on the extension.
ERROR - Static variable in class databionics.esom.gui.util.MessagePanel
static types
errorReader - Variable in class databionics.runner.MatlabRunner
error output of process
errorReader - Variable in class databionics.runner.Runner
error output of process
ev - Variable in class databionics.esom.train.Descriptives
Normalized Eigenvectors
evd - Variable in class databionics.esom.train.Descriptives
Eigenvalues
exit(int) - Method in class databionics.Application
Really exit if run in standalone mode, otherwise only set done flag for frontend.
exit - Variable in class databionics.esom.tool.slideshow.SlideShow
 
exit(int) - Method in class databionics.GraphicalApplication
Really exit if run in standalone mode, otherwise only set done flag for frontend and hide mai window.
ExitAction - Class in databionics.esom.util.actions
Exit program
ExitAction(Application) - Constructor for class databionics.esom.util.actions.ExitAction
 
exitCode - Variable in class databionics.Application
exit code of application, < 0 for not set, 0 for no error
exitOnInterruption() - Method in class databionics.Application
Exit application if current thread is interrupted
ExitSlideShowAction - Class in databionics.esom.tool.slideshow
action for closing the slide show
ExitSlideShowAction(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.ExitSlideShowAction
constructor with given slideShow
Explanation - Class in databionics.io
The explanation why a rule could not classify a data point.
Explanation() - Constructor for class databionics.io.Explanation
Standard constructor
Explanation(int, String, String, String) - Constructor for class databionics.io.Explanation
Constructor with all fields
ExplFile - Class in databionics.io
File that stores explanations why certain rules could not classify some data points.
ExplFile() - Constructor for class databionics.io.ExplFile
Standard constructor
ExplFile(String) - Constructor for class databionics.io.ExplFile
Constructor with a filename
ExponentialCooling - Class in databionics.esom.cooling
Exponential cooling of a parameter.
ExponentialCooling(double, int, double) - Constructor for class databionics.esom.cooling.ExponentialCooling
Create a new exponential cooling object
ext - Variable in class databionics.io.FileType
 
extension - Variable in class databionics.util.FileExtensionFilter
 
extNGramMetric(int, String) - Method in class databionics.text.SimilarString
Calculate extended n-grams metric distance of string and argument.
extNGramMetric(int, String, String) - Static method in class databionics.text.StringUtils
Calculate extended n-grams metric distance of two strings.

F

failingCondition - Variable in class databionics.io.Explanation
Failing condition.
failingRule - Variable in class databionics.io.Explanation
Failing rule.
fallback() - Method in class databionics.esom.renderer.background.BackgroundTool
If for any reason a Background might not work, this can be called as a fallback on the UMatrix.
favoriteColor - Variable in class databionics.esom.renderer.foreground.ForegroundRenderer
the color to choose if none is given
favoriteColor - Variable in class databionics.esom.tool.AbstractToolRenderer
 
fgRenderer - Variable in class databionics.esom.tool.AbstractToolRenderer
 
file - Variable in class databionics.esom.tool.projection.ProjectCallback
 
file - Variable in class databionics.io.BaseFile
Path of file.
file - Variable in class databionics.project.FileSlot
the data of the first file in this slot
FileAction - Class in databionics.esom.util.actions
Parent class for actions needing a filetype.
FileAction(FileType) - Constructor for class databionics.esom.util.actions.FileAction
Constructor with file type
FileExtensionFilter - Class in databionics.io
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
FileExtensionFilter() - Constructor for class databionics.io.FileExtensionFilter
Creates a file filter.
FileExtensionFilter(String) - Constructor for class databionics.io.FileExtensionFilter
Creates a file filter that accepts files with the given extension.
FileExtensionFilter(String, String) - Constructor for class databionics.io.FileExtensionFilter
Creates a file filter that accepts the given file type.
FileExtensionFilter(String[]) - Constructor for class databionics.io.FileExtensionFilter
Creates a file filter from the given string array.
FileExtensionFilter(String[], String) - Constructor for class databionics.io.FileExtensionFilter
Creates a file filter from the given string array and description.
FileExtensionFilter - Class in databionics.util
Filenamefilter that accepts files based on the extension
FileExtensionFilter(String) - Constructor for class databionics.util.FileExtensionFilter
 
fileMenu - Variable in class databionics.esom.tool.AbstractTool
fileMenu to be inserted into Main Menu.
filename - Variable in class databionics.esom.tool.AbstractTool
to be removed.
FileParameter - Class in databionics.modules
Parameter with filename argument.
FileParameter() - Constructor for class databionics.modules.FileParameter
 
FileSlot - Class in databionics.project
A FileSlot holds several filenames for a FileType.
FileSlot() - Constructor for class databionics.project.FileSlot
Default constructor
FileSlot(FileType) - Constructor for class databionics.project.FileSlot
Constructor with type
FileSlot(boolean, int) - Constructor for class databionics.project.FileSlot
Constructor without type
FileSlot(FileType, boolean, int) - Constructor for class databionics.project.FileSlot
Constructor with all parameters
FileType - Class in databionics.io
Class to describe file types
FileType() - Constructor for class databionics.io.FileType
 
fillBMMatrix() - Method in class databionics.io.BMFile
 
fillCache(int) - Method in class databionics.esom.cooling.CachedCooling
Fill the cache with precalculated values.
fillNames() - Method in class databionics.esom.tool.data.DataTool
fill empty names
finalName - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
findBackgrounds(String, String, String, String) - Method in class databionics.esom.renderer.background.BackgroundTool
Finds classes that render backgrounds from *.jar file.
findBestMatch(int, LrnFile, RectangularGrid) - Method in class databionics.esom.tool.projection.ProjectionTool
Find best matching weight for data vector.
findBestmatch(int, int) - Method in class databionics.esom.train.search.BmSearch
 
findBestmatch(int, int) - Method in class databionics.esom.train.search.LocalBmSearch
Find best matching weight for data vector.
findBestmatch(int, int) - Method in class databionics.esom.train.search.NoBmSearch
 
findBestmatch(int, int) - Method in class databionics.esom.train.search.SimpleBmSearch
Find best matching weight for data vector.
findClassesInJar(String, String, String, String, String) - Static method in class databionics.util.Utils
Find all classes in *.jar files, optionally restrict to a package, direct subclasses of a given class or classes implementing a given interface.
findNeighbors(int, int, IntArrayList, IntArrayList) - Method in class databionics.esom.grid.CircularGrid1D
Find all neighbors of a neuron within a given radius along with the distance from the center.
findNeighbors(int, int, IntArrayList, IntArrayList) - Method in class databionics.esom.grid.Grid
Find all neighbors of a neuron within a given radius along with the distance from the center.
findNeighbors(int, int, IntArrayList, IntArrayList) - Method in class databionics.esom.grid.Grid1D
Find all neighbors of a neuron within a given radius along with the distance from the center.
findNeighbors(int, int, IntArrayList, IntArrayList) - Method in class databionics.esom.grid.PlanarGrid
Find all neighbors of a neuron within a given radius along with the distance from the center.
findNeighbors(int, int, IntArrayList, IntArrayList) - Method in class databionics.esom.grid.ToroidGrid
Find all neighbors of a neuron within a given radius along with the distance from the center.
findToolByName(String) - Method in class databionics.modules.Modules
Find a tool by its name
finished() - Method in class databionics.esom.tool.projection.ClassifyCallback
react on finishing projection
finished() - Method in class databionics.esom.tool.projection.ProjectCallback
react on finishing projection
finished() - Method in class databionics.esom.tool.slideshow.SlideShowCallback
react on finishing projection
finished() - Method in class databionics.esom.train.TrainCallback
react after finishing
finished() - Method in interface databionics.gui.CallBack
reacts on finishing
fireChangeListener(ChangeEvent) - Method in class databionics.project.Project
Informs all classes contained in list changeListeners that something in this project has changed
first - Variable in class databionics.esom.tool.slideshow.SlideShow
 
FloatParameter - Class in databionics.modules
Parameter with floating point number argument.
FloatParameter() - Constructor for class databionics.modules.FloatParameter
 
floodFill - Variable in class databionics.esom.tool.classmask.ClassmaskTool
Floodfill or not.
flush() - Method in class databionics.gui.LogPanelWriter
Ignore call to flush
FolderFilter - Class in databionics.util
FileFilter that accepts only folders.
FolderFilter() - Constructor for class databionics.util.FolderFilter
 
FolderParameter - Class in databionics.modules
Parameter with string argument for folders.
FolderParameter() - Constructor for class databionics.modules.FolderParameter
 
fontSize - Variable in class databionics.esom.renderer.foreground.NamesRenderer
size of bestmatch
ForegroundList - Class in databionics.esom.renderer.foreground
List that holds ForegroundRenderers.
ForegroundList() - Constructor for class databionics.esom.renderer.foreground.ForegroundList
Standard constructor.
ForegroundList(int) - Constructor for class databionics.esom.renderer.foreground.ForegroundList
Constructor.
foregroundList - Variable in class databionics.esom.renderer.foreground.ForegroundTool
foregrounds
foregroundLists - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
foregroundNames - Variable in class databionics.esom.renderer.foreground.ForegroundTool
foreground names
ForegroundRenderer - Class in databionics.esom.renderer.foreground
Base class for all foreground renderers.
ForegroundRenderer() - Constructor for class databionics.esom.renderer.foreground.ForegroundRenderer
Standard constructor.
foregroundTool - Variable in class databionics.esom.gui.ToolLoader
 
foregroundTool - Variable in class databionics.esom.renderer.foreground.ForegroundRenderer
points to the foregroundTool.
ForegroundTool - Class in databionics.esom.renderer.foreground
GUI-interface to manage the various foregrounds.
ForegroundTool(boolean, Application) - Constructor for class databionics.esom.renderer.foreground.ForegroundTool
Constructor with application
foregroundTool - Variable in class databionics.esom.renderer.Renderer
 
foregroundTool - Variable in class databionics.esom.tool.AbstractToolRenderer
 
formatFilesize(int) - Static method in class databionics.text.StringUtils
Format file size
forward - Variable in class databionics.esom.tool.slideshow.SlideShow
 
fourtimes - Variable in class databionics.esom.tool.island.IslandTool
 
frame - Variable in class databionics.esom.renderer.Renderer
 
frame - Variable in class databionics.GraphicalApplication
main program window
frameColor - Variable in class databionics.esom.renderer.foreground.ForegroundTool
color of Frame
frameColor - Variable in class databionics.esom.renderer.foreground.FrameRenderer
 
frameRenderer - Variable in class databionics.esom.renderer.foreground.ForegroundTool
special case: frame renderer
FrameRenderer - Class in databionics.esom.renderer.foreground
Render frame of original map in tiled mode.
FrameRenderer() - Constructor for class databionics.esom.renderer.foreground.FrameRenderer
Standard constructor

G

g - Variable in class databionics.esom.renderer.foreground.BestmatchRenderer
graphic to draw on
g - Variable in class databionics.esom.renderer.foreground.LineRenderer
graphic to draw on
g - Variable in class databionics.esom.renderer.foreground.NamesRenderer
graphic to draw on
GapRenderer - Class in databionics.esom.renderer.background
Gap background renderer.
GapRenderer() - Constructor for class databionics.esom.renderer.background.GapRenderer
Standard constructor
GaussNeighborhood - Class in databionics.esom.neighborhood
Gaussian neighborhood kernel
GaussNeighborhood() - Constructor for class databionics.esom.neighborhood.GaussNeighborhood
Create a new neighborhood object.
GaussNeighborhood(int) - Constructor for class databionics.esom.neighborhood.GaussNeighborhood
Create a new neighborhood object.
GaussNeighborhood(int, double, int) - Constructor for class databionics.esom.neighborhood.GaussNeighborhood
Create a new neighborhood object.
GaussNeighborhood(int, double) - Constructor for class databionics.esom.neighborhood.GaussNeighborhood
Create a new neighborhood object.
generateFileName(Job) - Method in class databionics.modules.OutputFileParameter
Generate filename based on template and parameters
generateIcon(String, ColorTable) - Method in class databionics.esom.gui.util.GradientComboBox
Generate the image to be displayed in the color combobox
generateImage() - Method in class databionics.esom.tool.legend.HeightsLegend
original Version.
get(int) - Method in class databionics.esom.cooling.CachedCooling
Get value of parameter by the step number.
get(int) - Method in class databionics.esom.cooling.Cooling
Get value of parameter by the step number.
get(int) - Method in class databionics.esom.neighborhood.CachedNeighborhood
Get weight for distance from kernel center
get(int) - Method in class databionics.esom.neighborhood.Neighborhood
Get weight for distance on grid from kernel center
get(int, int) - Method in class databionics.io.Array2DFile
Get element of matrix.
get(int) - Method in class databionics.io.ColorMapping
 
get(int, double) - Method in class databionics.io.ColorMapping
 
get(int, int) - Method in class databionics.math.Distances
Get the distance between row i and j of the original data matrix
get(String) - Static method in class databionics.project.DataManager
obtain an Object from workspace.
get(String, String) - Static method in class databionics.project.DataManager
 
getActCol() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
getActRow() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
getActualRenderer() - Method in class databionics.esom.renderer.background.BackgroundTool
workaround
getAll(int) - Method in class databionics.io.DiagnosisFile
Get all class numbers of a classification by its position in the list
getAllByIndex(int) - Method in class databionics.io.DiagnosisFile
Get all class numbers of a classification by its index
getAllClasses() - Method in class databionics.io.DiagnosisFile
Get list of IntArrayLists with all class numbers.
getAlpha() - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
getAlpha() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
getApp() - Method in class databionics.modules.Job
 
getApplication() - Method in interface databionics.esom.gui.AbstractGuiComponent
 
getApplication() - Method in class databionics.esom.gui.BottomBar
 
getApplication() - Method in class databionics.esom.gui.MainFrame
 
getApplication() - Method in class databionics.esom.gui.RenderPanel
 
getApplication() - Method in class databionics.esom.gui.ToolLoader
 
getApplication() - Method in class databionics.esom.tool.AbstractTool
 
getAsInt(int) - Method in class databionics.esom.cooling.Cooling
Get value of parameter rounded to the nearest int
getBackgroundByName(String) - Method in class databionics.esom.renderer.background.BackgroundTool
Get a Background by its name.
getBackgroundRenderer() - Method in class databionics.esom.renderer.Renderer
Get the background renderer
getBackgroundTool() - Method in class databionics.esom.gui.ToolLoader
 
getBanner() - Method in class databionics.Application
Get long program name with version.
getBestMatches() - Method in class databionics.esom.renderer.Renderer
Get the bestmatches in grid
getBestMatches(IntArrayList, RectangularGrid, LrnFile) - Method in class databionics.esom.tool.projection.ProjectionTool
Save indices of best matching neurons to a *.bm file Available after calling train().
getBestMatches() - Method in class databionics.esom.train.SOM
Get the indices of best matching neurons for data points Available after calling train().
getBgImage() - Method in class databionics.esom.renderer.Renderer
 
getBinSize() - Method in class databionics.esom.tool.legend.HeightsLegend
 
getBmFilename() - Method in class databionics.esom.renderer.Renderer
 
getBMIndexByCoordinates(int, int) - Method in class databionics.io.BMFile
 
getBmInfoTool() - Method in class databionics.esom.gui.ToolLoader
 
getBMRendererNames() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
getBmSearch() - Method in class databionics.esom.train.SOM
 
getBmSize() - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Get the bestmatch size
getBmSize() - Method in class databionics.esom.renderer.foreground.ForegroundList
 
getBmSize() - Method in class databionics.esom.renderer.Renderer
 
getBoldClasses() - Method in class databionics.io.ClsFile
Get highlighted classes.
getBottomBar() - Method in class databionics.esom.gui.MainFrame
returns the bottomBar
getBottomTab() - Method in class databionics.esom.tool.AbstractTool
 
getBtnStartShow() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getByIndex(int) - Method in class databionics.io.BMFile
Get a best match by its index.
getByIndex(int) - Method in class databionics.io.ClassmaskFile
Get class number of a classification by its index
getByIndex(int) - Method in class databionics.io.ClsFile
Get class number of a classification by its index
getByIndex(int) - Method in class databionics.io.LrnFile
Get a datavector by it's keyValue returns DoubleMatrix1D
getByIndex(int) - Method in class databionics.io.NamesFile
Get a key name by its index.
getByIndex(int) - Method in class databionics.io.PicturesFile
Get a key name by its index.
getCache() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getCallback() - Method in class databionics.esom.Cluster
 
getCallback() - Method in class databionics.esom.Project
 
getCallback() - Method in class databionics.esom.SlideShow
 
getCallback() - Method in class databionics.esom.tool.AbstractTool
 
getCaption(Renderer) - Method in class databionics.esom.renderer.background.BackgroundRenderer
Short description of the renderer.
getCaption(Renderer) - Method in class databionics.esom.renderer.background.ComponentRenderer
Short description of the renderer: the name or number of the component.
getCaseKey() - Method in class databionics.io.DiffCondition
Get CaseKey.
getCaseKey() - Method in class databionics.io.Rule
Get CaseKey.
getCaseName() - Method in class databionics.io.Rule
Get CaseName.
getCellEditorValue() - Method in class databionics.esom.gui.util.ColorEditor
 
getCenters() - Method in class databionics.math.ParetoDensity
 
getChoices() - Method in class databionics.modules.MultipleChoiceParameter
Get the list of allowed values
getClass(int) - Method in class databionics.io.ClassmaskFile
Get a data class by its position in the list
getClass(int) - Method in class databionics.io.ClsFile
Get a data class by its position in the list
getClassByIndex(int) - Method in class databionics.io.ClassmaskFile
Get a data class by its index
getClassByIndex(int) - Method in class databionics.io.ClsFile
Get a data class by its index
getClassColumnIndex() - Method in class databionics.io.LrnFile
Get class column index.
getClassColumnName() - Method in class databionics.io.LrnFile
Get class column name.
getClasses() - Method in class databionics.esom.renderer.Renderer
 
getClasses() - Method in class databionics.io.ClassmaskFile
Get classes.
getClasses() - Method in class databionics.io.ClsFile
Get classes.
getClasses() - Method in class databionics.io.LrnFile
Get classes.
getClassification() - Method in class databionics.esom.renderer.foreground.NamesRenderer
 
getClassification() - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
getClassList() - Method in class databionics.esom.train.BestMatchHit
 
getClassmask() - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
getClassmaskTool() - Method in class databionics.esom.gui.ToolLoader
 
getClassName() - Method in class databionics.io.DiffCondition
Get ClassName.
getClassName() - Method in class databionics.io.Rule
Get ClassName.
getClip() - Method in class databionics.esom.renderer.Renderer
 
getClonedBgImage() - Method in class databionics.esom.renderer.Renderer
 
getClrFourtimes() - Method in class databionics.esom.tool.island.IslandRenderer
 
getClrFourtimes() - Method in class databionics.esom.tool.island.IslandTool
 
getClrThreetimes() - Method in class databionics.esom.tool.island.IslandRenderer
 
getClrThreetimes() - Method in class databionics.esom.tool.island.IslandTool
 
getClrTwice() - Method in class databionics.esom.tool.island.IslandRenderer
 
getClrTwice() - Method in class databionics.esom.tool.island.IslandTool
 
getClrWater() - Method in class databionics.esom.tool.island.IslandRenderer
 
getClrWater() - Method in class databionics.esom.tool.island.IslandTool
 
getClrZeros() - Method in class databionics.esom.tool.island.IslandRenderer
 
getClrZeros() - Method in class databionics.esom.tool.island.IslandTool
 
getClusterFactor(int) - Method in class databionics.math.ParetoDensity
Lookup table for cluster correction factors.
getClusters() - Method in class databionics.math.ParetoDensity
 
getColData() - Method in class databionics.io.BMFile
 
getColor(int) - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Get the color for this bestmatch.
getColor(int) - Method in class databionics.esom.renderer.foreground.LineRenderer
Get the color for this bestmatch.
getColor(int) - Method in class databionics.esom.renderer.foreground.NamesRenderer
Get the color for this bestmatch.
getColor(int) - Method in class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
Calculate opinion color
getColor(int) - Method in class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
Calculate opinion color
getColor(int, Renderer) - Method in class databionics.esom.tool.data.HighlightRenderer
Get the color for this bestmatch.
getColor(int) - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
Get the color for this bestmatch by it's classification
getColor(int) - Method in class databionics.io.ColorTable
 
getColor() - Method in class databionics.io.DataClass
Get the class number.
getColorGradient(String) - Static method in class databionics.Application
Get path to color gradient.
getColorify() - Method in class databionics.esom.renderer.Renderer
 
getColorMap() - Method in class databionics.esom.renderer.Renderer
 
getColorPath() - Static method in class databionics.Application
Get path to color tables
getColors() - Method in class databionics.esom.renderer.Renderer
Get the color table
getColorStats() - Method in class databionics.io.ColorMapping
 
getColorSteps() - Method in class databionics.esom.renderer.Renderer
Returns the Number of Colorsteps to be made
getColorTable(int) - Method in class databionics.esom.gui.util.GradientComboBox
Get a color table by index
getColorTable() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
getColorTable() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
getCols() - Method in class databionics.io.BMFile
Get the value of cols.
getColumn() - Method in class databionics.io.Bestmatch
Get column of best match.
getColumnClass(int) - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
returns the file type of one column
getColumnClass(int) - Method in class databionics.esom.tool.component.ComponentTableModel
returns kind of dataType in column
getColumnClass(int) - Method in class databionics.esom.tool.data.DataTableModel
returns the kind of dataType in each column
getColumnClass(int) - Method in class databionics.esom.tool.dataclass.DataclassTableModel
returns type of one column
getColumnClass(int) - Method in class databionics.esom.tool.info.InfoToolTableModel
 
getColumnClass(int) - Method in class databionics.esom.tool.island.IslandTableModel
returns type of one column
getColumnClass(int) - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
getColumnCount() - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
returns number of columns
getColumnCount() - Method in class databionics.esom.tool.component.ComponentTableModel
returns number of columns
getColumnCount() - Method in class databionics.esom.tool.data.DataTableModel
returns the number of columns
getColumnCount() - Method in class databionics.esom.tool.data.SelectedDataTableModel
returns the number of columns
getColumnCount() - Method in class databionics.esom.tool.dataclass.DataclassTableModel
returns the number of columns
getColumnCount() - Method in class databionics.esom.tool.info.InfoToolTableModel
 
getColumnCount() - Method in class databionics.esom.tool.island.IslandTableModel
 
getColumnCount() - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
getColumnName(int) - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
returns name of one column
getColumnName(int) - Method in class databionics.esom.tool.component.ComponentTableModel
returns name of column
getColumnName(int) - Method in class databionics.esom.tool.data.DataTableModel
returns the name of each column
getColumnName(int) - Method in class databionics.esom.tool.data.SelectedDataTableModel
returns the name of each column
getColumnName(int) - Method in class databionics.esom.tool.dataclass.DataclassTableModel
returns the name of one column
getColumnName(int) - Method in class databionics.esom.tool.info.InfoToolTableModel
 
getColumnName(int) - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
getColumns() - Method in class databionics.esom.grid.RectangularGrid
Get number of columns
getColumns() - Method in class databionics.io.Array2DFile
Get number of columns in matrix.
getColumns() - Method in class databionics.io.Array3DFile
Get number of columns of the pseudo 3d matrix.
getCommand() - Method in class databionics.modules.Tool
Get command to run this tool
getComment() - Method in class databionics.io.BaseFile
Get the comment of file.
getComponents() - Method in class databionics.esom.renderer.Renderer
Get the selected weight components.
getComponentTool() - Method in class databionics.esom.gui.ToolLoader
 
getConditions() - Method in class databionics.io.Rule
Get Conditions.
getConfigPath() - Static method in class databionics.Application
Get path to configuration files
getConstant() - Method in class databionics.esom.train.search.LocalBmSearch
 
getControlButton() - Method in class databionics.esom.tool.AbstractTool
 
getCopy(String) - Static method in class databionics.project.DataManager
obtain a copy of specified Object.
getCopy(String, String) - Static method in class databionics.project.DataManager
 
getCount(int) - Method in class databionics.io.ColorStatistics
 
getCount(String) - Method in class databionics.text.StringCounter
 
getCovariance() - Method in class databionics.esom.train.Descriptives
Returns covariance matrix of data
getCreatorPanel() - Method in class databionics.esom.tool.AbstractTool
Get the CreatorPanel belonging to this tool.
getCurrentClass() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
getCurrentclass() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
getData() - Method in interface databionics.esom.tool.AbstractCallback
 
getData() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
getData() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
getData() - Method in class databionics.esom.tool.island.IslandTool
 
getData() - Method in class databionics.esom.train.SOM
Get the matrix with the training data.
getData() - Method in class databionics.io.Array2DFile
Get 2D matrix.
getData() - Method in class databionics.io.ListFile
Get the data list.
getData() - Method in class databionics.math.Distances
 
getDataclassTool() - Method in class databionics.esom.gui.ToolLoader
 
getDataTable() - Method in class databionics.esom.tool.AbstractTool
 
getDataTableModel() - Method in class databionics.esom.tool.AbstractTool
 
getDataTableModel() - Method in class databionics.esom.tool.data.DataTool
 
getDataTool() - Method in class databionics.esom.gui.ToolLoader
 
getDefault() - Method in class databionics.modules.AbstractStringParameter
Get the default value
getDefault() - Method in class databionics.modules.FloatParameter
Get the default value
getDefault() - Method in class databionics.modules.IntParameter
Get the default value
getDefault() - Method in class databionics.modules.MultipleChoiceParameter
Get the default value
getDefault() - Method in class databionics.modules.SwitchParameter
Get the default value
getDefaultInstance() - Static method in class databionics.project.DataManager
returns the default instance identifier
getDefines() - Method in class databionics.io.LrnFile
Get defines.
getDensities() - Method in class databionics.math.ParetoDensity
Return all Pareto density values of the rows in matrix.
getDensityQuantiles() - Method in class databionics.math.ParetoDensity
returning quantiles of calculated densities.
getDescription() - Method in class databionics.io.FileExtensionFilter
Returns the human readable description of this filter.
getDescription() - Method in class databionics.io.FileType
Get the description of file type
getDescription() - Method in class databionics.io.KeyName
Get description of key.
getDescription() - Method in class databionics.modules.Module
Get the description
getDescription() - Method in class databionics.modules.MultipleChoiceElement
Get the description, if empty use value instead
getDescription() - Method in class databionics.modules.Parameter
Get decription to be displayed in dialogs
getDescription() - Method in class databionics.modules.Tool
Get the description
getDescription() - Method in class databionics.project.Project
Get description of project
getDescriptives() - Method in class databionics.esom.train.SOM
Get the statistics about the training data.
getDimensions() - Method in class databionics.io.Array3DFile
Get number of dimensions of the pseudo 3d matrix.
getDimName() - Method in class databionics.io.Condition
Get DimName.
getDimName() - Method in class databionics.io.IntervalCondition
Get DimName.
getDisplayPanel() - Method in class databionics.esom.tool.AbstractTool
 
getDistance(int, int, LrnFile, RectangularGrid) - Method in class databionics.esom.tool.projection.ProjectionTool
Get the distance between a data row and a neuron.
getDistance(int, int) - Method in class databionics.esom.train.SOM
Get the distance between a data row and a neuron.
getDistance(DoubleMatrix1D, int) - Method in class databionics.esom.train.SOM
Get the distance between a dataVector and a neuron.
getDistance() - Method in class databionics.io.WtsFile
Get the name of the dataspace distance function.
getDistance(String) - Static method in class databionics.math.DistanceFactory
Get a distance function by name.
getDistance(String, boolean) - Static method in class databionics.math.DistanceFactory
Get a distance function by name with flag whether to ignore NaN.
getDistanceFunction() - Method in class databionics.esom.grid.Grid
Get the distance function in data space
getDistanceFunction() - Method in class databionics.esom.renderer.Renderer
Get the distance function in data space
getDistanceFunction() - Method in class databionics.esom.train.SOM
Get the distance function in data space
getDistanceFunction() - Method in class databionics.math.Distances
 
getDistanceFunctionName() - Method in class databionics.esom.grid.Grid
Get the name distance function in data space
getDistanceMatrix() - Method in class databionics.math.Distances
getting the pairwise distances from matrix/vector set in setData().
getDistancePercentiles() - Method in class databionics.math.ParetoDensity
 
getDistances() - Method in class databionics.esom.train.SOM
 
getDistances() - Method in class databionics.math.Distances
getting the pairwise distances from matrix/vector invoked in setData().
getDistinct() - Method in class databionics.text.StringList
Get StringList without duplicates.
getDistinct() - Method in class databionics.util.IntegerList
Get IntegerList without duplicates.
getDistinctCount() - Method in class databionics.text.StringList
Get count of distinct strings.
getDistinctCount() - Method in class databionics.util.IntegerList
Get count of distinct numbers.
getDoubleImage(int) - Method in class databionics.esom.tool.legend.Legend
 
getDoubleImage2(int) - Method in class databionics.esom.tool.legend.Legend
 
getEigenValue(int) - Method in class databionics.esom.train.Descriptives
Returns i-th largest eigenvalue
getEigenValues() - Method in class databionics.esom.train.Descriptives
Returns EigenValues of data
getEigenVector(int) - Method in class databionics.esom.train.Descriptives
Returns eigenvector of i-th largest eigenvalue
getEigenVectors() - Method in class databionics.esom.train.Descriptives
Returns Eigenvectors of data
getEnd() - Method in class databionics.modules.Job
Get date and time when job ended
getEnvironmentVariable(String) - Static method in class databionics.util.Utils
Get value of an environment variable.
getEpochs() - Method in class databionics.esom.train.SOM
Get the number of training epochs.
getExitCode() - Method in class databionics.Application
Get exit code after app is done.
getExt() - Method in class databionics.io.FileType
Get the extension of file type
getExtension(File) - Method in class databionics.io.FileExtensionFilter
Return the extension portion of the file's name .
getFailingCondition() - Method in class databionics.io.Explanation
Get the failing condition.
getFailingRule() - Method in class databionics.io.Explanation
Get the failing rule.
getFavoriteColor() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Get the favorite Color
getFavoriteColor() - Method in class databionics.esom.tool.AbstractToolRenderer
 
getFgRenderer() - Method in class databionics.esom.tool.AbstractToolRenderer
 
getFile() - Method in class databionics.io.BaseFile
Get the file.
getFile() - Method in class databionics.project.FileSlot
Get the file object
getFileData(FileType) - Method in class databionics.project.Project
Get data of first filename for slot with FileType type
getFileMenu() - Method in class databionics.esom.tool.AbstractTool
 
getFilename() - Method in class databionics.esom.tool.AbstractTool
 
getFilename() - Method in class databionics.io.BaseFile
Get the name of file.
getFileName(FileType) - Method in class databionics.project.Project
Get first filename for slot with FileType type
getFileName(FileType, int) - Method in class databionics.project.Project
Get a filename for slot with FileType type
getFileSlot(FileType) - Method in class databionics.project.Project
Get FileSlot for FileType type
getFileType() - Static method in class databionics.io.ArffFile
Get the type of file.
getFileType() - Static method in class databionics.io.BMFile
Get the type of file.
getFileType() - Static method in class databionics.io.ClassmaskFile
Get the type of file.
getFileType() - Static method in class databionics.io.ClsFile
Get the type of file.
getFileType() - Static method in class databionics.io.ColorTable
Get the type of file.
getFileType() - Static method in class databionics.io.CsvFile
Get the type of file.
getFileType() - Static method in class databionics.io.DiagnosisFile
Get the type of file.
getFileType() - Static method in class databionics.io.ExplFile
Get the type of file.
getFileType() - Static method in class databionics.io.ImxFile
Get the type of file.
getFileType() - Static method in class databionics.io.LrnFile
Get the type of file.
getFileType() - Static method in class databionics.io.ModFile
Get the type of file.
getFileType() - Static method in class databionics.io.NamesFile
Get the type of file.
getFileType() - Static method in class databionics.io.PicturesFile
Get the type of file.
getFileType() - Static method in class databionics.io.PngFile
Get the type of file.
getFileType() - Static method in class databionics.io.RuleFile
Get the type of file.
getFileType() - Static method in class databionics.io.TxtFile
Get the type of file.
getFileType() - Static method in class databionics.io.UmxFile
Get the type of file.
getFileType() - Static method in class databionics.io.WtsFile
Get the type of file.
getFilter() - Method in class databionics.io.FileType
Get the extension as a filter for fiel dialogs
getFirstEigenValue() - Method in class databionics.esom.train.Descriptives
Returns largest eigenvalue
getFirstEigenVector() - Method in class databionics.esom.train.Descriptives
Returns eigenvector of largest eigenvalue
getFirstInt() - Method in class databionics.util.IntegerList
Get first number without casting.
getFirstInteger() - Method in class databionics.util.IntegerList
Get first number without casting.
getFirstString() - Method in class databionics.text.StringList
Get first string without casting.
getFlag(String, String) - Static method in class databionics.project.DataManager
 
getFlag(String, String, String) - Static method in class databionics.project.DataManager
 
getFontSize() - Method in class databionics.esom.renderer.foreground.NamesRenderer
Get the bestmatch size
getForeground(int) - Method in class databionics.esom.renderer.foreground.ForegroundList
Get a foregroundrenderer with casting
getForegroundByName(String) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Get foreground by name
getForegroundNames() - Method in class databionics.esom.renderer.foreground.ForegroundTool
Get the foreground names
getForegroundTool() - Method in class databionics.esom.gui.ToolLoader
 
getForegroundTool() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
 
getForegroundTool() - Method in class databionics.esom.tool.AbstractToolRenderer
 
getFourtimes() - Method in class databionics.esom.tool.island.IslandTool
 
getFrame() - Method in class databionics.GraphicalApplication
Get main program window.
getFrameColor() - Method in class databionics.esom.renderer.foreground.ForegroundTool
Get frame color
getFrameColor() - Method in class databionics.esom.renderer.foreground.FrameRenderer
Get the frame color
getFriends(RectangularGrid, BMFile, int, int, int) - Static method in class databionics.esom.tool.similarity.SimilarityTool
returns n-bms with shortest distance to given bm
getGrid() - Method in class databionics.esom.renderer.Renderer
Get the grid of weight vectors.
getGrid() - Method in class databionics.esom.train.SOM
Get the grid of weight vectors.
getGrid() - Method in class databionics.io.WtsFile
Get the class of the grid used in training.
getHeader() - Method in class databionics.io.BaseFile
Get the header of file.
getHelpFile() - Static method in class databionics.Application
Get help file.
getHighestClassIndex() - Method in class databionics.io.ClassmaskFile
 
getHighestClassIndex() - Method in class databionics.io.ClsFile
 
getHighlightedBms() - Method in class databionics.esom.tool.data.DataTool
 
getHighlightedBms() - Method in class databionics.esom.tool.data.HighlightRenderer
 
getHistory() - Method in class databionics.project.Project
Get history with executed jobs
getHits() - Method in class databionics.esom.train.BestMatchHit
gives number of BestMatchHits
getHome() - Static method in class databionics.Application
Get value of environment variable
getIcon() - Method in class databionics.modules.Module
Get the icon or null if the path was invalid.
getIdxs() - Method in class databionics.esom.tool.data.SelectedDataTableModel
 
getImage() - Method in class databionics.esom.renderer.Renderer
Get the generated image
getImage(int) - Method in class databionics.esom.tool.legend.ColorLegend
 
getImage(int) - Method in class databionics.esom.tool.legend.HeightsLegend
 
getImage() - Method in class databionics.esom.tool.legend.Legend
 
getImage(int) - Method in class databionics.esom.tool.legend.LegendRenderer
 
getImage(int) - Method in class databionics.esom.tool.legend.PictureLegend
return the Image with the wanted heights
getImage2(int) - Method in class databionics.esom.tool.legend.ColorLegend
 
getImage2(int) - Method in class databionics.esom.tool.legend.HeightsLegend
 
getImage2(int) - Method in class databionics.esom.tool.legend.LegendRenderer
 
getImage2(int) - Method in class databionics.esom.tool.legend.PictureLegend
 
getIndex() - Method in class databionics.io.DataItem
Get the index of data point.
getIndices() - Method in class databionics.io.BMFile
 
getInfoTool() - Method in class databionics.esom.gui.ToolLoader
 
getInputFileParameter(FileType) - Method in class databionics.modules.Tool
Get an InputFileParameter by the FileType
getInputFileParameters() - Method in class databionics.modules.Tool
Get the fileparameters, which are used as inputfiles for the tool
getInputTypes() - Method in class databionics.modules.Module
Get a List with the union of all FileTypes needed as inputfiles for the tools in this module
getInputTypes() - Method in class databionics.modules.Tool
Get the list of file types needed when running this tool
getInstance() - Static method in class databionics.esom.Analyze
Returns the application instance
getInstance() - Static method in class databionics.esom.Cluster
Returns the application instance
getInstance() - Static method in class databionics.esom.Project
Returns the application instance
getInstance() - Static method in class databionics.esom.Render
Returns the application instance
getInstance() - Static method in class databionics.esom.SlideShow
Returns the application instance
getInstance() - Static method in class databionics.esom.Train
Returns the application instance
getInstance() - Static method in class databionics.runner.MatlabRunner
Returns the application instance
getInstance() - Static method in class databionics.runner.Runner
Returns the application instance
getInt(int) - Method in class databionics.util.IntegerList
Get a number by index without casting.
getInteger(int) - Method in class databionics.util.IntegerList
Get a number by index without casting.
getInteractiveParams() - Method in class databionics.modules.Tool
Get the number of interactive parameters, i.e.
getIslandMatrix() - Method in class databionics.esom.tool.island.IslandRenderer
 
getIslandTool() - Method in class databionics.esom.gui.ToolLoader
 
getItems() - Method in class databionics.esom.tool.legend.LegendTool
 
getJob() - Method in class databionics.esom.gui.util.RunDialog
Get job
getJob() - Method in class databionics.gui.RunDialog
Get job
getK() - Method in class databionics.esom.train.KBatchSOM
 
getKeyColumnIndex() - Method in class databionics.io.LrnFile
Get key column index.
getKeyColumnName() - Method in class databionics.io.LrnFile
Get key column nams.
getKeys() - Method in class databionics.esom.train.SOM
Get the keys for the data patterns.
getKeys() - Method in class databionics.io.ClassmaskFile
Get keys.
getKeys() - Method in class databionics.io.ClsFile
Get keys.
getKeys() - Method in class databionics.io.LrnFile
Get keys.
getLastInt() - Method in class databionics.util.IntegerList
Get last number without casting.
getLastInteger() - Method in class databionics.util.IntegerList
Get last number without casting.
getLastString() - Method in class databionics.text.StringList
Get last string without casting.
getLeastFrequent() - Method in class databionics.text.StringCounter
 
getLeastFrequent() - Method in class databionics.text.StringList
Find least frequent string in list.
getLeastFrequent() - Method in class databionics.util.IntegerList
Find least frequent number in list.
getLegendTool() - Method in class databionics.esom.gui.ToolLoader
 
getLibPath() - Static method in class databionics.Application
Get path to *.jar files
getLibPath() - Method in class databionics.esom.gui.MainFrame
 
getLineSize() - Method in class databionics.esom.renderer.foreground.LineRenderer
Get the bestmatch size
getListOfNames() - Method in class databionics.esom.renderer.foreground.ForegroundList
Get a list of the names of the forgrounds
getLoader() - Method in class databionics.esom.Analyze
 
getLoader() - Method in class databionics.esom.tool.AbstractTool
 
getLoader() - Method in class databionics.esom.train.TrainAction
 
getLoader() - Method in class databionics.esom.train.TrainCallback
 
getLoadItm() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
getLocale() - Method in class databionics.io.BaseFile
Get the current locale.
getLog() - Static method in class databionics.esom.renderer.Renderer
 
getLogPanel() - Method in class databionics.esom.Analyze
returns the logPanel
getLogPanel() - Method in class databionics.esom.gui.ToolLoader
 
getLongName() - Method in class databionics.modules.Parameter
Get the long name to be used as "--longname"
getLRenderer() - Method in class databionics.esom.tool.legend.Legend
 
getLrnAbsIdx() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
getLrnCount() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
getLrnFile() - Method in class databionics.esom.renderer.Renderer
 
getLrnFile() - Method in class databionics.esom.tool.data.DataTableModel
 
getLrnFile() - Method in class databionics.esom.tool.data.DataTool
 
getLrnFile() - Method in class databionics.esom.tool.data.SelectedDataTableModel
 
getLrnFilename() - Method in class databionics.esom.renderer.Renderer
 
getLrnIdx() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
getLrnIdxs() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
getMainFrame() - Method in class databionics.esom.Analyze
returns the main Frame
getMainMenu() - Method in class databionics.esom.gui.MainFrame
retirns the mainMenu
getManualKeys() - Method in class databionics.esom.tool.data.DataTool
 
getManualNames() - Method in class databionics.esom.tool.data.DataTool
 
getManualNamesFile() - Method in class databionics.esom.tool.data.DataTool
 
getMap() - Method in class databionics.io.MapFile
Get the data in the map.
getMapspace() - Method in class databionics.io.DataClass
 
getMatrix() - Method in class databionics.esom.renderer.Renderer
Get the matrix
getMatrix() - Method in class databionics.esom.tool.ProtoPanel
 
getMax(int) - Method in class databionics.esom.train.Descriptives
Returns max of data
getMax(int) - Method in class databionics.io.ColorStatistics
 
getMax() - Method in class databionics.math.ParetoDensity
maximum of calculated densities
getMax() - Method in class databionics.modules.FloatParameter
Get the maximum value
getMax() - Method in class databionics.modules.IntParameter
Get the maximum value
getMax() - Method in class databionics.project.FileSlot
 
getMax() - Method in class databionics.util.IntegerList
Get maximum number in list.
getMaxCount() - Method in class databionics.io.ColorStatistics
 
getMaxDensityIndex() - Method in class databionics.math.ParetoDensity
 
getMaximum() - Method in class databionics.io.Condition
Get Max.
getMaximum() - Method in class databionics.io.IntervalCondition
Get Max.
getMaxPercentage() - Method in class databionics.io.ColorStatistics
 
getMean() - Method in class databionics.esom.train.BestMatchHit
Calculate the mean vector
getMean(int) - Method in class databionics.esom.train.Descriptives
Returns mean of data
getMessage(String) - Method in class databionics.Application
Get localized message from file defined in consructor.
getMessage(String) - Method in class databionics.esom.gui.MainMenu
 
getMessage(String) - Method in class databionics.esom.gui.RenderPanel
Get localized message from file defined in consructor.
getMessage() - Method in class databionics.esom.gui.util.MessagePanel
 
getMessage(String) - Method in class databionics.esom.tool.AbstractTool
Get a Message from the running application.
getMessage(String) - Method in class databionics.esom.tool.AbstractToolTable
 
getMessage(String) - Method in class databionics.esom.tool.island.IslandTable
 
getMessage() - Method in exception databionics.modules.GreaterThanMaxException
 
getMessage() - Method in exception databionics.modules.LessThanMinException
Warning message
getMethod() - Method in class databionics.esom.tool.slideshow.SlideShow
 
getMin() - Method in class databionics.esom.renderer.HeightStatistics
 
getMin(int) - Method in class databionics.esom.train.Descriptives
Returns min of data
getMin(int) - Method in class databionics.io.ColorStatistics
 
getMin() - Method in class databionics.math.ParetoDensity
minimum of calculated densities
getMin() - Method in class databionics.modules.FloatParameter
Get the minimum value
getMin() - Method in class databionics.modules.IntParameter
Get the minimum value
getMin() - Method in class databionics.util.IntegerList
Get minimum number in list.
getMinimum() - Method in class databionics.io.Condition
Get Min.
getMinimum() - Method in class databionics.io.IntervalCondition
Get Min.
getMnuFrameColor() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
getModules() - Method in class databionics.esom.Analyze
returns the module
getMostFrequent() - Method in class databionics.text.StringCounter
 
getMostFrequent() - Method in class databionics.text.StringList
Find most frequent string in list.
getMostFrequent() - Method in class databionics.util.IntegerList
Find most frequent number in list.
getMoveCallback() - Method in class databionics.esom.tool.AbstractTool
 
getName() - Method in class databionics.Application
Get short program name.
getName(int) - Method in class databionics.esom.gui.util.GradientComboBox
Get a color table name by index
getName() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Get the name by removing the "Renderer" from the class name.
getName() - Method in class databionics.io.DataClass
Get the name of DataClass.
getName() - Method in class databionics.io.FileType
Get the name of file type
getName() - Method in class databionics.io.KeyName
Get name of key.
getName() - Method in class databionics.io.Rule
Get name of rule.
getName() - Method in class databionics.modules.Module
Get the name
getName() - Method in class databionics.modules.Parameter
Get the name to be used as "-name"
getName() - Method in class databionics.modules.Tool
Get the name
getName(int) - Method in class databionics.project.FileSlot
Get a filename
getName() - Method in class databionics.project.FileSlot
Get the first filename in the slot
getName() - Method in class databionics.project.Project
Get name of project
getNames() - Method in class databionics.esom.renderer.Renderer
get names
getNames() - Method in class databionics.esom.tool.bminfo.BMInfoTool
 
getNames() - Method in class databionics.io.LrnFile
Get names.
getNamesFilename() - Method in class databionics.esom.renderer.Renderer
 
getNearestOnMap(RectangularGrid, BMFile, int, int, int) - Static method in class databionics.esom.tool.similarity.SimilarityTool
returns n-bms with shortest u-way to given bm
getNeighborhood() - Method in class databionics.esom.train.SOM
Get the neighborhood kernel function.
getNeighbours(RectangularGrid, BMFile, int, int, int) - Static method in class databionics.esom.tool.similarity.SimilarityTool
returns n-bms in the neighborhood of given bm
getNeuron(int) - Method in class databionics.esom.grid.Grid
Access to a weight vector by the neuron's index.
getNeuron(int) - Method in class databionics.esom.grid.MatrixGrid
Access to a weight vector by the neuron's index
getNeuron(int, int) - Method in class databionics.esom.grid.RectangularGrid
Access to a weight vector by coordinates
getNotClassName() - Method in class databionics.io.DiffCondition
Get name of class excluded by this rule.
getNotClassName() - Method in class databionics.io.DiffRule
Get name of class excluded by this rule.
getNotIn() - Method in class databionics.io.Explanation
Get the class not in.
getNumberFormat() - Method in class databionics.esom.train.SOM
Get the number format
getNumberFormat() - Method in class databionics.io.BaseFile
Get the current number format.
getOldBestmatches() - Method in class databionics.esom.train.SOM
 
getOnce() - Method in class databionics.esom.tool.island.IslandTool
 
getOperatingSystem() - Method in class databionics.modules.Tool
Get the os
getOperator() - Method in class databionics.io.Rule
Get Operator.
getOptionValue(String) - Method in class databionics.cli.PropertyCommandLine
Retrieve the argument, if any, of this option.
getOptionValue(String, String) - Method in class databionics.cli.PropertyCommandLine
Retrieve the argument, if any, of this option.
getOptionValueAsDouble(String, double) - Method in class databionics.cli.PropertyCommandLine
Retrieve the argument as double
getOptionValueAsInt(String, int) - Method in class databionics.cli.PropertyCommandLine
Retrieve the argument as int
getOutputFileParameters() - Method in class databionics.modules.Tool
Get the fileparameters representing the created files
getOutputTypes() - Method in class databionics.modules.Module
Get a List with the union of all FileTypes created as outputfiles by the tools in this module
getOutputTypes() - Method in class databionics.modules.Tool
Get the list of file type created by this tool
getOverlapMatrix() - Method in class databionics.esom.tool.island.IslandRenderer
 
getOverlapMatrix() - Method in class databionics.esom.tool.island.IslandTool
 
getParameterByName(String) - Method in class databionics.modules.Tool
Get a parameter by name
getParameters() - Method in class databionics.modules.Tool
Get the list of parameters
getParetoDensity() - Method in class databionics.esom.renderer.background.PMatrixRenderer
Get the densitsy estimation used for the P-Matrix
getParetoRadius() - Method in class databionics.math.ParetoDensity
Calculate Pareto radius.
getPartCls() - Method in class databionics.esom.tool.data.DataTool
 
getPartLrn() - Method in class databionics.esom.tool.data.DataTool
 
getPattern(int, LrnFile) - Method in class databionics.esom.tool.projection.ProjectionTool
Access to a data pattern by row number
getPattern(int) - Method in class databionics.esom.train.SOM
Access to a data pattern by row number
getPercentage(int) - Method in class databionics.io.ColorStatistics
 
getPercentile() - Method in class databionics.esom.renderer.background.PMatrixRenderer
Get the percentile parameter
getPercentile() - Method in class databionics.math.ParetoDensity
Get current percentile (closest to current radius)
getPermutation() - Method in class databionics.esom.train.SOM
Get the current permuation
getPermute() - Method in class databionics.esom.train.SOM
Get the flag whether to permute data vectors before each epoch.
getPicPanel() - Method in class databionics.esom.gui.RenderPanel
returns the picPanel
getPictures() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getPicturesFilename() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getPnlBmSize() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
getPnlControl() - Method in class databionics.esom.tool.AbstractTool
 
getPnlControl2() - Method in class databionics.esom.renderer.RendererTool
 
getPnlFGColor() - Method in class databionics.esom.renderer.foreground.ForegroundTool
Get the fg color panel
getPnlForeground() - Method in class databionics.esom.renderer.foreground.ForegroundTool
Getr the panel
getPnlFrame() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
getPnlMenu() - Method in class databionics.esom.renderer.foreground.ForegroundTool
Get the panel menu
getPolygon(int, int) - Method in class databionics.esom.gui.util.DoublePolygon
Returns the actual polygon
getPopMenu() - Method in class databionics.esom.tool.AbstractTool
 
getPopup() - Method in class databionics.esom.tool.data.DataTool
 
getPosition() - Method in class databionics.esom.tool.slideshow.SlideShow
 
getPrefix() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getProject() - Method in class databionics.Application
Returns the current project holding filename of different types and optionally the data from the files.
getProject() - Method in class databionics.esom.Analyze
returns the project
getProject() - Method in class databionics.esom.gui.ToolLoader
 
getProjection() - Method in class databionics.esom.Analyze
returns the projection
getProjectionTool() - Method in class databionics.esom.gui.ToolLoader
 
getPromapspace() - Method in class databionics.io.DataClass
 
getPropertyValue(String) - Method in class databionics.cli.PropertyOptions
Get a property value for an option
getQuadrantOfPixel(int, int) - Method in class databionics.esom.renderer.Renderer
returns the Quadrant of the map.
getQuantil(int) - Method in class databionics.esom.renderer.HeightStatistics
 
getQuick(int) - Method in class databionics.io.ClassmaskFile
Get class number of a classification by its position in the list
getQuick(int) - Method in class databionics.io.ClsFile
Get class number of a classification by its position in the list
getRadius() - Method in class databionics.esom.renderer.background.PMatrixRenderer
Get the radius parameter.
getRadius() - Method in class databionics.esom.train.SOM
 
getRadius() - Method in class databionics.math.ParetoDensity
Get current radius
getRadiusCooling() - Method in class databionics.esom.train.SOM
Get the cooling strategy of the neighborhood radius.
getRange(int, int) - Method in class databionics.esom.train.search.Constant
returns constant
getRange(int, int) - Method in class databionics.esom.train.search.LocalBmSearch
 
getRange(int, int) - Method in class databionics.esom.train.search.MuchFasterLearning
returns range for local bm search
getRange(int, int) - Method in class databionics.esom.train.search.MuchFasterLearning2
returns range for local bm search
getRange(int, int) - Method in class databionics.esom.train.search.QuickLearning
specify the range of searching
getRange(int, int) - Method in class databionics.esom.train.search.QuickLearning2
specify the range of searching
getRateCooling() - Method in class databionics.esom.train.SOM
Get the cooling strategy of learning rate.
getRegExp(String) - Static method in class databionics.text.StringUtils
Build a regular expression that matches this String and similar ones, e.g.
getRelation() - Method in class databionics.io.ArffFile
Get relation name
getRenderer() - Method in class databionics.esom.Analyze
returns the renderer
getRenderer() - Method in class databionics.esom.gui.MainFrame
 
getRenderer() - Method in class databionics.esom.gui.RenderPanel
returns the renderer
getRenderer() - Method in class databionics.esom.gui.ToolLoader
 
getRenderer() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Get reference to the main renderer.
getRenderer() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Get the renderer
getRenderer() - Method in class databionics.esom.tool.AbstractTool
 
getRenderer() - Method in class databionics.esom.tool.legend.Legend
 
getRenderer() - Method in class databionics.esom.train.TrainCallback
 
getRendererTool() - Method in class databionics.esom.gui.ToolLoader
 
getRenderPanel() - Method in class databionics.esom.gui.MainFrame
returns the renderPanel
getRenderPanel() - Method in class databionics.esom.gui.ToolLoader
 
getRenderPanel() - Method in class databionics.esom.tool.ProtoPanel
 
getRenderPosition() - Method in class databionics.esom.renderer.foreground.ForegroundList
Set the RenderPosition.
getRndLayer() - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Rank of this foreground
getRndLayer() - Method in class databionics.esom.renderer.foreground.ColorizeRenderer
 
getRndLayer() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Determines which foreground is renderered first.
getRndLayer() - Method in class databionics.esom.renderer.foreground.FrameRenderer
 
getRndLayer() - Method in class databionics.esom.renderer.foreground.LineRenderer
Rank of this foreground
getRndLayer() - Method in class databionics.esom.renderer.foreground.NamesRenderer
Rank of this foreground
getRndLayer() - Method in class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
The rendering layer
getRndLayer() - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
getRndLayer() - Method in class databionics.esom.tool.data.HighlightRenderer
 
getRndLayer() - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
getRndLayer() - Method in class databionics.esom.tool.island.IslandRenderer
 
getRndPosition() - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
 
getRndPosition() - Method in class databionics.esom.renderer.foreground.ColorizeRenderer
 
getRndPosition() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
 
getRndPosition() - Method in class databionics.esom.renderer.foreground.FrameRenderer
 
getRndPosition() - Method in class databionics.esom.renderer.foreground.LineRenderer
 
getRndPosition() - Method in class databionics.esom.renderer.foreground.NamesRenderer
 
getRndPosition() - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
getRndPosition() - Method in class databionics.esom.tool.data.HighlightRenderer
 
getRndPosition() - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
getRndPosition() - Method in class databionics.esom.tool.island.IslandRenderer
 
getRow() - Method in class databionics.io.Bestmatch
Get row of best match.
getRowCount() - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
returns number of rows
getRowCount() - Method in class databionics.esom.tool.component.ComponentTableModel
returns number of rows
getRowCount() - Method in class databionics.esom.tool.data.DataTableModel
returns the number of rows
getRowCount() - Method in class databionics.esom.tool.data.SelectedDataTableModel
returns the number of rows
getRowCount() - Method in class databionics.esom.tool.dataclass.DataclassTableModel
returns the number of rows
getRowCount() - Method in class databionics.esom.tool.info.InfoToolTableModel
 
getRowCount() - Method in class databionics.esom.tool.island.IslandTableModel
 
getRowCount() - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
getRowData() - Method in class databionics.io.BMFile
 
getRowName(int) - Method in class databionics.esom.tool.island.IslandTableModel
 
getRows() - Method in class databionics.esom.grid.RectangularGrid
Get number of rows
getRows() - Method in class databionics.io.Array2DFile
Get number of rows in matrix.
getRows() - Method in class databionics.io.Array3DFile
Get number of rows of the pseudo 3d matrix.
getRows() - Method in class databionics.io.BMFile
Get the number of rows in the map
getRuntime() - Method in class databionics.modules.Job
Get runtime !!! This could be done with: Calendar.getTime().getTime() - Calendar.getTime().get(Time) + 24*60*60*1000 and reformatting
getSameHits() - Method in class databionics.esom.train.BestMatchHit
gives the number of hits to neurons which are hit before
getSaveItm() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
getSecondEigenValue() - Method in class databionics.esom.train.Descriptives
Returns 2nd largest eigenvalue
getSecondEigenVector() - Method in class databionics.esom.train.Descriptives
Returns eigenvector of 2nd largest eigenvalue
getSelectedDataTableModel() - Method in class databionics.esom.tool.data.DataTool
 
getSelectedIndexes() - Method in class databionics.esom.tool.data.DataTable
 
getSelectedTool() - Method in class databionics.esom.gui.RenderPanel
 
getShiftX() - Method in class databionics.esom.renderer.Renderer
get shiftX
getShiftY() - Method in class databionics.esom.renderer.Renderer
get shiftY
getShortTitle() - Method in class databionics.esom.renderer.background.BackgroundTool
 
getShortTitle() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
getShortTitle() - Method in class databionics.esom.renderer.RendererTool
 
getShortTitle() - Method in class databionics.esom.tool.AbstractTool
 
getShortTitle() - Method in class databionics.esom.tool.bminfo.BMInfoTool
returns the short title of the bottom tab
getShortTitle() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
getShortTitle() - Method in class databionics.esom.tool.component.ComponentTool
 
getShortTitle() - Method in class databionics.esom.tool.data.DataTool
 
getShortTitle() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
getShortTitle() - Method in class databionics.esom.tool.info.InfoTool
 
getShortTitle() - Method in class databionics.esom.tool.island.IslandTool
 
getShortTitle() - Method in class databionics.esom.tool.legend.LegendTool
 
getShortTitle() - Method in class databionics.esom.tool.mapview.MapViewTool
 
getShortTitle() - Method in class databionics.esom.tool.options.OptionsTool
 
getShortTitle() - Method in class databionics.esom.tool.projection.ProjectionTool
 
getShortTitle() - Method in class databionics.esom.tool.similarity.SimilarityTool
 
getShortTitle() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getShow() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getSignificance() - Method in class databionics.io.Condition
Get significance.
getSignificance() - Method in class databionics.io.IntervalCondition
Get significance.
getSize() - Method in class databionics.esom.renderer.HeightStatistics
 
getSize() - Method in class databionics.io.Array2DFile
Get the number of lines in file.
getSize() - Method in class databionics.io.BaseFile
Get the number of lines in file.
getSize() - Method in class databionics.io.ClassmaskFile
Get the number of lines in file.
getSize() - Method in class databionics.io.ClsFile
Get the number of lines in file.
getSize() - Method in class databionics.io.ColorMapping
 
getSize() - Method in class databionics.io.ListFile
Get the number of lines in file.
getSlideCacheBm() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getSlideList() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getSlideListBm() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getSlidePictures() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getSlideshowTool() - Method in class databionics.esom.gui.ToolLoader
 
getSlideWts() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
getSmoothFactor() - Method in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
Get the smooth parameter
getSpeed() - Method in class databionics.esom.tool.slideshow.SlideShow
 
getStandardDeviation(int) - Method in class databionics.esom.train.Descriptives
Returns standard deviation
getStart() - Method in class databionics.modules.Job
Get date and time when the job was started
getStats() - Method in class databionics.esom.renderer.Renderer
 
getString(int) - Method in class databionics.text.StringList
Get a string by index without casting.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class databionics.esom.gui.util.ColorEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class databionics.esom.gui.util.ColorRenderer
 
getTemplate() - Method in class databionics.modules.OutputFileParameter
Get the filename template
getTextArea() - Method in class databionics.gui.LogPanel
Get the text area
getThirdEigenValue() - Method in class databionics.esom.train.Descriptives
Returns 3rd largest eigenvalue
getThirdEigenVector() - Method in class databionics.esom.train.Descriptives
Returns eigenvector of 3rd largest eigenvalue
getThread() - Method in class databionics.Application
 
getThread() - Method in class databionics.esom.tool.slideshow.SlideShow
 
getThreetimes() - Method in class databionics.esom.tool.island.IslandTool
 
getThresholdDistance(String) - Static method in class databionics.math.DistanceFactory
Get a thresholded distance function by name.
getThresholdDistance(String, boolean) - Static method in class databionics.math.DistanceFactory
Get a thresholded distance function by name with flag whether to ignore NaN.
getTiledImage() - Method in class databionics.esom.renderer.Renderer
 
getToolBar() - Method in class databionics.esom.tool.AbstractTool
 
getToolByName(String) - Method in class databionics.esom.gui.ToolLoader
 
getToolLoader() - Method in class databionics.esom.tool.bminfo.BMInfoTool
 
getToolRenderer() - Method in class databionics.esom.tool.AbstractTool
 
getTools() - Method in class databionics.modules.Module
Get the list of tools
getToroidLayout() - Method in class databionics.esom.renderer.Renderer
Get the toroid layout
getTotalCount() - Method in class databionics.io.ColorStatistics
 
getTotalMax() - Method in class databionics.io.ColorStatistics
 
getTreshold() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
getTwice() - Method in class databionics.esom.tool.island.IslandTool
 
getType() - Method in class databionics.esom.gui.util.MessagePanel
 
getType() - Method in class databionics.modules.AbstractFileParameter
Get the file type
getType() - Method in class databionics.project.FileSlot
Get the file type
getUmxFilename() - Method in class databionics.esom.renderer.Renderer
 
getUsableTools(Project) - Method in class databionics.modules.Module
Given the types of the files existing in the project, returns a List containing all tools of this module, that can be started because they only need files as input that are already present in the project.
getValue() - Method in class databionics.modules.AbstractStringParameter
Get the value or, if value is not defined, the default value
getValue() - Method in class databionics.modules.FloatParameter
Get the value or, if value is not defined, the default value
getValue() - Method in class databionics.modules.IntParameter
Get the value or, if value is not defined, the default value
getValue() - Method in class databionics.modules.MultipleChoiceElement
Get the value
getValue() - Method in class databionics.modules.MultipleChoiceParameter
Get the value or, if value is not defined, the default value
getValue() - Method in class databionics.modules.SwitchParameter
Get the value or, if value is not defined, the default value
getValueAsString() - Method in class databionics.modules.AbstractStringParameter
String representation of value.
getValueAsString() - Method in class databionics.modules.FloatParameter
String representation of value.
getValueAsString() - Method in class databionics.modules.IntParameter
String representation of value.
getValueAsString() - Method in class databionics.modules.MultipleChoiceParameter
String representation of value.
getValueAsString() - Method in class databionics.modules.Parameter
String representation of argument value.
getValueAsString() - Method in class databionics.modules.SwitchParameter
String representation of value.
getValueAt(int, int) - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
sets values to the table
getValueAt(int, int) - Method in class databionics.esom.tool.component.ComponentTableModel
gets value for cell
getValueAt(int, int) - Method in class databionics.esom.tool.data.DataTableModel
sets the value to each cell
getValueAt(int, int) - Method in class databionics.esom.tool.data.SelectedDataTableModel
returns the value of the wanted cell
getValueAt(int, int) - Method in class databionics.esom.tool.dataclass.DataclassTableModel
sets values to the table
getValueAt(int, int) - Method in class databionics.esom.tool.info.InfoToolTableModel
 
getValueAt(int, int) - Method in class databionics.esom.tool.island.IslandTableModel
 
getValueAt(int, int) - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
getWater() - Method in class databionics.esom.tool.island.IslandTool
 
getWaterColor(int, int) - Method in class databionics.esom.tool.island.IslandRenderer
 
getWaterColor(int, int) - Method in class databionics.esom.tool.island.IslandTool
 
getWeights() - Method in class databionics.esom.grid.MatrixGrid
Get weights
getWorkDir() - Method in class databionics.Application
Returns the current working directory.
getWts() - Method in class databionics.esom.grid.RectangularGrid
Convert grid to wts file
getWtsFilename() - Method in class databionics.esom.renderer.Renderer
 
getX() - Method in class databionics.esom.tool.bminfo.BMInfoPanel
 
getY() - Method in class databionics.esom.tool.bminfo.BMInfoPanel
 
getZeros() - Method in class databionics.esom.tool.island.IslandTool
 
getZoom() - Method in class databionics.esom.renderer.Renderer
Get the zoom factor
getZoomedMatrix() - Method in class databionics.esom.renderer.Renderer
 
GlobalNInfoRenderer - Class in databionics.esom.tool.pointinfo
Shows the Data of the actual Mouse-Point as a graph the Data is global normalized over the wts-Data (not the lrn-Data)
GlobalNInfoRenderer() - Constructor for class databionics.esom.tool.pointinfo.GlobalNInfoRenderer
Basic constructor
globalWTSMax - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
globalWTSMin - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
go() - Method in class databionics.esom.Analyze
 
GradientComboBox - Class in databionics.esom.gui.util
Combobox with all gradients
GradientComboBox(String) - Constructor for class databionics.esom.gui.util.GradientComboBox
Standard constructor
GraphicalApplication - Class in databionics
Base class for graphical applications.
GraphicalApplication() - Constructor for class databionics.GraphicalApplication
Standard constructor.
GraphicalApplication(boolean) - Constructor for class databionics.GraphicalApplication
Constructor with flag for standalone mode.
GreaterThanMaxException - Exception in databionics.modules
Thrown when the value of an IntParameter or FloatParameter is greater than the allowed maximum.
GreaterThanMaxException() - Constructor for exception databionics.modules.GreaterThanMaxException
Default constructor
Grid - Class in databionics.esom.grid
Abstract base class for a grid structure.
Grid() - Constructor for class databionics.esom.grid.Grid
Standard constructor
Grid(int, int) - Constructor for class databionics.esom.grid.Grid
Constructor with size
grid - Variable in class databionics.esom.renderer.Renderer
The grid of neurons
grid - Variable in class databionics.esom.SlideShow
 
grid - Variable in class databionics.esom.tool.legend.LegendRenderer
 
grid - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
grid - Variable in class databionics.esom.train.SOM
grid of weight vectors
grid - Variable in class databionics.io.WtsFile
Grid class used in training created from comment
Grid1D - Class in databionics.esom.grid
One dimensional line of neurons
Grid1D() - Constructor for class databionics.esom.grid.Grid1D
Standard constructor
Grid1D(int, int) - Constructor for class databionics.esom.grid.Grid1D
Constructor with sizes
gridChanged - Variable in class databionics.esom.renderer.Renderer
Flag for show changes on actual grid TODO: only the setter is needed right now.
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.PlanarEuclideanGrid
Squared Euclidean distance on rectangular grids.
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.PlanarManhattanGrid
Manhattan distance on rectangular grids.
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.PlanarMaxGrid
Maximum distance on rectangular grids.
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.RectangularGrid
Distance of two neurons on the grid
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.ToroidEuclideanGrid
Squared Euclidean distance on toroid rectangular grids.
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.ToroidManhattanGrid
Manhattan distance on rectangular grids.
gridDistance(int, int, int, int) - Method in class databionics.esom.grid.ToroidMaxGrid
Maximum distance on rectangular grids.
gui - Variable in class databionics.esom.gui.ToolLoader
 
gui - Variable in class databionics.esom.tool.AbstractTool
Flag showing if the Tool is used in GUI-mode.

H

h - Variable in class databionics.esom.tool.ProtoPanel
 
h - Variable in class databionics.esom.train.HybridBatchSOM
 
hasClass(int) - Method in class databionics.io.ClsFile
 
hashMap - Variable in class databionics.esom.train.BatchSOM
Hash map to connect bm index and bm hitcount
hashMap - Variable in class databionics.esom.train.HybridBatchSOM
Hash map to connect bm index and bm hitcount
hashMap - Variable in class databionics.esom.train.KBatchSOM
Hash map to connect bm index and bm hitcount
hasInteractiveParams() - Method in class databionics.modules.Tool
Check if there are parameters to be set by the user
hasOption(String) - Method in class databionics.cli.PropertyCommandLine
Query to see if an option has been set.
header - Variable in class databionics.io.BaseFile
Header of file.
header(String) - Method in class databionics.io.CharRule
Generate start of rule.
header(String) - Method in class databionics.io.DiffRule
Generate start of rule.
header(String) - Method in class databionics.io.Rule
Generate start of rule.
headerPrefix - Variable in class databionics.io.BaseFile
Header prefix.
height - Variable in class databionics.esom.renderer.Renderer
The original height of the display in 2D
heights - Variable in class databionics.esom.tool.legend.LegendRenderer
 
HeightsLegend - Class in databionics.esom.tool.legend
legend with differnet bins for different number of pixel colored in this color
HeightsLegend() - Constructor for class databionics.esom.tool.legend.HeightsLegend
 
HeightsLegend(Renderer) - Constructor for class databionics.esom.tool.legend.HeightsLegend
 
HeightStatistics - Class in databionics.esom.renderer
 
HeightStatistics(DoubleMatrix2D) - Constructor for class databionics.esom.renderer.HeightStatistics
 
hexagonal - Variable in class databionics.esom.renderer.Renderer
Flag for hexagonal neurons
highlight() - Method in class databionics.esom.tool.data.DataTool
highlights every bm of selected row in data Table
highlightedBms - Variable in class databionics.esom.tool.data.DataTool
list with bms, which have to be highlighted
highlightedBms - Variable in class databionics.esom.tool.data.HighlightRenderer
 
highlightPoint(IntArrayList) - Method in class databionics.esom.tool.data.DataTool
highlights the selected point on the map
HighlightRenderer - Class in databionics.esom.tool.data
 
HighlightRenderer() - Constructor for class databionics.esom.tool.data.HighlightRenderer
Standard Constructor.
history - Variable in class databionics.project.Project
list with finished and active jobs
hitCount - Variable in class databionics.esom.train.BestMatchHit
counter for hits on neuron
hitcounter - Variable in class databionics.esom.train.HybridBatchSOM
 
home - Static variable in class databionics.Application
value of environment variable
HybridBatchSOM - Class in databionics.esom.train
batch version, which goes online, if too many same hits are realized
HybridBatchSOM() - Constructor for class databionics.esom.train.HybridBatchSOM
Standard constructor

I

iconName - Variable in class databionics.modules.Module
name of the icon file
idxs - Variable in class databionics.esom.tool.data.SelectedDataTableModel
the selected Indexes
image - Variable in class databionics.esom.renderer.Renderer
The image to render to
imageLabel - Variable in class databionics.esom.gui.util.MessagePanel
 
imagePanel - Variable in class databionics.esom.tool.slideshow.SlideShow
 
img - Variable in class databionics.esom.gui.AboutDialog
background image
ImportExaFile - Class in databionics.io
imports a *.exa file int a *.lrn file
ImportExaFile() - Constructor for class databionics.io.ImportExaFile
 
ImxFile - Class in databionics.io
File that stores an island mask for an ESOM.
ImxFile() - Constructor for class databionics.io.ImxFile
 
ImxFile(String) - Constructor for class databionics.io.ImxFile
 
ImxFile(int, int) - Constructor for class databionics.io.ImxFile
 
incCount(int) - Method in class databionics.io.ColorStatistics
 
index - Variable in class databionics.io.DataItem
Index of data point.
index2col(int, int) - Static method in class databionics.esom.grid.RectangularGrid
Convert unique index on grid to column coordinate
index2col(int) - Method in class databionics.esom.grid.RectangularGrid
Convert unique index on grid to column coordinate
index2row(int, int) - Static method in class databionics.esom.grid.RectangularGrid
Convert unique index on grid to row coordinate
index2row(int) - Method in class databionics.esom.grid.RectangularGrid
Convert unique index on grid to row coordinate
INFO - Static variable in class databionics.esom.gui.util.MessagePanel
 
infoTool - Variable in class databionics.esom.gui.ToolLoader
 
infoTool - Variable in class databionics.esom.renderer.Renderer
 
InfoTool - Class in databionics.esom.tool.info
 
InfoTool(boolean, Application) - Constructor for class databionics.esom.tool.info.InfoTool
 
InfoToolTable - Class in databionics.esom.tool.info
 
InfoToolTable(AbstractTool) - Constructor for class databionics.esom.tool.info.InfoToolTable
 
InfoToolTableModel - Class in databionics.esom.tool.info
 
InfoToolTableModel(AbstractTool) - Constructor for class databionics.esom.tool.info.InfoToolTableModel
 
init(String[]) - Method in class databionics.Application
Init Log4J logging system and parse command line.
init() - Method in class databionics.Application
Init without command line parameters.
init(String[]) - Method in class databionics.esom.Analyze
init
init(String[]) - Method in class databionics.esom.Cluster
init
init() - Method in class databionics.esom.cooling.CachedCooling
Initialize the cache
init() - Method in class databionics.esom.cooling.CenterCooling
Initialize the constants and the cache
init() - Method in class databionics.esom.cooling.ExponentialCooling
Initialize constants and the cache.
init() - Method in class databionics.esom.cooling.LinearCooling
Initialize constants and the cache.
init(Descriptives) - Method in class databionics.esom.grid.Grid
Initialize all weights by a normal distribution.
init(String, Descriptives) - Method in class databionics.esom.grid.Grid
Initialize all weights by a given method.
init(String, Descriptives, RandomEngine) - Method in class databionics.esom.grid.Grid
Initialize all weights by a given method.
init() - Method in class databionics.esom.grid.MatrixGrid
Initialize the matrix
init(String, Descriptives, RandomEngine) - Method in class databionics.esom.grid.RectangularGrid
Initialize the dimensions of the weights by pca
init() - Method in interface databionics.esom.gui.AbstractGuiComponent
 
init() - Method in class databionics.esom.gui.BottomBar
 
init() - Method in class databionics.esom.gui.MainFrame
 
init() - Method in class databionics.esom.gui.RenderPanel
 
init() - Method in class databionics.esom.gui.ToolLoader
 
init(DataClass) - Method in class databionics.esom.gui.util.ClassNameDialog
 
init(String, int) - Method in class databionics.esom.gui.util.MessagePanel
 
init() - Method in class databionics.esom.neighborhood.BubbleNeighborhood
No initialization needed.
init() - Method in class databionics.esom.neighborhood.CachedNeighborhood
Initialize the neighborhood.
init() - Method in class databionics.esom.neighborhood.EpanechicovNeighborhood
Initialize constants and the cache
init() - Method in class databionics.esom.neighborhood.GaussNeighborhood
Initialize constants and the cache
init() - Method in class databionics.esom.neighborhood.MexicanHatNeighborhood
Initialize constants and the cache
init() - Method in class databionics.esom.neighborhood.Neighborhood
Initialize the neighborhood.
init(String[]) - Method in class databionics.esom.Project
init
init(String[]) - Method in class databionics.esom.Render
init
init() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Optional initialization of background renderer.
init() - Method in class databionics.esom.renderer.background.BackgroundTool
Find backgrounds automatically.
init() - Method in class databionics.esom.renderer.background.GapRenderer
 
init() - Method in class databionics.esom.renderer.background.OpinionRenderer
 
init(Renderer) - Method in class databionics.esom.renderer.background.PMatrixRenderer
 
init() - Method in class databionics.esom.renderer.background.PMatrixRenderer
 
init() - Method in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
 
init() - Method in class databionics.esom.renderer.background.TwoMatchRenderer
 
init() - Method in class databionics.esom.renderer.background.UMatrixRenderer
 
init() - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Optional initialization of foreground renderer.
init() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
init() - Method in class databionics.esom.renderer.RendererTool
init the tool
init(String[]) - Method in class databionics.esom.SlideShow
init
init() - Method in class databionics.esom.tool.AbstractTool
Initialize what needs to be Initialized.
init() - Method in class databionics.esom.tool.AbstractToolRenderer
initialize foregroundrenderer.
init() - Method in class databionics.esom.tool.bminfo.BMInfoTool
inits the tool
init() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
init() - Method in class databionics.esom.tool.classmask.ClassmaskToolRenderer
 
init() - Method in class databionics.esom.tool.component.ComponentTool
 
init() - Method in class databionics.esom.tool.data.DataTool
 
init() - Method in class databionics.esom.tool.data.DataToolRenderer
 
init() - Method in class databionics.esom.tool.dataclass.DataclassRenderer
 
init() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
init() - Method in class databionics.esom.tool.info.InfoTool
 
init() - Method in class databionics.esom.tool.island.IslandTool
 
init() - Method in class databionics.esom.tool.island.IslandToolRenderer
 
init(int, int) - Method in class databionics.esom.tool.legend.ColorLegend
 
init(int, int) - Method in class databionics.esom.tool.legend.HeightsLegend
 
init() - Method in class databionics.esom.tool.legend.Legend
 
init(int, int) - Method in class databionics.esom.tool.legend.LegendRenderer
 
init() - Method in class databionics.esom.tool.legend.LegendTool
 
init(int, int) - Method in class databionics.esom.tool.legend.PictureLegend
 
init() - Method in class databionics.esom.tool.mapview.MapViewTool
 
init() - Method in class databionics.esom.tool.options.OptionsTool
 
init() - Method in class databionics.esom.tool.pointinfo.GlobalNInfoRenderer
Init the image and the graphics object
init() - Method in class databionics.esom.tool.pointinfo.LocalNInfoRenderer
Init the image and the graphics object
init() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
init() - Method in class databionics.esom.tool.pointinfo.ValueInfoRenderer
Init the image and the graphics object
init() - Method in class databionics.esom.tool.projection.ProjectionTool
 
init() - Method in class databionics.esom.tool.similarity.SimilarityTool
 
init() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
init(String[]) - Method in class databionics.esom.Train
init
init() - Method in class databionics.esom.train.search.BmSearch
 
init() - Method in class databionics.esom.train.search.LocalBmSearch
init needed stuff
init() - Method in class databionics.esom.train.search.NoBmSearch
 
init() - Method in class databionics.esom.train.search.SimpleBmSearch
nothing to init
init() - Method in class databionics.esom.train.SOM
Initialize the grid of weight vectors with the current initialization method.
init(int, int) - Method in class databionics.io.ArffFile
Initialize 2D array and class and key columns.
init(int, int) - Method in class databionics.io.Array2DFile
Initialize 2D array.
init(int, int, int) - Method in class databionics.io.Array3DFile
Initialize 3D as 2D array.
init(int, int) - Method in class databionics.io.BaseFile
Init data structures in subclasses given the number of lines in the file and the number of tokens in the first line after header and comments.
init() - Method in class databionics.io.CsvFile
Init data fields.
init(int, int) - Method in class databionics.io.LrnFile
Initialize 2D array and class and key columns.
init(String[]) - Method in class databionics.runner.MatlabRunner
init
init(String[]) - Method in class databionics.runner.Runner
init
initForegrounds() - Method in class databionics.esom.renderer.foreground.ForegroundTool
This is a quick and dirty workaround, Loading Bestmatch- and OpinionBestmatchRenderer.
initGui(RenderPanel, BottomBar) - Method in class databionics.esom.gui.ToolLoader
 
initGui(RenderPanel, BottomBar) - Method in class databionics.esom.renderer.background.BackgroundTool
Let the tool know the references to relevant GUI elements.
initGui(RenderPanel, BottomBar) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Init GUI elements
initGui(RenderPanel, BottomBar) - Method in class databionics.esom.tool.AbstractTool
init the Tool and register its components to the Gui when this method is overriden, inheritors should call super.initGui().
initLayout() - Method in class databionics.esom.tool.BottomTab
 
initMethod - Variable in class databionics.esom.train.SOM
kind of initialising
initRenderer(Renderer) - Method in class databionics.esom.gui.ToolLoader
 
initRenderer() - Method in class databionics.esom.renderer.background.BackgroundTool
Initialize the main renderer with the current settings.
initRenderer(Renderer) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
initRenderer() - Method in class databionics.esom.renderer.RendererTool
 
initRenderer(Renderer) - Method in class databionics.esom.renderer.RendererTool
 
initTest() - Method in class databionics.io.LrnFile
 
InputFileParameter - Class in databionics.modules
FileParameter for input files.
InputFileParameter() - Constructor for class databionics.modules.InputFileParameter
 
inputTypes - Variable in class databionics.modules.Tool
list of file types needed when running this tool
IntegerList - Class in databionics.util
LinkedList of Integers.
IntegerList() - Constructor for class databionics.util.IntegerList
Standard constructor without arguments.
IntegerList(IntegerList) - Constructor for class databionics.util.IntegerList
 
IntegerList(Collection) - Constructor for class databionics.util.IntegerList
Constructor with a collection of objects.
interactiveParams - Variable in class databionics.modules.Tool
number interactive (non-file and non-constant parameters)
interrupt() - Method in class databionics.Application
Stop app thread
interrupt() - Method in class databionics.modules.Job
Interrupt the job
interrupted() - Method in class databionics.Application
Check for interruption of current thread an reset interrupted flag
IntervalCondition - Class in databionics.io
Condition on a variable being in an open or closed interval
IntervalCondition() - Constructor for class databionics.io.IntervalCondition
Standard constructor
IntervalCondition(String, Float, Float, Float) - Constructor for class databionics.io.IntervalCondition
Constructor with all fields.
IntParameter - Class in databionics.modules
Parameter with integer number argument.
IntParameter() - Constructor for class databionics.modules.IntParameter
 
invertSelection() - Method in class databionics.esom.tool.data.DataTable
 
isAutoFlood() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
isAutoRender() - Method in class databionics.esom.renderer.Renderer
Get the auto render flag
isBestMatch() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
isBmStatNeeded() - Method in class databionics.esom.train.SOM
 
isBold(int) - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Get the bold flag for this bestmatch.
isBold(int) - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
Get the bold flag for this bestmatch
isCellEditable(int, int) - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
returns true if this cell is editable
isCellEditable(int, int) - Method in class databionics.esom.tool.component.ComponentTableModel
returns true if cell is editable
isCellEditable(int, int) - Method in class databionics.esom.tool.data.DataTable
returns true if cell is editable
isCellEditable(int, int) - Method in class databionics.esom.tool.data.DataTableModel
returns true, if column is editable
isCellEditable(int, int) - Method in class databionics.esom.tool.dataclass.DataclassTableModel
returns true if cell is editable
isCellEditable(int, int) - Method in class databionics.esom.tool.info.InfoToolTableModel
 
isCellEditable(int, int) - Method in class databionics.esom.tool.island.IslandTableModel
returns true if this cell is editable
isCellEditable(int, int) - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
isCenter() - Method in class databionics.esom.train.SOM
 
isCircle() - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
 
isClean() - Method in class databionics.project.Project
Get boolean if project has to be named before saving
isClickMode() - Method in class databionics.esom.tool.AbstractTool
 
isClipping() - Method in class databionics.esom.renderer.Renderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Whether this background renderer returns color matrix.
isColorBackground() - Method in class databionics.esom.renderer.background.ComponentRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.GapRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.OpinionRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.PMatrixRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.RandomRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.TwoMatchRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.background.UMatrixRenderer
 
isColorBackground() - Method in class databionics.esom.renderer.Renderer
 
isColorifying() - Method in class databionics.esom.renderer.Renderer
 
isColorRenderer() - Method in class databionics.esom.renderer.RendererTool
 
isCompos() - Method in class databionics.esom.gui.RenderPanel
 
isConstant() - Method in class databionics.modules.Parameter
Get flag whether this parameter should be constant or changeable
isContours() - Method in class databionics.esom.renderer.Renderer
Get the contour flag
isCreating - Variable in class databionics.esom.tool.ProtoPanel
 
isDone() - Method in class databionics.Application
Get flag whether app is done.
isDone() - Method in class databionics.modules.Job
Returns true if application is finished,
isDragMode() - Method in class databionics.esom.tool.AbstractTool
 
isDrawing() - Method in class databionics.esom.tool.AbstractTool
 
isDrawing() - Method in class databionics.esom.tool.AbstractToolRenderer
 
isDrawingLetters - Variable in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
isDrawingLetters() - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
isEmtpy(int) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Check if list of foregrounds at this position is empty
isExtensionListInDescription() - Method in class databionics.io.FileExtensionFilter
Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFloodFill() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
isFrame() - Method in class databionics.esom.renderer.Renderer
Deprecated.  
isGridChanged() - Method in class databionics.esom.renderer.Renderer
 
isGui() - Method in class databionics.esom.tool.AbstractTool
 
isHeader(String) - Method in class databionics.io.BaseFile
Determine if a line still contains header information or whether the data lines started
isHeader(String) - Method in class databionics.io.CsvFile
Determine if a line still contains header information or whether the data lines started
isHeader(String) - Method in class databionics.io.ExplFile
Determine if a line still contains header information or whether the data lines started
isHeader(String) - Method in class databionics.io.RuleFile
Determine if a line still contains header information or whether the data lines started
isHexagonal() - Method in class databionics.esom.renderer.Renderer
Get the hexagonal flag
isInt(String) - Static method in class databionics.text.StringUtils
Text whether string is an integer
IslandCreatorPanel - Class in databionics.esom.tool.island
 
IslandCreatorPanel(AbstractTool) - Constructor for class databionics.esom.tool.island.IslandCreatorPanel
 
islandMatrix - Variable in class databionics.esom.tool.island.IslandRenderer
 
IslandRenderer - Class in databionics.esom.tool.island
 
IslandRenderer() - Constructor for class databionics.esom.tool.island.IslandRenderer
 
IslandTable - Class in databionics.esom.tool.island
 
IslandTable(AbstractTool) - Constructor for class databionics.esom.tool.island.IslandTable
 
IslandTableModel - Class in databionics.esom.tool.island
 
IslandTableModel(AbstractTool) - Constructor for class databionics.esom.tool.island.IslandTableModel
Basic constructor.
islandTool - Variable in class databionics.esom.gui.ToolLoader
 
IslandTool - Class in databionics.esom.tool.island
 
IslandTool(boolean, Application) - Constructor for class databionics.esom.tool.island.IslandTool
 
IslandToolRenderer - Class in databionics.esom.tool.island
 
IslandToolRenderer(AbstractTool) - Constructor for class databionics.esom.tool.island.IslandToolRenderer
 
isLrnChanged() - Method in class databionics.esom.renderer.Renderer
 
isManual() - Method in class databionics.esom.tool.data.DataTool
 
isNaN(String) - Static method in class databionics.io.BaseFile
Check if a string represents a NaN.
isNoForeground() - Method in class databionics.esom.renderer.Renderer
 
isNumber(String) - Method in class databionics.io.BaseFile
Check if a string represents a number
isOnly() - Method in class databionics.esom.util.actions.LoadUmxFileAction
 
isOnly() - Method in class databionics.esom.util.actions.LoadWtsFileAction
 
isOptional() - Method in class databionics.modules.Parameter
Get flag whether this parameter is optional or required
isOverlapMode() - Method in class databionics.esom.tool.island.IslandRenderer
 
isOverlapMode() - Method in class databionics.esom.tool.island.IslandTool
 
isPolygonMode() - Method in class databionics.esom.tool.AbstractTool
 
isPreTiled() - Method in class databionics.esom.tool.island.IslandToolRenderer
 
isReDraw() - Method in class databionics.esom.renderer.Renderer
 
isReMask() - Method in class databionics.esom.renderer.Renderer
 
isRePostFore() - Method in class databionics.esom.renderer.Renderer
 
isRePreFore() - Method in class databionics.esom.renderer.Renderer
 
isReRender() - Method in class databionics.esom.renderer.Renderer
 
isReTile() - Method in class databionics.esom.renderer.Renderer
 
isReZoom() - Method in class databionics.esom.renderer.Renderer
 
isSaved() - Method in class databionics.project.Project
Get boolean if something has changed after last saving
isSelected() - Method in class databionics.esom.tool.data.DataTool
 
isSimilarTo(String) - Method in class databionics.text.SimilarString
Check whether the String is similar to another String.
isSlideLoaded() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
isSlideShow() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
isStopped() - Method in class databionics.esom.tool.slideshow.SlideShow
 
isTiled() - Method in class databionics.esom.renderer.Renderer
Get the tiled flag
isToroid() - Method in class databionics.esom.renderer.Renderer
 
isXYselectableTiled(int, int) - Method in class databionics.esom.gui.ToolLoader
 
isXYSelectableTiled(int, int) - Method in class databionics.esom.tool.island.IslandTool
 
isZoomedByFromTo(int, DoubleMatrix2D, DoubleMatrix2D) - Static method in class databionics.esom.renderer.RendererTools
 
items - Variable in class databionics.esom.tool.legend.LegendTool
 
itemStateChanged(ItemEvent) - Method in class databionics.esom.tool.data.DataTool
 
itmSaveLegend - Variable in class databionics.esom.tool.legend.Legend
 

J

job - Variable in class databionics.esom.gui.util.RunDialog
Job created to run the tool
job - Variable in class databionics.gui.RunDialog
Job created to run the tool
Job - Class in databionics.modules
A job is the execution of a tool on a set of files.
Job() - Constructor for class databionics.modules.Job
standard constructor
Job(Tool) - Constructor for class databionics.modules.Job
Copy constructor to create a Job from a Tool.

K

k - Variable in class databionics.esom.train.KBatchSOM
parameter for k-batch training
KBatchSOM - Class in databionics.esom.train
version of batch training, updates map every k-th epoch
KBatchSOM() - Constructor for class databionics.esom.train.KBatchSOM
Standard constructor
key2pos - Variable in class databionics.io.ClassmaskFile
Column with data point keys
key2pos - Variable in class databionics.io.ClsFile
Column with data point keys
KEY_COLUMN - Static variable in class databionics.io.LrnFile
 
keyColumnIndex - Variable in class databionics.io.LrnFile
Index of key column.
keyColumnName - Variable in class databionics.io.LrnFile
Name of key column.
KeyName - Class in databionics.io
Detailed information about a data key.
KeyName() - Constructor for class databionics.io.KeyName
Standard constructor
KeyName(int, String, String) - Constructor for class databionics.io.KeyName
Constructor with all fields
keyPressed(KeyEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
donothing.
keyPressed(KeyEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
keyPressed(KeyEvent) - Method in class databionics.esom.tool.ProtoPanel
 
keyPressed(KeyEvent) - Method in class databionics.esom.tool.slideshow.PngPrefixQuestion
handles event for pressed key
keyReleased(KeyEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
Event handling for edit fields.
keyReleased(KeyEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
keyReleased(KeyEvent) - Method in class databionics.esom.tool.ProtoPanel
 
keyReleased(KeyEvent) - Method in class databionics.esom.tool.slideshow.PngPrefixQuestion
handles event for released key
keys - Variable in class databionics.esom.train.SOM
list with unique keys
keys - Variable in class databionics.io.ClassmaskFile
Column with data point keys
keys - Variable in class databionics.io.ClsFile
Column with data point keys
keys - Variable in class databionics.io.LrnFile
Column with unique keys, not stored in the main array.
keysMatch(IntArrayList) - Method in class databionics.io.BMFile
 
keyTyped(KeyEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
donothing.
keyTyped(KeyEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
keyTyped(KeyEvent) - Method in class databionics.esom.tool.ProtoPanel
 
keyTyped(KeyEvent) - Method in class databionics.esom.tool.slideshow.PngPrefixQuestion
handles event for typed key

L

lblFGColor - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
lblPath - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
lblPrefix - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
lblRemoveCol - Variable in class databionics.esom.tool.data.DataTool
 
lblSaveAs - Variable in class databionics.esom.tool.data.DataTool
 
lblTreshold - Variable in class databionics.esom.tool.classmask.ClassmaskTool
Label for sldTreshold.
left - Variable in class databionics.esom.cooling.CenterCooling
start of linear cooling
Legend - Class in databionics.esom.tool.legend
 
Legend(AbstractTool) - Constructor for class databionics.esom.tool.legend.Legend
 
Legend(Renderer, AbstractTool) - Constructor for class databionics.esom.tool.legend.Legend
constructor with given renderer
legend - Variable in class databionics.esom.tool.legend.LegendTool
 
LegendRenderer - Class in databionics.esom.tool.legend
abstract class for different legends
LegendRenderer() - Constructor for class databionics.esom.tool.legend.LegendRenderer
 
LegendRenderer(Renderer) - Constructor for class databionics.esom.tool.legend.LegendRenderer
 
legendTool - Variable in class databionics.esom.gui.ToolLoader
 
legendTool - Variable in class databionics.esom.renderer.Renderer
 
LegendTool - Class in databionics.esom.tool.legend
 
LegendTool(boolean, Application) - Constructor for class databionics.esom.tool.legend.LegendTool
 
LessThanMinException - Exception in databionics.modules
Thrown when the value of an IntParameter or FloatParameter is less than the allowed minimum.
LessThanMinException() - Constructor for exception databionics.modules.LessThanMinException
Default constructor
LinearCooling - Class in databionics.esom.cooling
Linear cooling of a parameter.
LinearCooling(double, int, double) - Constructor for class databionics.esom.cooling.LinearCooling
Create a new linear cooling object
LineRenderer - Class in databionics.esom.renderer.foreground
Line connecting bestmatches.
LineRenderer() - Constructor for class databionics.esom.renderer.foreground.LineRenderer
Standard constructor
lineSeparator - Static variable in class databionics.project.Project
the line separator used for writing a xml-document
lineSize - Variable in class databionics.esom.renderer.foreground.LineRenderer
size of bestmatch
ListFile - Class in databionics.io
Base class for files with lists.
ListFile() - Constructor for class databionics.io.ListFile
Standard constructor
ListFile(String) - Constructor for class databionics.io.ListFile
Constructor with a filename
load(String) - Method in class databionics.esom.tool.AbstractLoadAction
 
load(String) - Method in class databionics.esom.tool.classmask.ClassmaskLoadAction
 
load(String) - Method in class databionics.esom.tool.classmask.ClassmaskTool
load the neuron classification from a *.cls file
load(String) - Method in class databionics.esom.tool.component.ComponentTool
 
load(String) - Method in class databionics.esom.tool.data.DataTool
 
load(String) - Method in class databionics.esom.tool.dataclass.DataclassLoadAction
 
load(String) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
load(String) - Method in class databionics.esom.tool.info.InfoTool
donothing
load(String) - Method in class databionics.esom.tool.island.IslandTool
 
load(String) - Method in class databionics.esom.tool.island.LoadImxFileAction
 
load(String) - Method in class databionics.esom.tool.legend.LegendTool
 
load(String) - Method in class databionics.esom.tool.projection.ProjectionTool
 
load(String) - Method in class databionics.esom.tool.slideshow.LoadPicturesAction
Load the file into the renderer
load(String) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
load(String) - Method in class databionics.esom.util.actions.LoadBMFileAction
Load the file into the renderer
load(String) - Method in class databionics.esom.util.actions.LoadFileAction
Really load the file in subclasses.
load(String) - Method in class databionics.esom.util.actions.LoadLrnFileAction
Load the file into the renderer
load(String) - Method in class databionics.esom.util.actions.LoadNamesFileAction
Load the file into the renderer
load(String) - Method in class databionics.esom.util.actions.LoadUmxFileAction
Load the file into the renderer
load(String) - Method in class databionics.esom.util.actions.LoadWtsFileAction
Load the file into the renderer
load() - Method in class databionics.io.BaseFile
Load data.
load(String) - Method in class databionics.io.BaseFile
Load data from this file
load(String, String) - Static method in class databionics.io.ImportExaFile
 
load(String) - Method in class databionics.modules.Modules
Load the modules out of an XML document
load(InputStream) - Method in class databionics.modules.Modules
Load the modules out of an XML document
load() - Method in class databionics.project.FileSlot
Load the data of the first file in the slot
load(String) - Method in class databionics.project.Project
Load a project from a XML-File
load(InputStream, String) - Method in class databionics.project.Project
Load a project from a XML-File
loadAllInDir(FileType) - Method in class databionics.project.Project
load all files in same directory as file in slot with FileType type
loadBestMatches(String) - Method in class databionics.esom.renderer.Renderer
Load the indices of the bestmatches from a *.bm file
loadBM - Variable in class databionics.esom.tool.projection.ClassifyAction
 
LoadBMFileAction - Class in databionics.esom.util.actions
Load a *.bm file
LoadBMFileAction() - Constructor for class databionics.esom.util.actions.LoadBMFileAction
Standard contructor
loadCls(String) - Method in class databionics.esom.train.SOM
 
loadData(String) - Method in class databionics.esom.renderer.Renderer
Load the training data and keys from a *.lrn file
loadData(String) - Method in class databionics.esom.train.SOM
Load the training data and keys from a *.lrn file
loader - Variable in class databionics.esom.Analyze
the tools
loader - Variable in class databionics.esom.gui.MainFrame
 
loader - Variable in class databionics.esom.gui.MainMenu
 
loader - Variable in class databionics.esom.gui.RenderPanel
 
loader - Variable in class databionics.esom.gui.util.RunDialog
 
loader - Variable in class databionics.esom.tool.AbstractTool
Somanas ToolLoader
loader - Variable in class databionics.esom.tool.projection.ClassifyAction
 
loader - Variable in class databionics.esom.tool.projection.ClassifyCallback
the toll loader
loader - Variable in class databionics.esom.tool.projection.ProjectAction
 
loader - Variable in class databionics.esom.tool.projection.ProjectCallback
the toll loader
loader - Variable in class databionics.esom.tool.slideshow.PngPrefixQuestion
the global tool loader
loader - Variable in class databionics.esom.tool.slideshow.SlideShowCallback
the toll loader
loader - Variable in class databionics.esom.train.TrainAction
 
loader - Variable in class databionics.esom.train.TrainCallback
 
loader - Variable in class databionics.esom.util.actions.LoadUmxFileAction
 
loader - Variable in class databionics.esom.util.actions.LoadWtsFileAction
 
loader - Variable in class databionics.esom.util.actions.ResetAction
 
LoadFileAction - Class in databionics.esom.util.actions
Show a dialog to load a file of the specific filetype.
LoadFileAction(FileType) - Constructor for class databionics.esom.util.actions.LoadFileAction
Constructor with file tpye
LoadImxFileAction - Class in databionics.esom.tool.island
 
LoadImxFileAction(AbstractTool) - Constructor for class databionics.esom.tool.island.LoadImxFileAction
 
loadItm - Variable in class databionics.esom.tool.AbstractTool
 
loadLrn - Variable in class databionics.esom.tool.projection.ProjectAction
 
loadLrn - Variable in class databionics.esom.train.TrainAction
action for loading lrn, if no one is loaded
LoadLrnFileAction - Class in databionics.esom.util.actions
Load a *.lrn file
LoadLrnFileAction(AbstractTool) - Constructor for class databionics.esom.util.actions.LoadLrnFileAction
Standard contructor
loadMatrix(String) - Method in class databionics.esom.renderer.Renderer
Load the matrix from a *.umx file
loadNames(String) - Method in class databionics.esom.renderer.Renderer
Load the data names from a *.names file
LoadNamesFileAction - Class in databionics.esom.util.actions
Load a *.names file
LoadNamesFileAction() - Constructor for class databionics.esom.util.actions.LoadNamesFileAction
Standard contructor
loadNewFromJob(Job) - Method in class databionics.project.Project
load all files possibly created by a job
loadPictures(String) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
LoadPicturesAction - Class in databionics.esom.tool.slideshow
Loading *.pictures file, holding the absolute path of the slide show images
LoadPicturesAction(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.LoadPicturesAction
Standard contructor
loadProperties(File) - Static method in class databionics.util.Utils
Load properties from a file into System properties
loadUMXAction - Variable in class databionics.esom.gui.MainMenu
 
LoadUmxFileAction - Class in databionics.esom.util.actions
Load a *.umx file
LoadUmxFileAction(ToolLoader) - Constructor for class databionics.esom.util.actions.LoadUmxFileAction
Standard contructor
LoadUmxFileAction(ToolLoader, boolean) - Constructor for class databionics.esom.util.actions.LoadUmxFileAction
 
loadWeights(String) - Static method in class databionics.esom.grid.RectangularGrid
Load the weight vectors from a *.wts file
loadWts - Variable in class databionics.esom.tool.projection.ClassifyAction
 
loadWts - Variable in class databionics.esom.tool.projection.ProjectAction
 
loadWTSAction - Variable in class databionics.esom.gui.MainMenu
 
LoadWtsFileAction - Class in databionics.esom.util.actions
Load a *.wts file
LoadWtsFileAction(ToolLoader) - Constructor for class databionics.esom.util.actions.LoadWtsFileAction
Standard contructor
LoadWtsFileAction(ToolLoader, boolean) - Constructor for class databionics.esom.util.actions.LoadWtsFileAction
constructor for loading only the *.wts file
loc - Variable in class databionics.io.BaseFile
Current locale.
LocalBmSearch - Class in databionics.esom.train.search
special kind of bm search, searches in local range of old bm
LocalBmSearch() - Constructor for class databionics.esom.train.search.LocalBmSearch
 
LocalNInfoRenderer - Class in databionics.esom.tool.pointinfo
Shows the Data of the actual Mouse-Point as a graph the Data is local normalized over the wts-Data (not the lrn-Data)
LocalNInfoRenderer() - Constructor for class databionics.esom.tool.pointinfo.LocalNInfoRenderer
Basic constructor
localWTSMax - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
localWTSMin - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
log - Static variable in class databionics.Application
interface to log4j system
log - Static variable in class databionics.esom.Analyze
interface to log4j system
log - Static variable in class databionics.esom.Cluster
interface to log4j system
log - Static variable in class databionics.esom.cooling.CachedCooling
interface to log4j system
log - Static variable in class databionics.esom.cooling.CenterCooling
interface to log4j system
log - Static variable in class databionics.esom.cooling.Cooling
interface to log4j system
log - Static variable in class databionics.esom.cooling.ExponentialCooling
interface to log4j system
log - Static variable in class databionics.esom.cooling.LinearCooling
interface to log4j system
log - Static variable in class databionics.esom.cooling.NoCooling
interface to log4j system
log - Static variable in class databionics.esom.grid.CircularGrid1D
interface to log4j system
log - Static variable in class databionics.esom.grid.Grid
interface to log4j system
log - Static variable in class databionics.esom.grid.Grid1D
interface to log4j system
log - Static variable in class databionics.esom.grid.MatrixGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.PlanarEuclideanGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.PlanarGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.PlanarManhattanGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.PlanarMaxGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.RectangularGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.ToroidEuclideanGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.ToroidGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.ToroidManhattanGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.ToroidMaxGrid
interface to log4j system
log - Static variable in class databionics.esom.grid.ToroidRectangularGrid
interface to log4j system
log - Static variable in class databionics.esom.gui.AboutDialog
log4j logging
log - Static variable in class databionics.esom.gui.MainFrame
interface to log4j system
log - Static variable in class databionics.esom.gui.MainMenu
log4j logging
log - Static variable in class databionics.esom.gui.PicPanel
interface to log4j system
log - Static variable in class databionics.esom.gui.RenderPanel
interface to log4j system
log - Static variable in class databionics.esom.gui.ToolLoader
interface to log4j system
log - Static variable in class databionics.esom.gui.util.ClassComboBox
interface to log4j system
log - Static variable in class databionics.esom.gui.util.ClassNameDialog
interface to log4j system
log - Static variable in class databionics.esom.gui.util.DoublePolygon
 
log - Static variable in class databionics.esom.gui.util.GradientComboBox
interface to log4j system
log - Static variable in class databionics.esom.gui.util.MessagePanel
interface to log4j system
log - Static variable in class databionics.esom.gui.util.RunDialog
log4j logging
log - Static variable in class databionics.esom.neighborhood.BubbleNeighborhood
interface to log4j system
log - Static variable in class databionics.esom.neighborhood.CachedNeighborhood
interface to log4j system
log - Static variable in class databionics.esom.neighborhood.ConeNeighborhood
interface to log4j system
log - Static variable in class databionics.esom.neighborhood.EpanechicovNeighborhood
interface to log4j system
log - Static variable in class databionics.esom.neighborhood.GaussNeighborhood
interface to log4j system
log - Static variable in class databionics.esom.neighborhood.MexicanHatNeighborhood
interface to log4j system
log - Static variable in class databionics.esom.neighborhood.Neighborhood
interface to log4j system
log - Static variable in class databionics.esom.Project
interface to log4j system
log - Static variable in class databionics.esom.Render
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.BackgroundTool
interface to log4j system.
log - Static variable in class databionics.esom.renderer.background.ComponentRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.GapRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.OpinionRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.PMatrixRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.TwoMatchRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.background.UMatrixRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.BestmatchRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.BoundaryList
 
log - Static variable in class databionics.esom.renderer.foreground.ForegroundList
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.ForegroundTool
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.FrameRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.LineRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.NamesRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.HeightStatistics
interface to log4j system
log - Static variable in class databionics.esom.renderer.Renderer
interface to log4j system
log - Static variable in class databionics.esom.renderer.RendererTools
 
log - Static variable in class databionics.esom.SlideShow
interface to log4j system
log - Static variable in class databionics.esom.tool.AbstractTool
 
log - Static variable in class databionics.esom.tool.AbstractToolRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.AbstractToolTable
 
log - Variable in class databionics.esom.tool.BottomTab
 
log - Static variable in class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
log - Static variable in class databionics.esom.tool.classmask.ClassmaskLoadAction
 
log - Static variable in class databionics.esom.tool.classmask.ClassmaskRenderer
 
log - Static variable in class databionics.esom.tool.classmask.ClassmaskSaveAction
 
log - Static variable in class databionics.esom.tool.classmask.ClassmaskTableModel
interface to log4j system
log - Static variable in class databionics.esom.tool.classmask.ClassmaskTool
 
log - Static variable in class databionics.esom.tool.component.ComponentTableModel
interface to log4j system
log - Static variable in class databionics.esom.tool.component.ComponentTool
Interface to log4j system
log - Static variable in class databionics.esom.tool.data.DataTable
interface to log4j system
log - Static variable in class databionics.esom.tool.data.DataTableModel
interface to log4j system
log - Static variable in class databionics.esom.tool.data.DataTool
interface to log4j system
log - Static variable in class databionics.esom.tool.data.SelectedDataTableModel
interface to log4j system
log - Static variable in class databionics.esom.tool.data.SelectionPanel
Interface to log4j system
log - Static variable in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.dataclass.DataclassTableModel
interface to log4j system
log - Static variable in class databionics.esom.tool.island.IslandCreatorPanel
interface to log4j system
log - Static variable in class databionics.esom.tool.island.IslandRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.island.IslandTool
interface to log4j system
log - Static variable in class databionics.esom.tool.island.IslandToolRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.island.SaveImxFileAction
interface to log4j system
log - Static variable in class databionics.esom.tool.legend.Legend
interface to log4j system
log - Static variable in class databionics.esom.tool.legend.LegendRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.mapview.MapViewTool
interface to log4j system
log - Static variable in class databionics.esom.tool.pointinfo.GlobalNInfoRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.pointinfo.LocalNInfoRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.pointinfo.ValueInfoRenderer
interface to log4j system
log - Static variable in class databionics.esom.tool.projection.ClassifyAction
 
log - Static variable in class databionics.esom.tool.projection.ClassifyCallback
interface to log4j system
log - Static variable in class databionics.esom.tool.projection.ProjectAction
 
log - Static variable in class databionics.esom.tool.projection.ProjectCallback
interface to log4j system
log - Static variable in class databionics.esom.tool.projection.ProjectionTool
 
log - Static variable in class databionics.esom.tool.ProtoPanel
 
log - Static variable in class databionics.esom.tool.slideshow.LoadPicturesAction
interface to log4j system
log - Static variable in class databionics.esom.tool.slideshow.PngPrefixQuestion
interface to log4j system
log - Static variable in class databionics.esom.tool.slideshow.SavePicturesAction
interface to log4j system
log - Static variable in class databionics.esom.tool.slideshow.SlideShowCallback
interface to log4j system
log - Static variable in class databionics.esom.train.Batch2SOM
interface to log4j system
log - Static variable in class databionics.esom.train.BatchSOM
interface to log4j system
log - Static variable in class databionics.esom.train.Descriptives
interface to log4j system
log - Static variable in class databionics.esom.train.HybridBatchSOM
interface to log4j system
log - Static variable in class databionics.esom.train.KBatchSOM
interface to log4j system
log - Static variable in class databionics.esom.Train
interface to log4j system
log - Static variable in class databionics.esom.train.OnlineSOM
interface to log4j system
log - Static variable in class databionics.esom.train.search.BmSearchStat
interface to log4j system
log - Static variable in class databionics.esom.train.search.LocalBmSearch
interface to log4j system
log - Static variable in class databionics.esom.train.SlowBatchSOM
interface to log4j system
log - Static variable in class databionics.esom.train.SOM
interface to log4j system
log - Static variable in class databionics.esom.train.TrainAction
log4j logging
log - Static variable in class databionics.esom.train.TrainCallback
log4j logging
log - Static variable in class databionics.esom.util.actions.ExitAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.FileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.LoadBMFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.LoadFileAction
log4j logging
log - Static variable in class databionics.esom.util.actions.LoadLrnFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.LoadNamesFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.LoadUmxFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.LoadWtsFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.ResetAction
Interface to log4j system
log - Static variable in class databionics.esom.util.actions.SaveBMFileAction
log4j logging
log - Static variable in class databionics.esom.util.actions.SaveFileAction
log4j logging
log - Static variable in class databionics.esom.util.actions.SaveLrnFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.SaveNamesFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.SavePngFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.SaveUmxFileAction
interface to log4j system
log - Static variable in class databionics.esom.util.actions.ShowAboutAction
log4j logging
log - Static variable in class databionics.esom.util.actions.ShowHelpAction
log4j logging
log - Static variable in class databionics.GraphicalApplication
interface to log4j system
log - Static variable in class databionics.gui.BaseMainFrame
 
log - Static variable in class databionics.gui.LogPanel
 
log - Static variable in class databionics.gui.LogPanelWriter
interface to log4j system
log - Static variable in class databionics.gui.RunDialog
log4j logging
log - Static variable in class databionics.io.ArffFile
Log4j logging.
log - Static variable in class databionics.io.Array2DFile
Log4j logging.
log - Static variable in class databionics.io.Array3DFile
Log4j logging.
log - Static variable in class databionics.io.BaseFile
Log4j logging.
log - Static variable in class databionics.io.Bestmatch
Log4j logging.
log - Static variable in class databionics.io.BMFile
Log4j logging.
log - Static variable in class databionics.io.CharRule
Log4j logging.
log - Static variable in class databionics.io.ClassmaskFile
Log4j logging.
log - Static variable in class databionics.io.ClsFile
Log4j logging.
log - Static variable in class databionics.io.ColorMapping
interface to log4j system
log - Static variable in class databionics.io.ColorStatistics
 
log - Static variable in class databionics.io.ColorTable
Log4j logging.
log - Static variable in class databionics.io.Condition
Log4j logging.
log - Static variable in class databionics.io.CsvFile
Log4j logging.
log - Static variable in class databionics.io.DataClass
Log4j logging.
log - Static variable in class databionics.io.DataItem
Log4j logging.
log - Static variable in class databionics.io.DiagnosisFile
Log4j logging.
log - Static variable in class databionics.io.DiffCondition
Log4j logging.
log - Static variable in class databionics.io.DiffRule
Log4j logging.
log - Static variable in class databionics.io.Explanation
Log4j logging.
log - Static variable in class databionics.io.ExplFile
Log4j logging.
log - Static variable in class databionics.io.FileType
log4j logging
log - Static variable in class databionics.io.IntervalCondition
Log4j logging.
log - Static variable in class databionics.io.KeyName
Log4j logging.
log - Static variable in class databionics.io.ListFile
Log4j logging.
log - Static variable in class databionics.io.LrnFile
Log4j logging.
log - Static variable in class databionics.io.MapFile
Log4j logging.
log - Static variable in class databionics.io.NamesFile
Log4j logging.
log - Static variable in class databionics.io.PicturesFile
Log4j logging.
log - Static variable in class databionics.io.Rule
Log4j logging.
log - Static variable in class databionics.io.RuleFile
Log4j logging.
log - Static variable in class databionics.io.UmxFile
Log4j logging.
log - Static variable in class databionics.io.WtsFile
Log4j logging.
log - Static variable in class databionics.math.DistanceFactory
 
log - Static variable in class databionics.math.Distances
 
log - Static variable in class databionics.modules.AbstractFileParameter
log4j logging
log - Static variable in class databionics.modules.AbstractStringParameter
log4j logging
log - Static variable in class databionics.modules.FileParameter
log4j logging
log - Static variable in class databionics.modules.FloatParameter
log4j logging
log - Static variable in class databionics.modules.FolderParameter
log4j logging
log - Static variable in exception databionics.modules.GreaterThanMaxException
log4j logging
log - Static variable in class databionics.modules.InputFileParameter
log4j logging
log - Static variable in class databionics.modules.IntParameter
log4j logging
log - Static variable in class databionics.modules.Job
log4j logging
log - Static variable in exception databionics.modules.LessThanMinException
log4j logging
log - Static variable in class databionics.modules.Module
log4j logging
log - Static variable in class databionics.modules.Modules
log4j logging
log - Static variable in class databionics.modules.MultipleChoiceElement
log4j logging
log - Static variable in class databionics.modules.MultipleChoiceParameter
log4j logging
log - Static variable in class databionics.modules.OutputFileParameter
log4j logging
log - Static variable in class databionics.modules.Parameter
log4j logging
log - Static variable in class databionics.modules.StringParameter
log4j logging
log - Static variable in class databionics.modules.SwitchParameter
log4j logging
log - Static variable in class databionics.modules.Tool
log4j logging
log - Static variable in class databionics.project.DataManager
 
log - Static variable in class databionics.project.FileSlot
log4j logging
log - Static variable in class databionics.project.Project
log4j logging
log - Static variable in class databionics.runner.MatlabRunner
interface to log4j system
log - Static variable in class databionics.runner.Runner
interface to log4j system
log - Static variable in class databionics.util.Utils
logging
logger - Variable in class databionics.gui.LogPanel
logger to add appender to
logPanel - Variable in class databionics.esom.Analyze
the panel for logging all messages
logPanel - Variable in class databionics.esom.gui.ToolLoader
link to the LogPanel
logPanel - Variable in class databionics.esom.gui.util.RunDialog
Panel to display messages in
LogPanel - Class in databionics.gui
A panel to displays log messages from log4j.
LogPanel() - Constructor for class databionics.gui.LogPanel
Create the panel and a correspoding appender but do not add to any logger yet.
LogPanel(Logger) - Constructor for class databionics.gui.LogPanel
Create and add to given logger
LogPanel(String) - Constructor for class databionics.gui.LogPanel
Create and add to given logger
LogPanel(Class) - Constructor for class databionics.gui.LogPanel
Create and add to given logger
logPanel - Variable in class databionics.gui.LogPanelWriter
panel to write to
logPanel - Variable in class databionics.gui.RunDialog
Panel to display messages in
LogPanel.ClearAction - Class in databionics.gui
 
LogPanel.ClearAction(String, JTextArea) - Constructor for class databionics.gui.LogPanel.ClearAction
 
LogPanelWriter - Class in databionics.gui
A writer that writes to a LogPanel
LogPanelWriter(LogPanel) - Constructor for class databionics.gui.LogPanelWriter
constructor with panel to write to
longer(String, String) - Static method in class databionics.text.StringUtils
Return longer of two strings.
longName - Variable in class databionics.modules.Parameter
long name
lRenderer - Variable in class databionics.esom.tool.legend.Legend
 
lrn - Variable in class databionics.esom.renderer.Renderer
LrnFile with data
lrn - Variable in class databionics.esom.tool.data.DataTableModel
 
lrn - Variable in class databionics.esom.tool.data.SelectedDataTableModel
the underlying data
lrn - Variable in class databionics.esom.train.SOM
 
lrn - Variable in class databionics.esom.util.actions.LoadUmxFileAction
flag for loading other fileType
lrn - Variable in class databionics.esom.util.actions.LoadWtsFileAction
flag for loading other fileType
lrnChanged - Variable in class databionics.esom.renderer.background.BackgroundRenderer
flag wether lrn-data changed.
lrnChanged() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Called when the data changed.
lrnChanged - Variable in class databionics.esom.renderer.Renderer
Flag for show changes on actual lrn file
lrnChanged() - Method in interface databionics.esom.util.LrnChangeListener
Called when the data has changed.
LrnChangeListener - Interface in databionics.esom.util
Listener for changes of data.
lrnFile - Variable in class databionics.esom.SlideShow
 
LrnFile - Class in databionics.io
File that stores multivariate data sets in a 2D array.
LrnFile() - Constructor for class databionics.io.LrnFile
Standard constructor
LrnFile(String) - Constructor for class databionics.io.LrnFile
Constructor with a filename
LrnFile(int, int) - Constructor for class databionics.io.LrnFile
Constructor with size for an empty array.
LrnFile(LrnFile) - Constructor for class databionics.io.LrnFile
Clone constructor
lrnFilename - Variable in class databionics.esom.renderer.Renderer
 
lrnIdxList - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
lrnLength - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
lrnListeners - Variable in class databionics.esom.renderer.Renderer
 

M

main(String[]) - Static method in class databionics.Application
Main method, only for testing in this class
main(String[]) - Static method in class databionics.esom.Analyze
main method
main(String[]) - Static method in class databionics.esom.Cluster
main method
main(String[]) - Static method in class databionics.esom.Project
main method
main(String[]) - Static method in class databionics.esom.Render
main method
main(String[]) - Static method in class databionics.esom.SlideShow
main method
main(String[]) - Static method in class databionics.esom.Train
main method
main(String[]) - Static method in class databionics.runner.MatlabRunner
main method
main(String[]) - Static method in class databionics.runner.Runner
main method
mainFrame - Variable in class databionics.esom.Analyze
the main frame holding the panels
MainFrame - Class in databionics.esom.gui
The main frame
MainFrame(ToolLoader) - Constructor for class databionics.esom.gui.MainFrame
constructor with logPanel given by Analyze
mainMenu - Variable in class databionics.esom.gui.MainFrame
the main menu
MainMenu - Class in databionics.esom.gui
main menu
MainMenu(ToolLoader) - Constructor for class databionics.esom.gui.MainMenu
Default constructor Sets up the whole menubar with actionlisteners for all menuitems
makeComponentsImage() - Method in class databionics.esom.tool.component.ComponentTool
called if ComponentRenderer was chosen (flag:if(controlPanel.inCompos)).
makePictures() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
manageNewShowitem(boolean) - Method in class databionics.esom.tool.slideshow.SlideshowTool
switch newShowItem between enabled and disabled
manageShowitem(boolean) - Method in class databionics.esom.tool.slideshow.SlideshowTool
switch showItem between enabled and disabled
manageSlideLists(int) - Method in class databionics.esom.tool.slideshow.SlideshowTool
sorts the slide lists to manage linux and windows differences
manageSlideShow() - Method in class databionics.esom.tool.slideshow.SlideshowTool
builts the slidePictures
manhattanGridDistance(int, int, int, int) - Static method in class databionics.esom.grid.RectangularGrid
Manhattan distance on rectangular grids.
manual - Variable in class databionics.esom.tool.data.DataTool
flag for new names
manualKeys - Variable in class databionics.esom.tool.data.DataTool
manuel keys
manualNames - Variable in class databionics.esom.tool.data.DataTool
manuel names
manualNamesFile - Variable in class databionics.esom.tool.data.DataTool
manuel NamesFile
map - Variable in class databionics.io.MapFile
Hashtable with data.
MapFile - Class in databionics.io
Base class for files with lists that need fast access by index.
MapFile() - Constructor for class databionics.io.MapFile
Standard constructor
MapFile(String) - Constructor for class databionics.io.MapFile
Constructor with a filename
mapspace - Variable in class databionics.esom.tool.dataclass.DataclassTool
 
mapspace - Variable in class databionics.io.DataClass
size of space of this class on current map
mapViewTool - Variable in class databionics.esom.gui.ToolLoader
 
MapViewTool - Class in databionics.esom.tool.mapview
 
MapViewTool(boolean, Application) - Constructor for class databionics.esom.tool.mapview.MapViewTool
 
maskForegrounds - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
maskForegrounds - Variable in class databionics.esom.renderer.Renderer
 
MatlabRunner - Class in databionics.runner
Runs a script in Matlab.
MatlabRunner() - Constructor for class databionics.runner.MatlabRunner
standard constructor.
matrix - Variable in class databionics.esom.renderer.Renderer
The height above each neuron
matrix - Variable in class databionics.esom.tool.ProtoPanel
 
MatrixGrid - Class in databionics.esom.grid
Abstract base class for all grid structures that can store the weight vectors in a 2D matrix.
MatrixGrid() - Constructor for class databionics.esom.grid.MatrixGrid
Standard constructor
MatrixGrid(int, int) - Constructor for class databionics.esom.grid.MatrixGrid
Constructor with sizes
max - Variable in class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
 
max - Variable in class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
 
max - Variable in class databionics.modules.FloatParameter
maximum value
max - Variable in class databionics.modules.IntParameter
maximum value
max - Variable in class databionics.project.FileSlot
maximum size of history
maxima - Variable in class databionics.esom.train.Descriptives
vector of maxima
maximum - Variable in class databionics.io.Condition
The maximum value.
maximum - Variable in class databionics.io.IntervalCondition
The maximum value.
maximumGridDistance(int, int, int, int) - Static method in class databionics.esom.grid.RectangularGrid
Maximum distance on rectangular grids.
means - Variable in class databionics.esom.train.Descriptives
vector of means
message - Variable in class databionics.esom.gui.util.MessagePanel
error message
MessagePanel - Class in databionics.esom.gui.util
class for react on errors
MessagePanel(int, int) - Constructor for class databionics.esom.gui.util.MessagePanel
 
messages - Variable in class databionics.Application
localized messages
metaPanel - Variable in class databionics.esom.tool.BottomTab
 
method - Variable in class databionics.esom.tool.slideshow.SlideShow
 
method - Variable in class databionics.esom.util.actions.SaveLrnFileAction
string to differ between different kinds saving
method - Variable in class databionics.esom.util.actions.SavePngFileAction
string with kind of saving
MexicanHatNeighborhood - Class in databionics.esom.neighborhood
MexicanHatian neighborhood kernel
MexicanHatNeighborhood() - Constructor for class databionics.esom.neighborhood.MexicanHatNeighborhood
Create a new neighborhood object.
MexicanHatNeighborhood(int, double) - Constructor for class databionics.esom.neighborhood.MexicanHatNeighborhood
Create a new neighborhood object.
min - Variable in class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
 
min - Variable in class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
 
min - Variable in class databionics.modules.FloatParameter
minimum value
min - Variable in class databionics.modules.IntParameter
minimum value
minBMSize - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
minima - Variable in class databionics.esom.train.Descriptives
vector of minima
minimum - Variable in class databionics.io.Condition
The minimum value.
minimum - Variable in class databionics.io.IntervalCondition
The minimum value.
mnuFGColor - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
mnuFrameColor - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
mnuSavePictures - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
ModFile - Class in databionics.io
Dummy class to provide this FileType for WEKA model files.
ModFile() - Constructor for class databionics.io.ModFile
 
Module - Class in databionics.modules
A group of tools with similar functions.
Module() - Constructor for class databionics.modules.Module
Default constructor
modules - Variable in class databionics.esom.Analyze
the modul needed for training
Modules - Class in databionics.modules
List of all BDM modules.
Modules() - Constructor for class databionics.modules.Modules
Default constructor
modules - Variable in class databionics.project.Project
list of modules with tools needed for loading
mouseClicked(MouseEvent) - Method in class databionics.esom.gui.AboutDialog
 
mouseClicked(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
mouseClicked(MouseEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
donothing.
mouseClicked(MouseEvent) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
mouseClicked(MouseEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
mouseClicked(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
mouseClicked(MouseEvent) - Method in class databionics.esom.tool.legend.Legend
 
mouseClicked(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mouseClicked(ActionEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
mouseClicked(MouseEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
mouseDragged(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
mouseDragged(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mouseEntered(MouseEvent) - Method in class databionics.esom.gui.AboutDialog
 
mouseEntered(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
Show the infoPanel when the mouse coordinates are in the RenderPanel
mouseEntered(MouseEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
donothing.
mouseEntered(MouseEvent) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
mouseEntered(MouseEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
mouseEntered(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
mouseEntered(MouseEvent) - Method in class databionics.esom.tool.legend.Legend
 
mouseEntered(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mouseEntered(MouseEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
mouseExited(MouseEvent) - Method in class databionics.esom.gui.AboutDialog
 
mouseExited(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
Hide the infoPanel when the mouse coordinates are out of the RenderPanel
mouseExited(MouseEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
donothing.
mouseExited(MouseEvent) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
mouseExited(MouseEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
mouseExited(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
mouseExited(MouseEvent) - Method in class databionics.esom.tool.legend.Legend
 
mouseExited(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mouseExited(MouseEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
mouseMoved(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
If mouse tool is in info mode update the infoPanel if the mouse has been moved
mouseMoved(MouseEvent) - Method in class databionics.esom.tool.data.SelectionPanel
 
mouseMoved(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mousePressed(MouseEvent) - Method in class databionics.esom.gui.AboutDialog
 
mousePressed(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
mousePressed(MouseEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
donothing.
mousePressed(MouseEvent) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
mousePressed(MouseEvent) - Method in class databionics.esom.renderer.RendererTool
donothing
mousePressed(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
mousePressed(MouseEvent) - Method in class databionics.esom.tool.legend.Legend
 
mousePressed(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mousePressed(MouseEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
mouseReleased(MouseEvent) - Method in class databionics.esom.gui.AboutDialog
If mouse button released, close dialog
mouseReleased(MouseEvent) - Method in class databionics.esom.gui.RenderPanel
Handle Event
mouseReleased(MouseEvent) - Method in class databionics.esom.renderer.background.BackgroundTool
Event handling for the sliders.
mouseReleased(MouseEvent) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
mouseReleased(MouseEvent) - Method in class databionics.esom.renderer.RendererTool
handle sliderevents here
mouseReleased(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
mouseReleased(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
mouseReleased(MouseEvent) - Method in class databionics.esom.tool.data.SelectionPanel
 
mouseReleased(MouseEvent) - Method in class databionics.esom.tool.legend.Legend
 
mouseReleased(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
mouseReleased(MouseEvent) - Method in class databionics.esom.tool.slideshow.SlideShow
 
moveCallback - Variable in class databionics.esom.tool.AbstractTool
 
moveSelection(int) - Method in class databionics.esom.tool.AbstractTool
activates move callback, with bm under mouse
msgfile - Variable in class databionics.Application
name of properties file with messages
MuchFasterLearning - Class in databionics.esom.train.search
local bm search, depending on distance between last two bms on this data point
MuchFasterLearning() - Constructor for class databionics.esom.train.search.MuchFasterLearning
 
MuchFasterLearning2 - Class in databionics.esom.train.search
simple variation of MuchFasterLearning
MuchFasterLearning2() - Constructor for class databionics.esom.train.search.MuchFasterLearning2
 
MultipleChoiceElement - Class in databionics.modules
Possible argument for a MultipleChoiceParameter
MultipleChoiceElement() - Constructor for class databionics.modules.MultipleChoiceElement
Default constructor
MultipleChoiceParameter - Class in databionics.modules
Parameter with a multiple choice argument.
MultipleChoiceParameter() - Constructor for class databionics.modules.MultipleChoiceParameter
Default constructor
myFileType - Variable in class databionics.esom.util.actions.FileAction
corresponding file type

N

n - Variable in class databionics.math.Distances
 
name - Variable in class databionics.Application
short program name
name - Variable in class databionics.io.DataClass
Name of class
name - Variable in class databionics.io.FileType
 
name - Variable in class databionics.io.KeyName
Name of key.
name - Variable in class databionics.io.Rule
The name of rule.
name - Variable in class databionics.modules.Module
name of the module
name - Variable in class databionics.modules.Parameter
short name
name - Variable in class databionics.modules.Tool
name
name - Variable in class databionics.project.Project
name of the project
names - Variable in class databionics.esom.gui.util.GradientComboBox
list with all color table names
names - Variable in class databionics.esom.renderer.Renderer
names of bestmatches
names - Variable in class databionics.esom.tool.bminfo.BMInfoTool
 
names - Variable in class databionics.esom.util.actions.LoadUmxFileAction
flag for loading other fileType
names - Variable in class databionics.esom.util.actions.LoadWtsFileAction
flag for loading other fileType
names - Variable in class databionics.io.LrnFile
Names of data columns from header.
NamesFile - Class in databionics.io
File that stores detailled information about datasets.
NamesFile() - Constructor for class databionics.io.NamesFile
Standard constructor
NamesFile(String) - Constructor for class databionics.io.NamesFile
Constructor with a filename
namesFilename - Variable in class databionics.esom.renderer.Renderer
 
NamesRenderer - Class in databionics.esom.renderer.foreground
Names foreground renderer.
NamesRenderer() - Constructor for class databionics.esom.renderer.foreground.NamesRenderer
Standard constructor
Neighborhood - Class in databionics.esom.neighborhood
Abstract base class for neighborhood kernels on a SOM grid.
Neighborhood() - Constructor for class databionics.esom.neighborhood.Neighborhood
Create a new neighborhood object
Neighborhood(int, double) - Constructor for class databionics.esom.neighborhood.Neighborhood
Create a new neighborhood object
neighborhood - Variable in class databionics.esom.train.SOM
neighborhood kernel function
neuron - Variable in class databionics.esom.train.SOM
current neuron, only used internally
newProject() - Method in class databionics.project.Project
Creates a new project with empty filesets and empty history
newShow - Variable in class databionics.esom.tool.slideshow.SlideShowAction
 
nf - Variable in class databionics.Application
number format
nf - Variable in class databionics.esom.train.SOM
number format for messages
nf - Variable in class databionics.io.BaseFile
Current number format.
nGramMetric(int, String) - Method in class databionics.text.SimilarString
Calculate n-grams metric distance of string and argument.
nGramMetric(int, String, String) - Static method in class databionics.text.StringUtils
Calculate n-grams metric distance of two strings.
noBmCapture - Variable in class databionics.esom.renderer.background.BackgroundTool
This Action will load a *.bm into if the Background is missing one.
NoBmSearch - Class in databionics.esom.train.search
Dummy bm search, not searching at all
NoBmSearch() - Constructor for class databionics.esom.train.search.NoBmSearch
 
NoCooling - Class in databionics.esom.cooling
Constant 'cooling' of a parameter.
NoCooling(double) - Constructor for class databionics.esom.cooling.NoCooling
Create a new non-cooling object
noForeground - Variable in class databionics.esom.renderer.Renderer
 
noLrnCapture - Variable in class databionics.esom.renderer.background.BackgroundTool
This Action will load a *.lrn into if the Background is missing one.
norm - Variable in class databionics.esom.neighborhood.EpanechicovNeighborhood
normalization factor
norm - Variable in class databionics.esom.neighborhood.GaussNeighborhood
normalization factor
norm - Variable in class databionics.esom.neighborhood.MexicanHatNeighborhood
normalization factor
normalize() - Method in class databionics.text.SimilarString
Normalize the String, that is make it lowercase, remove all no word characters like spacec and punctuation, remove articles replace German Umlaute
normalize(String) - Static method in class databionics.text.StringUtils
Normalize a String, that is make it lowercase, remove all no word characters like spacec and punctuation, remove articles replace German Umlaute
normCursor - Variable in class databionics.esom.gui.RenderPanel
 
notClassName - Variable in class databionics.io.DiffCondition
The class name excluded by this rule.
notClassName - Variable in class databionics.io.DiffRule
The class name excluded by this rule.
notifyBmListeners() - Method in class databionics.esom.renderer.Renderer
 
notifyLrnListeners() - Method in class databionics.esom.renderer.Renderer
 
notifyWtsListeners() - Method in class databionics.esom.renderer.Renderer
 
notIn - Variable in class databionics.io.Explanation
Class the data point is not in.
noWtsFileCapture - Variable in class databionics.esom.renderer.background.BackgroundTool
This Action will load a *.wts file if the Background is missing one.
npoints - Variable in class databionics.esom.gui.util.DoublePolygon
 
NUL_COLUMN - Static variable in class databionics.io.LrnFile
constants for column definitions.
nullColumns - Variable in class databionics.io.LrnFile
Column to be ignored.

O

occurrences(String, String) - Static method in class databionics.text.StringUtils
Count number of occurences of one String int another.
offline - Variable in class databionics.esom.train.SOM
 
offset - Variable in class databionics.esom.cooling.CachedCooling
step number of first element of cache
ok - Variable in class databionics.esom.gui.util.MessagePanel
 
oldBestmatches - Variable in class databionics.esom.train.search.LocalBmSearch
 
oldBestmatches - Variable in class databionics.esom.train.SOM
indices of best matching neurons for data points of last epoch
olderBestmatches - Variable in class databionics.esom.train.search.MuchFasterLearning
 
olderBestmatches - Variable in class databionics.esom.train.search.MuchFasterLearning2
 
once - Variable in class databionics.esom.tool.island.IslandTool
 
online - Variable in class databionics.esom.train.SOM
 
OnlineSOM - Class in databionics.esom.train
Implementation of the standard SOM training by pattern: The update of the best matching neuron and its neighbors is done right after the best match search for the curent pattern.
OnlineSOM() - Constructor for class databionics.esom.train.OnlineSOM
Standard constructor
only - Variable in class databionics.esom.util.actions.LoadUmxFileAction
 
only - Variable in class databionics.esom.util.actions.LoadWtsFileAction
flag for loading only a wts file
openPicturesItem - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
openUMXItem - Variable in class databionics.esom.gui.MainMenu
 
openWTSItem - Variable in class databionics.esom.gui.MainMenu
 
operator - Variable in class databionics.io.Rule
The operator between the conditions
OpinionBestmatch2Renderer - Class in databionics.esom.renderer.foreground
Render bestmatches in opinion color.
OpinionBestmatch2Renderer() - Constructor for class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
Standard constructor
OpinionBestmatchRenderer - Class in databionics.esom.renderer.foreground
Render bestmatches in opinion color.
OpinionBestmatchRenderer() - Constructor for class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
Standard constructor
opinionMatrix - Variable in class databionics.esom.renderer.Renderer
The Place to store the calculated OpinionMatrix
OpinionRenderer - Class in databionics.esom.renderer.background
OpinionRenderer background renderer.
OpinionRenderer() - Constructor for class databionics.esom.renderer.background.OpinionRenderer
Standard constructor
optional - Variable in class databionics.modules.Parameter
flag whether this parameter is optional or required
options - Variable in class databionics.Application
interface option definition
optionsTool - Variable in class databionics.esom.gui.ToolLoader
 
OptionsTool - Class in databionics.esom.tool.options
 
OptionsTool(boolean, Application) - Constructor for class databionics.esom.tool.options.OptionsTool
 
orderBmSizes() - Method in class databionics.esom.renderer.foreground.ForegroundList
Orders the Sizes of eventually contained Bestmatchrenderers descending.
os - Variable in class databionics.modules.Tool
run only on this operating system if set
OutputFileParameter - Class in databionics.modules
FileParameter for output files.
OutputFileParameter() - Constructor for class databionics.modules.OutputFileParameter
 
outputTypes - Variable in class databionics.modules.Tool
list of file type created by this tool
overlapMatrix - Variable in class databionics.esom.tool.island.IslandRenderer
 
overlapMatrix - Variable in class databionics.esom.tool.island.IslandTool
 
overlapMode - Variable in class databionics.esom.tool.island.IslandRenderer
 
overlapMode - Variable in class databionics.esom.tool.island.IslandTool
 

P

p - Variable in class databionics.esom.tool.AbstractToolTable
 
paint(Graphics) - Method in class databionics.esom.gui.AboutDialog
Paint the image and text
paint(Graphics) - Method in class databionics.esom.gui.PicPanel
Paint the imag on the given graphic object
paint(Graphics) - Method in class databionics.esom.tool.bminfo.BMInfoPanel
 
paint(Graphics) - Method in class databionics.esom.tool.legend.Legend
Show the actual used Legend
paint(Graphics) - Method in class databionics.esom.tool.ProtoPanel
Draws the actual Polygon
paramChanged - Variable in class databionics.esom.renderer.background.BackgroundRenderer
flag wether parameters changed.
paramChanged() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Called when the parameters changed.
paramChanged() - Method in interface databionics.esom.util.ParamChangeListener
Called when a parameter is changed.
ParamChangeListener - Interface in databionics.esom.util
Listener for changes of parameter settings.
Parameter - Class in databionics.modules
Base class for all parameters.
Parameter() - Constructor for class databionics.modules.Parameter
 
parameters - Variable in class databionics.modules.Tool
for calling the tool, these parameters are needed
ParetoDensity - Class in databionics.math
Compute the Pareto Density for all row vectors of a DoubleMatrix2D.
ParetoDensity() - Constructor for class databionics.math.ParetoDensity
 
parseCondition(String) - Static method in class databionics.io.Condition
Parse a condition from a string.
parseError(int, int, String) - Static method in class databionics.io.BaseFile
Report a parsing error
parseHeader() - Method in class databionics.io.ArffFile
Parse the header.
parseHeader() - Method in class databionics.io.Array3DFile
Parse the header.
parseHeader() - Method in class databionics.io.BaseFile
Parse the header in subclasses.
parseHeader() - Method in class databionics.io.BMFile
Parse the header.
parseHeader() - Method in class databionics.io.ClassmaskFile
Parse the header.
parseHeader() - Method in class databionics.io.ClsFile
Parse the header.
parseHeader() - Method in class databionics.io.CsvFile
Parse the header.
parseHeader() - Method in class databionics.io.LrnFile
Parse the header.
parseHeader() - Method in class databionics.io.WtsFile
Parse the header.
parseLine(int, String) - Method in class databionics.io.Array2DFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.BaseFile
Parse a line in subclasses to fill the data structures with values.
parseLine(int, String) - Method in class databionics.io.BMFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.ClassmaskFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.ClsFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.ColorTable
Parse a line.
parseLine(int, String) - Method in class databionics.io.CsvFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.DiagnosisFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.ExplFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.LrnFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.NamesFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.PicturesFile
Parse a line.
parseLine(int, String) - Method in class databionics.io.RuleFile
Parse a line.
parseNames(String) - Method in class databionics.io.ArffFile
Parse line for names with custom delimiters.
parseNames(String) - Method in class databionics.io.LrnFile
Parse line for names with custom delimiters.
parseRule(String) - Static method in class databionics.io.Rule
Parse a rule from a string.
partBm - Variable in class databionics.esom.tool.data.DataTool
 
partCls - Variable in class databionics.esom.tool.data.DataTool
 
partLrn - Variable in class databionics.esom.tool.data.DataTool
 
pattern - Variable in class databionics.esom.train.SOM
current data pattern, only used internally
pca() - Method in class databionics.esom.train.Descriptives
Perform PCA
pdens - Variable in class databionics.esom.renderer.background.PMatrixRenderer
cache distance percentiles
percentile - Variable in class databionics.esom.renderer.background.PMatrixRenderer
percentile parameter
permutation - Variable in class databionics.esom.train.SOM
current permutation of the data vectors, only used internally
permutations - Variable in class databionics.esom.train.SOM
number of possible permutations of the data vectors, only used internally
permute - Variable in class databionics.esom.train.SOM
flag whether to permute data vectors before each epoch
PicPanel - Class in databionics.esom.gui
Mario Noecker, Martin Kuemmerer Panel to display the renderer image
PicPanel() - Constructor for class databionics.esom.gui.PicPanel
Basic contructor
PictureLegend - Class in databionics.esom.tool.legend
generates the legend for adding to png file
PictureLegend() - Constructor for class databionics.esom.tool.legend.PictureLegend
standard constructor, needed for Instance
PictureLegend(Renderer) - Constructor for class databionics.esom.tool.legend.PictureLegend
 
pictures - Variable in class databionics.esom.tool.slideshow.SlideshowTool
PicturesFile for slideshow
PicturesFile - Class in databionics.io
File to store picture names for a slidewhow.
PicturesFile() - Constructor for class databionics.io.PicturesFile
Standard constructor
PicturesFile(String) - Constructor for class databionics.io.PicturesFile
Constructor with a filename
picturesFilename - Variable in class databionics.esom.tool.slideshow.SlideshowTool
PicturesFilename
PlanarEuclideanGrid - Class in databionics.esom.grid
Planar grid with euclidean distance.
PlanarEuclideanGrid() - Constructor for class databionics.esom.grid.PlanarEuclideanGrid
Standard constructor
PlanarEuclideanGrid(int, int, int) - Constructor for class databionics.esom.grid.PlanarEuclideanGrid
Constructor with sizes
PlanarGrid - Class in databionics.esom.grid
Planar grid.
PlanarGrid() - Constructor for class databionics.esom.grid.PlanarGrid
Standard constructor
PlanarGrid(int, int, int) - Constructor for class databionics.esom.grid.PlanarGrid
Constructor with sizes
PlanarManhattanGrid - Class in databionics.esom.grid
Planar grid with manhattan distance.
PlanarManhattanGrid() - Constructor for class databionics.esom.grid.PlanarManhattanGrid
Standard constructor
PlanarManhattanGrid(int, int, int) - Constructor for class databionics.esom.grid.PlanarManhattanGrid
Constructor with sizes
PlanarMaxGrid - Class in databionics.esom.grid
Planar grid with maximum distance.
PlanarMaxGrid() - Constructor for class databionics.esom.grid.PlanarMaxGrid
Standard constructor
PlanarMaxGrid(int, int, int) - Constructor for class databionics.esom.grid.PlanarMaxGrid
Constructor with sizes
PLAY_BACK - Variable in class databionics.esom.tool.slideshow.SlideShow
 
PLAY_FOR - Variable in class databionics.esom.tool.slideshow.SlideShow
 
PlayThread - Class in databionics.esom.tool.slideshow
 
PlayThread(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.PlayThread
 
PMatrixRenderer - Class in databionics.esom.renderer.background
P-Matrix background renderer.
PMatrixRenderer() - Constructor for class databionics.esom.renderer.background.PMatrixRenderer
Standard constructor
PMatrixRenderer(double) - Constructor for class databionics.esom.renderer.background.PMatrixRenderer
Constructor with radius.
PMatrixRenderer(int) - Constructor for class databionics.esom.renderer.background.PMatrixRenderer
Constructor with percentile.
PngFile - Class in databionics.io
Dummy class to provide this FileType for image files.
PngFile() - Constructor for class databionics.io.PngFile
 
PngPrefixQuestion - Class in databionics.esom.tool.slideshow
dialog that asks for name to set
PngPrefixQuestion(ToolLoader) - Constructor for class databionics.esom.tool.slideshow.PngPrefixQuestion
 
pnlBackgroundChooser - Variable in class databionics.esom.renderer.background.BackgroundTool
Panel containing the different GUI elements.
pnlBmSize - Variable in class databionics.esom.renderer.foreground.ForegroundTool
extra Panel for the BestmatchSize slider.
pnlControl - Variable in class databionics.esom.tool.AbstractTool
Panel containing control-elements for the ControlPanel.
pnlFGColor - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
pnlFGColor - Variable in class databionics.esom.tool.options.OptionsTool
 
pnlForeground - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
pnlForegroundChooser - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
pnlFrame - Variable in class databionics.esom.tool.options.OptionsTool
 
pnlMenu - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
pnlPath - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
pnlPathNPrefix - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
pnlPrefix - Variable in class databionics.esom.tool.options.OptionsTool
 
pnlPrefix - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
pnlSpace - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
PointInfoRenderer - Class in databionics.esom.tool.pointinfo
The parent-class for all Point-Info-Renderer
PointInfoRenderer() - Constructor for class databionics.esom.tool.pointinfo.PointInfoRenderer
 
polygonMode - Variable in class databionics.esom.tool.AbstractTool
 
popMenu - Variable in class databionics.esom.tool.AbstractTool
popup menu for the BottomTab.
popMenu - Variable in class databionics.esom.tool.legend.Legend
popup menu
position - Variable in class databionics.esom.tool.slideshow.SlideShow
 
postTileForegrounds - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
posttileForegrounds - Variable in class databionics.esom.renderer.Renderer
 
prefix - Variable in class databionics.esom.tool.options.OptionsTool
 
prefix - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
PrefixAction - Class in databionics.esom.tool.slideshow
action for showing dialog to set slide show prefix
PrefixAction(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.PrefixAction
standard constructor
PrefixAction - Class in databionics.esom.util.actions
 
PrefixAction(SlideshowTool) - Constructor for class databionics.esom.util.actions.PrefixAction
 
prefixitem - Variable in class databionics.esom.tool.options.OptionsTool
 
pRenderer - Variable in class databionics.esom.tool.legend.Legend
 
prepare(Object) - Method in class databionics.esom.tool.projection.ClassifyCallback
 
prepare(Object) - Method in class databionics.esom.tool.projection.ProjectCallback
 
prepare(Object) - Method in class databionics.esom.tool.slideshow.SlideShowCallback
 
prepare(Object) - Method in class databionics.esom.train.TrainCallback
 
prepare(Object) - Method in interface databionics.gui.CallBack
 
preTileForegrounds - Variable in class databionics.esom.renderer.foreground.ForegroundTool
 
pretileForegrounds - Variable in class databionics.esom.renderer.Renderer
The rendererlists for the foregrounds
printHelp() - Method in class databionics.Application
Print command line help and exit.
printVersion() - Method in class databionics.Application
Print version information and exit
processReader - Variable in class databionics.runner.MatlabRunner
standard output of process
processReader - Variable in class databionics.runner.Runner
standard output of process
progressBar - Variable in class databionics.gui.LogPanel
progress bar below messages
progressMatcher - Variable in class databionics.gui.LogPanel
regular expression matcher for parsing progress
progressPattern - Variable in class databionics.gui.LogPanel
regular expression for parsing progress
project - Variable in class databionics.Application
project holding files
project - Variable in class databionics.esom.Analyze
the project to hold the files
project - Variable in class databionics.esom.gui.ToolLoader
The Project containing most of the files
project - Variable in class databionics.esom.gui.util.RunDialog
Project to update after job is done (optional)
Project - Class in databionics.esom
Command line tool to project new data on an ESOM and optionally classify using a class mask.
Project() - Constructor for class databionics.esom.Project
standard constructor.
project - Variable in class databionics.esom.tool.projection.ProjectCallback
 
project - Variable in class databionics.esom.train.TrainCallback
 
project - Variable in class databionics.gui.RunDialog
Project to update after job is done (optional)
Project - Class in databionics.project
A Project contains a collection of file slots and the history of jobs.
Project() - Constructor for class databionics.project.Project
Default constructor
ProjectAction - Class in databionics.esom.tool.projection
action for start to project new data
ProjectAction(ToolLoader) - Constructor for class databionics.esom.tool.projection.ProjectAction
standard constructor
ProjectCallback - Class in databionics.esom.tool.projection
callback for project run dialog
ProjectCallback(ToolLoader) - Constructor for class databionics.esom.tool.projection.ProjectCallback
constructor
projection - Variable in class databionics.esom.Analyze
the class for projecting new data on a map and in a classification
projection(int) - Method in class databionics.esom.train.Descriptives
Projection of data with eigenvector of given eigenvalue
projectionTool - Variable in class databionics.esom.gui.ToolLoader
 
ProjectionTool - Class in databionics.esom.tool.projection
 
ProjectionTool(boolean, Application) - Constructor for class databionics.esom.tool.projection.ProjectionTool
 
promapspace - Variable in class databionics.io.DataClass
prozentual space of this class on current map
properties - Variable in class databionics.cli.PropertyOptions
hashtable for property names
PropertyCommandLine - Class in databionics.cli
Command line options class enhanced with default values from system properties.
PropertyCommandLine(CommandLine, PropertyOptions) - Constructor for class databionics.cli.PropertyCommandLine
Creates an PropertyCommandLine using the specified parameters.
PropertyOptions - Class in databionics.cli
Command line options class enhanced with default values from system properties
PropertyOptions() - Constructor for class databionics.cli.PropertyOptions
Defualt constructor
ProtoPanel - Class in databionics.esom.tool
 
ProtoPanel(AbstractTool) - Constructor for class databionics.esom.tool.ProtoPanel
 
put(String, Object) - Static method in class databionics.project.DataManager
put an Object into workspace (default instance)
put(String, Object, String) - Static method in class databionics.project.DataManager
put an Object in workspace at specified instance.
put(String, Object, String[]) - Static method in class databionics.project.DataManager
 

Q

qerror - Variable in class databionics.esom.train.SOM
current quantization error
QuickLearning - Class in databionics.esom.train.search
search for bm just in a range of the bm in last epoch
QuickLearning() - Constructor for class databionics.esom.train.search.QuickLearning
 
QuickLearning2 - Class in databionics.esom.train.search
simple variation of QuickLearnig
QuickLearning2() - Constructor for class databionics.esom.train.search.QuickLearning2
 

R

radius - Variable in class databionics.esom.neighborhood.Neighborhood
maximum distance from bestmatch on grid to be considered
radius - Variable in class databionics.esom.renderer.background.PMatrixRenderer
radius parameter
radius - Variable in class databionics.esom.train.SOM
current neighborhood radius, only used internally
radius - Variable in class databionics.math.ParetoDensity
the current radius
radiusCooling - Variable in class databionics.esom.train.SOM
cooling strategy of neighborhood radius
random - Variable in class databionics.esom.train.SOM
random number generator, only used internally
RandomRenderer - Class in databionics.esom.renderer.background
Random background renderer.
RandomRenderer() - Constructor for class databionics.esom.renderer.background.RandomRenderer
Standard constructor
rate - Variable in class databionics.esom.train.SOM
current learning rate, only used internally
rateCooling - Variable in class databionics.esom.train.SOM
cooling strategy of learning rate
reallyAppend(String) - Method in class databionics.gui.LogPanel
Add text to the panel
reAreas() - Method in class databionics.esom.tool.AbstractTool
 
reColorize() - Method in class databionics.esom.tool.AbstractTool
 
RectangularGrid - Class in databionics.esom.grid
Abstract base class for all grid structures with a rectangular shaped grid.
RectangularGrid() - Constructor for class databionics.esom.grid.RectangularGrid
Standard constructor
RectangularGrid(int, int, int) - Constructor for class databionics.esom.grid.RectangularGrid
Constructor with sizes
reDraw - Variable in class databionics.esom.renderer.Renderer
Flag whether drawBackground needs to be called again
reDraw() - Method in class databionics.esom.tool.AbstractTool
 
reDraw() - Method in class databionics.esom.tool.slideshow.SlideshowTool
overides super.reDraw with a donothing
reFore(int) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Redraw foregrounds.
reFore() - Method in class databionics.esom.tool.AbstractTool
Redraw all foregrounds.
refresh() - Method in class databionics.esom.tool.projection.ClassifyCallback
 
refresh() - Method in class databionics.esom.tool.projection.ProjectCallback
 
refresh() - Method in class databionics.esom.tool.slideshow.SlideShowCallback
 
refresh() - Method in class databionics.esom.train.TrainCallback
 
refresh() - Method in interface databionics.gui.CallBack
 
registerCallBack(CallBack) - Method in class databionics.esom.gui.util.RunDialog
 
registerCallback(CallBack) - Method in class databionics.gui.RunDialog
 
relation - Variable in class databionics.io.ArffFile
relation name from header
reMask - Variable in class databionics.esom.renderer.Renderer
Flag for drawing island/frame etc.
reMask() - Method in class databionics.esom.tool.AbstractTool
 
remove(int) - Method in class databionics.io.ClassmaskFile
Remove a class, set all corresponding class numbers to 0.
remove(DataClass) - Method in class databionics.io.ClassmaskFile
Remove a class, set all corresponding class numbers to 0
remove(int) - Method in class databionics.io.ClsFile
Remove a class, set all corresponding class numbers to 0.
remove(DataClass) - Method in class databionics.io.ClsFile
Remove a class, set all corresponding class numbers to 0
remove(DataItem) - Method in class databionics.io.MapFile
Remove item from list and map.
remove(int) - Method in class databionics.io.MapFile
Remove item by index from list and map.
remove(String) - Static method in class databionics.project.DataManager
remove an Object from default instance workspace, including all dependents.
remove(String, String) - Static method in class databionics.project.DataManager
remove an Object from workspace, including all dependents.
removeArticles(String) - Static method in class databionics.text.StringUtils
Remove all German, English and French articles from a String.
removeChangeListener(ChangeListener) - Method in class databionics.project.Project
Removes a class of list with changeListeners
removeClass(DataClass) - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
remove one class
removeClass(DataClass) - Method in class databionics.esom.tool.dataclass.DataclassTableModel
removes one class
removeColumn(int) - Method in class databionics.io.LrnFile
 
removeForeground(ForegroundRenderer) - Method in class databionics.esom.renderer.foreground.ForegroundList
Remove a Foreground from List.
removeFromBold(int) - Method in class databionics.io.ClsFile
Remove class from boldclasses
removeFromClassification(int, int) - Method in class databionics.esom.tool.dataclass.DataclassCreatorPanel
 
removeItm - Variable in class databionics.esom.tool.AbstractTool
 
removeNonWordChars(String) - Static method in class databionics.text.StringUtils
Remove all character from a string that don't match the regular expression \W+
removeOne(int, int) - Method in class databionics.io.ClassmaskFile
 
removeOne(int, int) - Method in class databionics.io.ClsFile
 
rename(String) - Method in class databionics.project.FileSlot
Rename first file in this slot
renameFileName(FileType, String) - Method in class databionics.project.Project
Rename filename for a filetype and fire ChangeEvent
Render - Class in databionics.esom
Command line tool for ESOM rendering
Render() - Constructor for class databionics.esom.Render
Standard constructor.
render(Renderer) - Method in class databionics.esom.renderer.background.BackgroundRenderer
Calculate the height above each neuron
render(Renderer) - Method in class databionics.esom.renderer.background.ComponentRenderer
The heights are simply a slice of the high dimensional grid by copying the value of a the selected dimension.
render(Renderer) - Method in class databionics.esom.renderer.background.GapRenderer
The heights are calculated as the distance of a prototype to a local centroid.
render(Renderer) - Method in class databionics.esom.renderer.background.OpinionRenderer
Calculate the color for each neuron with the Opinion method.
render(Renderer) - Method in class databionics.esom.renderer.background.PMatrixRenderer
Calculate the height above each neuron with the P-Matrix method.
render(Renderer) - Method in class databionics.esom.renderer.background.RandomRenderer
Calculate the height above each neuron randomly.
render(Renderer) - Method in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
Calculate the height above each neuron with the SDH method.
render(Renderer) - Method in class databionics.esom.renderer.background.TwoMatchRenderer
Calculate the height above each neuron with the TwoMatch method.
render(Renderer) - Method in class databionics.esom.renderer.background.UMatrixRenderer
Calculate the height above each neuron with the U-Matrix method.
render(Renderer) - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Draw colored square for each best match
render(Renderer) - Method in class databionics.esom.renderer.foreground.ColorizeRenderer
 
render(Renderer) - Method in class databionics.esom.renderer.foreground.ForegroundList
Let all contained Foregrounds render.
render(Renderer) - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Add foreground to the Image taken from the given renderer.
render(Renderer) - Method in class databionics.esom.renderer.foreground.FrameRenderer
 
render(Renderer) - Method in class databionics.esom.renderer.foreground.LineRenderer
Draw colored square for each best match
render(Renderer) - Method in class databionics.esom.renderer.foreground.NamesRenderer
Draw colored square for each best match
render(Renderer) - Method in class databionics.esom.renderer.foreground.OpinionBestmatch2Renderer
Uses super class for actual rendering, but calculates a columnwise-normalized matrix, which is neede for calls to this.getColor(i,);
render(Renderer) - Method in class databionics.esom.renderer.foreground.OpinionBestmatchRenderer
Uses super class for actual rendering, but calculates a columnwise-normalized matrix, which is neede for calls to this.getColor(i,);
render() - Method in class databionics.esom.renderer.Renderer
Render the image.
render(String) - Method in class databionics.esom.renderer.Renderer
Render the image to a file
render(int, int, int, BufferedImage) - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
render(Renderer) - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
render(int, int, int, BufferedImage) - Method in class databionics.esom.tool.classmask.ClassmaskToolRenderer
 
render(Renderer) - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
renders bestmatches in different color per class
render(int, int, int, BufferedImage) - Method in class databionics.esom.tool.island.IslandRenderer
 
render(Renderer) - Method in class databionics.esom.tool.island.IslandRenderer
 
render2(int, int, int, BufferedImage) - Method in class databionics.esom.tool.island.IslandRenderer
(non-Javadoc)
RENDER_MASK - Static variable in class databionics.esom.renderer.foreground.ForegroundRenderer
Indicates that a Foreground wants to be renderered at the very end.
RENDER_POSTTILE - Static variable in class databionics.esom.renderer.foreground.ForegroundRenderer
Indicates that a Foreground wants to be renderered after tiling the image is tiled.
RENDER_PRETILE - Static variable in class databionics.esom.renderer.foreground.ForegroundRenderer
Indicates that a Foreground wants to be renderered before the image is tiled.
renderBackground(Grid) - Method in class databionics.esom.renderer.Renderer
 
renderBackground() - Method in class databionics.esom.renderer.Renderer
If a grid of weights is available (field grid not null) let the background renderer caluclate the height values and store it in the field matrix.
renderer - Variable in class databionics.esom.Analyze
the main renderer
renderer - Variable in class databionics.esom.gui.MainFrame
 
renderer - Variable in class databionics.esom.gui.ToolLoader
link to the main Renderer
renderer - Variable in class databionics.esom.renderer.background.BackgroundRenderer
reference to the main renderer.
renderer - Variable in class databionics.esom.renderer.foreground.ForegroundRenderer
points on main renderer
Renderer - Class in databionics.esom.renderer
Render an ESOM to a 2D image.
Renderer() - Constructor for class databionics.esom.renderer.Renderer
Standard constructor
Renderer(Grid) - Constructor for class databionics.esom.renderer.Renderer
Constructor with weights
Renderer(DoubleMatrix2D) - Constructor for class databionics.esom.renderer.Renderer
Constructor with precalculated matrix
renderer - Variable in class databionics.esom.tool.AbstractTool
Somanas main Renderer
renderer - Variable in class databionics.esom.tool.component.ComponentTable
the main Renderer
renderer - Variable in class databionics.esom.tool.data.DataTableModel
 
renderer - Variable in class databionics.esom.tool.info.InfoToolTableModel
 
renderer - Variable in class databionics.esom.tool.legend.LegendRenderer
 
renderer - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
renderer - Variable in class databionics.esom.tool.ProtoPanel
 
renderer - Variable in class databionics.esom.tool.slideshow.SlideShow
 
renderer - Variable in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
renderer - Variable in class databionics.esom.train.TrainCallback
 
rendererTool - Variable in class databionics.esom.gui.ToolLoader
 
RendererTool - Class in databionics.esom.renderer
 
RendererTool(boolean, Application) - Constructor for class databionics.esom.renderer.RendererTool
Standard constructor initializa all gui-elements if the gui flag is set
RendererTools - Class in databionics.esom.renderer
 
RendererTools() - Constructor for class databionics.esom.renderer.RendererTools
 
rendererTools - Variable in class databionics.esom.tool.legend.LegendRenderer
 
renderLegend(String) - Method in class databionics.esom.tool.legend.Legend
Render the image to a file
renderPanel - Variable in class databionics.esom.gui.MainFrame
the render Panel, holding the ImagePanel
RenderPanel - Class in databionics.esom.gui
The RenderPanel is used to control the renderer and visualize its results.
RenderPanel() - Constructor for class databionics.esom.gui.RenderPanel
Standard Constructor
renderPanel - Variable in class databionics.esom.gui.ToolLoader
link to the RenderPanel
renderPanel - Variable in class databionics.esom.tool.AbstractTool
Somana's main RenderPanel.
renderPanel - Variable in class databionics.esom.tool.ProtoPanel
 
renderPosition - Variable in class databionics.esom.renderer.foreground.ForegroundList
One of the constants RENDER_POSTTILE,RENDER_MASK or RENDER_PRETILE from ForegroundRenderer.java.
replace(String, String, String) - Static method in class databionics.text.StringUtils
Replace parts of a string.
replaceUmlauts(String) - Static method in class databionics.text.StringUtils
Replace German Umlaute with official replacements.
rePostFore - Variable in class databionics.esom.renderer.Renderer
Flag for drawing cls/bm/opn etc.
rePostFore() - Method in class databionics.esom.tool.AbstractTool
 
rePreFore - Variable in class databionics.esom.renderer.Renderer
Flag for drawing areas/colorize etc.
rePreFore() - Method in class databionics.esom.tool.AbstractTool
this lauches a Rerender from those Foreground on, which are painted before the Image is tiled.
reRender - Variable in class databionics.esom.renderer.Renderer
Flag whether renderBackground needs to be called again
reRender() - Method in class databionics.esom.tool.AbstractTool
Set the main renderer's ReRender-flag true.
reset() - Method in class databionics.esom.gui.RenderPanel
Reset the ControlPane, UmxPanel, AreaInfoPanel, InfoPanel using the current renderer
reset() - Method in class databionics.esom.gui.util.RunDialog
Fill input fields with default values from tool or values from old job
reset() - Method in class databionics.esom.renderer.background.BackgroundTool
Reset the Cache of all Backgrounds.
reset() - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
reset() - Method in class databionics.esom.renderer.Renderer
 
reset() - Method in class databionics.esom.renderer.RendererTool
donothing atm TODO
reset() - Method in class databionics.esom.tool.AbstractTool
reset the tool.
reset() - Method in class databionics.esom.tool.AbstractToolRenderer
 
reset() - Method in class databionics.esom.tool.bminfo.BMInfoTool
resets the tool
reset() - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
 
reset() - Method in class databionics.esom.tool.classmask.ClassmaskTool
called when the actual renderer changed
reset() - Method in class databionics.esom.tool.classmask.ClassmaskToolRenderer
 
reset() - Method in class databionics.esom.tool.component.ComponentTool
 
reset() - Method in class databionics.esom.tool.data.DataTable
resets the classCount
reset() - Method in class databionics.esom.tool.data.DataTableModel
 
reset() - Method in class databionics.esom.tool.data.DataTool
 
reset() - Method in class databionics.esom.tool.data.DataToolRenderer
 
reset() - Method in class databionics.esom.tool.data.SelectedDataTableModel
resets the selected LrnFile
reset() - Method in class databionics.esom.tool.data.SelectionPanel
 
reset() - Method in class databionics.esom.tool.dataclass.DataclassRenderer
 
reset() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
reset() - Method in class databionics.esom.tool.info.InfoTool
 
reset() - Method in class databionics.esom.tool.island.IslandTool
 
reset() - Method in class databionics.esom.tool.island.IslandToolRenderer
 
reset() - Method in class databionics.esom.tool.legend.LegendTool
 
reset() - Method in class databionics.esom.tool.mapview.MapViewTool
 
reset() - Method in class databionics.esom.tool.options.OptionsTool
 
reset() - Method in class databionics.esom.tool.projection.ProjectionTool
 
reset() - Method in class databionics.esom.tool.ProtoPanel
Reset the CreatorPanel.
reset() - Method in class databionics.esom.tool.similarity.SimilarityTool
 
reset() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
reset() - Method in class databionics.gui.RunDialog
Fill input fields with default values from tool or values from old job
reset() - Method in class databionics.io.ColorMapping
 
reset() - Method in class databionics.project.FileSlot
empty the slot
reset(FileType) - Method in class databionics.project.Project
Reset slot
reset() - Method in class databionics.project.Project
Resets the project by invoking the methods:
ResetAction - Class in databionics.esom.util.actions
action for reseting renderer and somana gui
ResetAction(ToolLoader) - Constructor for class databionics.esom.util.actions.ResetAction
standard constructor
resetAll() - Method in class databionics.esom.gui.ToolLoader
 
resetButton - Variable in class databionics.esom.gui.util.RunDialog
 
resetButton - Variable in class databionics.gui.RunDialog
 
resetCache() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Reset the cache for the result matrix.
resetGuiElements() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
resizeCols() - Method in class databionics.esom.tool.AbstractToolTable
resizes the columns
resizeCols() - Method in class databionics.esom.tool.classmask.ClassmaskTable
resizes the columns
resizeCols() - Method in class databionics.esom.tool.component.ComponentTable
 
resizeCols() - Method in class databionics.esom.tool.data.DataTable
resizes the columns
resizeCols() - Method in class databionics.esom.tool.dataclass.DataclassTable
 
resizeCols() - Method in class databionics.esom.tool.info.InfoToolTable
 
resizeCols() - Method in class databionics.esom.tool.island.IslandTable
 
resizeCols() - Method in class databionics.esom.tool.slideshow.SlideShowInfoTable
 
resizeContent() - Method in class databionics.esom.gui.RenderPanel
resizing the components
result(int) - Method in class databionics.esom.train.search.BmSearchStat
 
reTile - Variable in class databionics.esom.renderer.Renderer
Flag whether tileBackground needs to be called again
reTile() - Method in class databionics.esom.tool.AbstractTool
 
reZoom - Variable in class databionics.esom.renderer.Renderer
Flag whether zoomBackground needs to be called again
reZoom() - Method in class databionics.esom.tool.AbstractTool
 
right - Variable in class databionics.esom.cooling.CenterCooling
end of linear cooling
row - Variable in class databionics.esom.tool.AbstractToolTable
 
row - Variable in class databionics.io.Bestmatch
Row of data point's best match.
rows - Variable in class databionics.esom.grid.RectangularGrid
rows of rectangle
rows - Variable in class databionics.io.Array3DFile
Number of rows of 3D array.
rows - Variable in class databionics.io.BMFile
Number of rows from header.
Rule - Class in databionics.io
Abstract base class for rules
Rule() - Constructor for class databionics.io.Rule
Standard constructor
Rule(String, String, String, String, String) - Constructor for class databionics.io.Rule
Constructor with all important fields.
RuleFile - Class in databionics.io
File that stores DataClass rules.
RuleFile() - Constructor for class databionics.io.RuleFile
Standard constructor
RuleFile(String) - Constructor for class databionics.io.RuleFile
Constructor with a filename
run() - Method in class databionics.Application
Run method for Interface Runnable.
run() - Method in class databionics.esom.Analyze
run
run() - Method in class databionics.esom.Cluster
run
run() - Method in class databionics.esom.gui.util.RunDialog
Watch the running job.
run() - Method in class databionics.esom.Project
run
run() - Method in class databionics.esom.Render
run
run() - Method in class databionics.esom.SlideShow
run
run() - Method in class databionics.esom.tool.slideshow.PlayThread
 
run() - Method in class databionics.esom.Train
run
run() - Method in class databionics.gui.RunDialog
Watch the running job.
run() - Method in class databionics.runner.MatlabRunner
run
run(String) - Method in class databionics.runner.Runner
run
run() - Method in class databionics.runner.Runner
run
RunDialog - Class in databionics.esom.gui.util
clone of databionics.gui.RunDialog Dialog to start a tool, thus create a job.
RunDialog(Tool, Project) - Constructor for class databionics.esom.gui.util.RunDialog
Constructor to initialize the dialog window
RunDialog - Class in databionics.gui
Dialog to start a Tool, thus create a Job.
RunDialog(Tool, Project) - Constructor for class databionics.gui.RunDialog
Constructor to initialize the dialog window
Runner - Class in databionics.runner
Application that runs an external program.
Runner() - Constructor for class databionics.runner.Runner
standard constructor.

S

sameHits - Static variable in class databionics.esom.train.BestMatchHit
counter for BestMatchHits
save(String) - Method in class databionics.esom.tool.AbstractSaveAction
 
save(String) - Method in class databionics.esom.tool.classmask.ClassmaskSaveAction
 
save(String) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
save(String) - Method in class databionics.esom.tool.component.ComponentTool
 
save(String) - Method in class databionics.esom.tool.data.DataTool
 
save(String) - Method in class databionics.esom.tool.data.SelectedBMsSaveFileAction
 
save(String) - Method in class databionics.esom.tool.data.SelectedClsSaveAction
 
save(String) - Method in class databionics.esom.tool.data.SelectedLrnSaveAction
 
save(String) - Method in class databionics.esom.tool.dataclass.DataclassSaveAction
 
save(String) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
save(String) - Method in class databionics.esom.tool.info.InfoTool
donothing
save(String) - Method in class databionics.esom.tool.island.IslandTool
 
save(String) - Method in class databionics.esom.tool.island.SaveImxFileAction
Save the file
save(String) - Method in class databionics.esom.tool.legend.LegendTool
 
save(String) - Method in class databionics.esom.tool.legend.SaveLegendAction
 
save(String) - Method in class databionics.esom.tool.legend.SavePictureWithLegendAction
 
save(String) - Method in class databionics.esom.tool.legend.SavePictureWithLegendAction2
 
save(String) - Method in class databionics.esom.tool.slideshow.SavePicturesAction
Save the file
save(String) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
save(String) - Method in class databionics.esom.util.actions.SaveBMFileAction
saves the file
save(String) - Method in class databionics.esom.util.actions.SaveFileAction
Really save the file in subclasses.
save(String) - Method in class databionics.esom.util.actions.SaveLrnFileAction
Save the file
save(String) - Method in class databionics.esom.util.actions.SaveNamesFileAction
Save the file
save(String) - Method in class databionics.esom.util.actions.SavePngFileAction
Save the file
save(String) - Method in class databionics.esom.util.actions.SaveUmxFileAction
Save the file
save() - Method in class databionics.io.BaseFile
Save the data to a file.
save(String) - Method in class databionics.io.BaseFile
Save data to this file.
save() - Method in class databionics.project.FileSlot
Save the data of the first file in the slot
save(String) - Method in class databionics.project.Project
Saves a project in a XML-document
saveBestMatches(String) - Method in class databionics.esom.train.SOM
Save indices of best matching neurons to a *.bm file Available after calling train().
SaveBMFileAction - Class in databionics.esom.util.actions
saves a new *.bm file
SaveBMFileAction() - Constructor for class databionics.esom.util.actions.SaveBMFileAction
standard constructor
saveBMs(String) - Method in class databionics.esom.tool.data.DataTool
 
saveCls(String) - Method in class databionics.esom.tool.data.DataTool
 
saved - Variable in class databionics.project.Project
flag whether anything has changed since the last saving
saveDoublePicture(String) - Method in class databionics.esom.tool.legend.LegendTool
generates a image with map and legend
saveDoublePicture2(String) - Method in class databionics.esom.tool.legend.LegendTool
generates a image with map and legend
savedTool - Variable in class databionics.esom.gui.RenderPanel
If components are shown, the currently active tool has to be deactivated.
saveEpoch - Variable in class databionics.esom.train.SOM
number of epochs after which a bm and wts file will be saved
saveEpoches - Variable in class databionics.esom.train.SOM
Boolean for saving during epochs
SaveFileAction - Class in databionics.esom.util.actions
Show a dialog to save a file of the specific filetype.
SaveFileAction(FileType) - Constructor for class databionics.esom.util.actions.SaveFileAction
Constructor with file tpye
SaveImxFileAction - Class in databionics.esom.tool.island
saves an island
SaveImxFileAction(AbstractTool) - Constructor for class databionics.esom.tool.island.SaveImxFileAction
Standard contructor
saveItm - Variable in class databionics.esom.tool.AbstractTool
 
saveItm2 - Variable in class databionics.esom.tool.legend.LegendTool
 
saveItm3 - Variable in class databionics.esom.tool.legend.LegendTool
 
saveItmLrn - Variable in class databionics.esom.tool.data.DataTool
 
SaveLegendAction - Class in databionics.esom.tool.legend
 
SaveLegendAction(AbstractTool) - Constructor for class databionics.esom.tool.legend.SaveLegendAction
 
saveLrn(String) - Method in class databionics.esom.tool.data.DataTool
 
saveLrn - Variable in class databionics.esom.tool.projection.ProjectAction
 
saveLrn - Variable in class databionics.esom.train.TrainAction
action for saving lrn, if it has been modified
SaveLrnFileAction - Class in databionics.esom.util.actions
Save a *.lrn file
SaveLrnFileAction() - Constructor for class databionics.esom.util.actions.SaveLrnFileAction
Standard contructor
SaveLrnFileAction(String) - Constructor for class databionics.esom.util.actions.SaveLrnFileAction
contructor with given kind of method
saveMatrix(String) - Method in class databionics.esom.renderer.Renderer
Save the matrix to a *.umx file
SaveNamesFileAction - Class in databionics.esom.util.actions
Save a *.names file
SaveNamesFileAction() - Constructor for class databionics.esom.util.actions.SaveNamesFileAction
Standard contructor
SavePicturesAction - Class in databionics.esom.tool.slideshow
saves a *.pictures file, with absolute pathes of slide show images
SavePicturesAction(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.SavePicturesAction
Standard contructor
SavePictureWithLegendAction - Class in databionics.esom.tool.legend
 
SavePictureWithLegendAction(AbstractTool) - Constructor for class databionics.esom.tool.legend.SavePictureWithLegendAction
 
SavePictureWithLegendAction2 - Class in databionics.esom.tool.legend
 
SavePictureWithLegendAction2(AbstractTool) - Constructor for class databionics.esom.tool.legend.SavePictureWithLegendAction2
 
SavePngFileAction - Class in databionics.esom.util.actions
Save a *.umx file
SavePngFileAction() - Constructor for class databionics.esom.util.actions.SavePngFileAction
Standard contructor
SavePngFileAction(String) - Constructor for class databionics.esom.util.actions.SavePngFileAction
constructor witrh given kind of saving
savePrefix - Variable in class databionics.esom.train.SOM
String with name of files during epochs
saveUMatrix - Variable in class databionics.esom.train.SOM
Boolean for saving U-Matrix during epochs
SaveUmxFileAction - Class in databionics.esom.util.actions
Save a *.umx file
SaveUmxFileAction() - Constructor for class databionics.esom.util.actions.SaveUmxFileAction
Standard contructor
saveWeights(String) - Method in class databionics.esom.grid.RectangularGrid
Save the weight vectors to a *.wts file
saveWeights(String, StringList) - Method in class databionics.esom.grid.RectangularGrid
Save the weight vectors to a *.wts file
scaling - Variable in class databionics.esom.neighborhood.Neighborhood
scaling factor for all weights
scrollPane - Variable in class databionics.esom.gui.MainFrame
the Java Swing ScrollPane
scrollPane - Variable in class databionics.esom.tool.BottomTab
 
scrollPane - Variable in class databionics.gui.LogPanel
scrolling around messages
scrollPane2 - Variable in class databionics.esom.tool.BottomTab
 
sdevs - Variable in class databionics.esom.train.Descriptives
vector of standard deviations
select() - Method in class databionics.esom.tool.AbstractTool
make this tool the active one, notify all relevant gui-components (ControlPanel, RenderPanel, BottomBar) when this method is overriden, it should call super.select()
select() - Method in class databionics.esom.tool.BottomTab
 
selected - Variable in class databionics.esom.tool.data.DataTool
flag for looking if selection active
SelectedBMsSaveFileAction - Class in databionics.esom.tool.data
 
SelectedBMsSaveFileAction(AbstractTool) - Constructor for class databionics.esom.tool.data.SelectedBMsSaveFileAction
 
selectedClasses - Variable in class databionics.esom.tool.data.SelectedDataTableModel
IntArrayList with selected classes
SelectedClsSaveAction - Class in databionics.esom.tool.data
 
SelectedClsSaveAction(AbstractTool) - Constructor for class databionics.esom.tool.data.SelectedClsSaveAction
 
selectedDataTableModel - Variable in class databionics.esom.tool.data.DataTool
model with selected data
SelectedDataTableModel - Class in databionics.esom.tool.data
 
SelectedDataTableModel(AbstractTool) - Constructor for class databionics.esom.tool.data.SelectedDataTableModel
constructor
selectedKeys - Variable in class databionics.esom.tool.data.SelectedDataTableModel
IntArray with selected keys
selectedLrn - Variable in class databionics.esom.tool.data.SelectedDataTableModel
the underlying data
SelectedLrnSaveAction - Class in databionics.esom.tool.data
 
SelectedLrnSaveAction(AbstractTool) - Constructor for class databionics.esom.tool.data.SelectedLrnSaveAction
 
selectedTool - Variable in class databionics.esom.gui.RenderPanel
 
selectGroup(int, int) - Method in class databionics.esom.tool.data.DataTable
selects group in all cases including start and end
selectIndex(int) - Method in class databionics.esom.tool.data.DataTable
selects index i in all cases
selection(IntArrayList) - Method in class databionics.esom.tool.data.DataTool
selects the rows which bms are selected
SelectionPanel - Class in databionics.esom.tool.data
 
SelectionPanel(AbstractTool) - Constructor for class databionics.esom.tool.data.SelectionPanel
 
set(int, int, double) - Method in class databionics.io.Array2DFile
Change element of matrix.
set(int, int) - Method in class databionics.io.ClassmaskFile
Set an index - class number pair
set(int, int) - Method in class databionics.io.ClsFile
Deprecated. is a wrapper to add only, wich should manage id right, check if code is still working. if yes change set to add. stammi
set(int, int, double) - Method in class databionics.math.Distances
set distance between i and j to d
setAllClasses(List) - Method in class databionics.io.DiagnosisFile
Set list of IntArrayLists with all class numbers.
setAlpha(float) - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
setApplication(Application) - Method in interface databionics.esom.gui.AbstractGuiComponent
 
setApplication(Application) - Method in class databionics.esom.gui.BottomBar
 
setApplication(Application) - Method in class databionics.esom.gui.MainFrame
 
setApplication(Application) - Method in class databionics.esom.gui.RenderPanel
 
setApplication(Application) - Method in class databionics.esom.gui.ToolLoader
 
setApplication(Application) - Method in class databionics.esom.tool.AbstractTool
 
setAutoRender(boolean) - Method in class databionics.esom.renderer.Renderer
Set the auto render flag
setBackgroundRenderer(BackgroundRenderer) - Method in class databionics.esom.renderer.Renderer
Set the background renderer
setBackgroundTool(BackgroundTool) - Method in class databionics.esom.renderer.Renderer
 
setBestMatches(BMFile) - Method in class databionics.esom.renderer.Renderer
Set the bestmatches in grid
setBestMatches(IntArrayList) - Method in class databionics.esom.train.SOM
Set the indices of best matching neurons for data points
setBestMatches(BMFile) - Method in class databionics.esom.train.SOM
Set the indices of best matching neurons for data points
setBinSize(int) - Method in class databionics.esom.tool.legend.HeightsLegend
 
setBmFilename(String) - Method in class databionics.esom.renderer.Renderer
 
setBMRenderers(StringList) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
setBmSearch(BmSearch) - Method in class databionics.esom.train.SOM
 
setBmSize(int) - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
Set the bestmatch size.
setBmSize(int) - Method in class databionics.esom.renderer.foreground.ForegroundList
 
setBmSize(int) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
setBmSize(int) - Method in class databionics.esom.renderer.Renderer
 
setBmStatNeeded(boolean) - Method in class databionics.esom.train.SOM
 
setBoldClasses(IntArrayList) - Method in class databionics.io.ClsFile
Set highlighted classes.
setBoldClasses(int[]) - Method in class databionics.io.ClsFile
Set highlighted classes.
setBottomTab(BottomTab) - Method in class databionics.esom.tool.AbstractTool
 
setCache(DoubleMatrix2D) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setCallback(CallBack) - Method in class databionics.esom.Cluster
 
setCallback(CallBack) - Method in class databionics.esom.Project
 
setCallback(CallBack) - Method in class databionics.esom.SlideShow
 
setCallback(CallBack) - Method in class databionics.esom.tool.AbstractTool
 
setCaseKey(String) - Method in class databionics.io.DiffCondition
Set CaseKey.
setCaseKey(String) - Method in class databionics.io.Rule
Set CaseKey.
setCaseName(String) - Method in class databionics.io.Rule
Set CaseName.
setCenter(boolean) - Method in class databionics.esom.train.SOM
 
setCenters(DoubleMatrix2D) - Method in class databionics.math.ParetoDensity
 
setCircle(boolean) - Method in class databionics.esom.renderer.foreground.BestmatchRenderer
 
setCircularBestmatches(boolean) - Method in class databionics.esom.renderer.foreground.ForegroundList
 
setCircularBestmatches(boolean) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
setClassColumnName(String) - Method in class databionics.io.LrnFile
Set class column nams.
setClasses(IntArrayList) - Method in class databionics.esom.renderer.Renderer
 
setClasses(IntArrayList) - Method in class databionics.io.ClassmaskFile
Set classes.
setClasses(int[]) - Method in class databionics.io.ClassmaskFile
Set classes.
setClasses(IntArrayList) - Method in class databionics.io.ClsFile
Set classes.
setClasses(int[]) - Method in class databionics.io.ClsFile
Set classes.
setClasses(IntArrayList) - Method in class databionics.io.LrnFile
Set classes.
setClasses(int[]) - Method in class databionics.io.LrnFile
Set classes.
setClassification(ClsFile) - Method in class databionics.esom.renderer.foreground.NamesRenderer
 
setClassification(ClsFile) - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
setClassList(IntArrayList) - Method in class databionics.esom.train.BestMatchHit
 
setClassmask(ClassmaskFile) - Method in class databionics.esom.tool.classmask.ClassmaskRenderer
 
setClassName(String) - Method in class databionics.io.DiffCondition
Set ClassName.
setClassName(String) - Method in class databionics.io.Rule
Set ClassName.
setClean(boolean) - Method in class databionics.project.Project
Set if project has to be named before saving
setClickMode(boolean) - Method in class databionics.esom.tool.AbstractTool
 
setClip(double) - Method in class databionics.esom.renderer.Renderer
Sets the height percentage where the heigths matrix shall be clipped
setClipping(boolean) - Method in class databionics.esom.renderer.Renderer
 
setClonedBgImage(BufferedImage) - Method in class databionics.esom.renderer.Renderer
 
setClrFourtimes(Color) - Method in class databionics.esom.tool.island.IslandRenderer
 
setClrFourtimes(Color) - Method in class databionics.esom.tool.island.IslandTool
 
setClrThreetimes(Color) - Method in class databionics.esom.tool.island.IslandRenderer
 
setClrThreetimes(Color) - Method in class databionics.esom.tool.island.IslandTool
 
setClrTwice(Color) - Method in class databionics.esom.tool.island.IslandRenderer
 
setClrTwice(Color) - Method in class databionics.esom.tool.island.IslandTool
 
setClrWater(Color) - Method in class databionics.esom.tool.island.IslandRenderer
 
setClrWater(Color) - Method in class databionics.esom.tool.island.IslandTool
 
setClrZeros(Color) - Method in class databionics.esom.tool.island.IslandRenderer
 
setClrZeros(Color) - Method in class databionics.esom.tool.island.IslandTool
 
setClusters(int) - Method in class databionics.math.ParetoDensity
Number of clusters, used for radius correction
setColor(Color) - Method in class databionics.io.DataClass
Set the class color.
setColorify(float) - Method in class databionics.esom.renderer.Renderer
 
setColorifying(boolean) - Method in class databionics.esom.renderer.Renderer
 
setColorMap(ColorMapping) - Method in class databionics.esom.renderer.Renderer
 
setColorRenderer(boolean) - Method in class databionics.esom.renderer.RendererTool
 
setColors(ColorTable) - Method in class databionics.esom.renderer.Renderer
Set the color table
setColorSteps(int) - Method in class databionics.esom.renderer.Renderer
Set the number of color-steps to be made
setColorTable(ColorTable) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
setColorTable(ColorTable) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
setCols(int) - Method in class databionics.io.BMFile
Set the value of cols.
setColumn(int) - Method in class databionics.io.Bestmatch
Set column of best match.
setColumns(int) - Method in class databionics.esom.grid.RectangularGrid
Set number of columns
setCommand(String) - Method in class databionics.modules.Tool
Set command to run this tool
setComment(StringList) - Method in class databionics.io.BaseFile
Change the comment of file.
setComponent(int) - Method in class databionics.esom.renderer.background.ComponentRenderer
Set the dimension to use for rendering.
setComponents(IntArrayList) - Method in class databionics.esom.renderer.Renderer
Set the selected weight components.
setComponents(String) - Method in class databionics.esom.renderer.Renderer
Set the selected weight components as a string.
setCompos(boolean) - Method in class databionics.esom.gui.RenderPanel
 
setConditions(List) - Method in class databionics.io.Rule
Set Conditions.
setConstant(int) - Method in class databionics.esom.train.search.BmSearch
 
setConstant(int) - Method in class databionics.esom.train.search.LocalBmSearch
 
setConstant(int) - Method in class databionics.esom.train.search.NoBmSearch
 
setConstant(int) - Method in class databionics.esom.train.search.SimpleBmSearch
 
setConstant(boolean) - Method in class databionics.modules.Parameter
Set flag whether this parameter should be constant or changeable
setContours(boolean) - Method in class databionics.esom.renderer.Renderer
Set the contour flag
setControlButton(JButton) - Method in class databionics.esom.tool.AbstractTool
 
setCounter(int) - Static method in class databionics.esom.train.search.BmSearchStat
 
setCreatorPanel(ProtoPanel) - Method in class databionics.esom.tool.AbstractTool
Set the CreatorPanel belonging to this tool.
setCtrlAccelerator(JMenuItem, char) - Method in class databionics.esom.tool.AbstractTool
Sets the ctrlaccelerator to the menuitems
setCurrentClass(DataClass) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
setCurrentclass(DataClass) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
setCustomCursor(boolean, boolean) - Method in class databionics.esom.gui.RenderPanel
sets the custom cursor
setCustomCursor(boolean, boolean) - Method in class databionics.esom.tool.ProtoPanel
 
setData(Object) - Method in interface databionics.esom.tool.AbstractCallback
 
setData(Object) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
setData(ClassmaskFile) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
setData(ClassmaskFile) - Method in class databionics.esom.tool.classmask.ClassmaskToolRenderer
 
setData(Object) - Method in class databionics.esom.tool.component.ComponentTool
 
setData(Object) - Method in class databionics.esom.tool.data.DataTool
 
setData(Object) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
setData(ClsFile) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
setData(Object) - Method in class databionics.esom.tool.info.InfoTool
donothing
setData(Object) - Method in class databionics.esom.tool.island.IslandTool
 
setData(DoubleMatrix2D) - Method in class databionics.esom.tool.island.IslandToolRenderer
 
setData(Object) - Method in class databionics.esom.tool.legend.LegendTool
 
setData(Object) - Method in class databionics.esom.tool.projection.ClassifyCallback
sets Data if needed
setData(Object) - Method in class databionics.esom.tool.projection.ProjectCallback
sets Data if needed
setData(Object) - Method in class databionics.esom.tool.projection.ProjectionTool
 
setData(Object) - Method in class databionics.esom.tool.slideshow.SlideShowCallback
sets Data if needed
setData(Object) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setData(DoubleMatrix2D) - Method in class databionics.esom.train.Descriptives
Set data and calculate statistics.
setData(DoubleMatrix2D) - Method in class databionics.esom.train.SOM
Set the matrix with the training data, patterns in rows.
setData(Object) - Method in class databionics.esom.train.TrainCallback
sets data if needed
setData(Object) - Method in interface databionics.gui.CallBack
sets data if needed
setData(DoubleMatrix2D) - Method in class databionics.io.Array2DFile
Set 2D matrix.
setData(double[][]) - Method in class databionics.io.Array2DFile
Set 2D matrix as array
setData(List) - Method in class databionics.io.ListFile
Set the data list.
setData(List) - Method in class databionics.io.MapFile
Change the data in the list and the map.
setData(DoubleMatrix2D) - Method in class databionics.math.Distances
 
setData(DoubleMatrix1D) - Method in class databionics.math.Distances
 
setData(DoubleMatrix1D[]) - Method in class databionics.math.Distances
 
setData(DenseDoubleMatrix1D) - Method in class databionics.math.ParetoDensity
set one dimensional data
setData(DenseDoubleMatrix1D[]) - Method in class databionics.math.ParetoDensity
set data matrix
setData(DoubleMatrix2D) - Method in class databionics.math.ParetoDensity
set data matrix with vectors in rows
setDataTable(AbstractToolTable) - Method in class databionics.esom.tool.AbstractTool
 
setDataTableModel(AbstractTableModel) - Method in class databionics.esom.tool.AbstractTool
Get the DataTabelModel.
setDataTool(DataTool) - Method in class databionics.esom.renderer.Renderer
 
setDefault(String) - Method in class databionics.modules.AbstractStringParameter
Set the default value
setDefault(float) - Method in class databionics.modules.FloatParameter
Set the default value
setDefault(Float) - Method in class databionics.modules.FloatParameter
Set the default value
setDefault(int) - Method in class databionics.modules.IntParameter
Set the default value
setDefault(Integer) - Method in class databionics.modules.IntParameter
Set the default value
setDefault(MultipleChoiceElement) - Method in class databionics.modules.MultipleChoiceParameter
Set the default value
setDefault(Boolean) - Method in class databionics.modules.SwitchParameter
Set the default value
setDefault(boolean) - Method in class databionics.modules.SwitchParameter
Set the default value
setDefaultInstance(String) - Static method in class databionics.project.DataManager
sets the default instance identifier
setDefines(IntArrayList) - Method in class databionics.io.LrnFile
Set defines.
setDefines(int[]) - Method in class databionics.io.LrnFile
Set defines.
setDefines() - Method in class databionics.io.LrnFile
Set automatically generated defines.
setDependency(String, String) - Static method in class databionics.project.DataManager
make an Object dependent to another Ovject, such that chaging the specified Object will remove the dependent
setDependency(String, String, String) - Static method in class databionics.project.DataManager
make an Object dependent to another Ovject, such that chaging the specified Object will remove the dependent.
setDependency(String, String[]) - Static method in class databionics.project.DataManager
make a list of Objects in workspace depending on another Object (s.
setDependency(String, String[], String) - Static method in class databionics.project.DataManager
make a list of Objects in workspace depending on another Object (s.
setDescription(String) - Method in class databionics.io.FileExtensionFilter
Sets the human readable description of this filter.
setDescription(String) - Method in class databionics.io.FileType
Set the description of file type
setDescription(String) - Method in class databionics.io.KeyName
Set description of key.
setDescription(String) - Method in class databionics.modules.Module
Set the description
setDescription(String) - Method in class databionics.modules.MultipleChoiceElement
Set the description
setDescription(String) - Method in class databionics.modules.Parameter
Set decription to be displayed in dialogs
setDescription(String) - Method in class databionics.modules.Tool
Set the description
setDescription(String) - Method in class databionics.project.Project
Set project's description
setDim(int) - Method in class databionics.esom.grid.Grid
Set the value of dim.
setDim(int) - Method in class databionics.esom.grid.MatrixGrid
Set the value of dim.
setDimName(String) - Method in class databionics.io.Condition
Set DimName.
setDimName(String) - Method in class databionics.io.IntervalCondition
Set DimName.
setDisplayPanel(JPanel) - Method in class databionics.esom.tool.AbstractTool
 
setDistanceFunction(VectorVectorFunction) - Method in class databionics.esom.grid.Grid
Set the distance function in data space
setDistanceFunction(VectorVectorFunction, String) - Method in class databionics.esom.grid.Grid
Set the distance function in data space
setDistanceFunction(ThresholdVectorVectorFunction) - Method in class databionics.esom.train.SOM
Set the distance function in data space
setDistanceFunction(VectorVectorFunction) - Method in class databionics.math.Distances
set the function to calculate distances.
setDistances(DoubleMatrix1D) - Method in class databionics.esom.train.SOM
 
setDragMode(boolean) - Method in class databionics.esom.tool.AbstractTool
 
setDrawing(boolean) - Method in class databionics.esom.tool.AbstractTool
set the drawing mode for this tool.
setDrawing(boolean) - Method in class databionics.esom.tool.AbstractToolRenderer
 
setDrawing(boolean) - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
setDrawing(boolean) - Method in class databionics.esom.tool.dataclass.DataclassTool
 
setDrawing(boolean) - Method in class databionics.esom.tool.island.IslandTool
 
setDrawingLetters(boolean) - Method in class databionics.esom.tool.dataclass.ClassBestmatchRenderer
 
setEnd() - Method in class databionics.modules.Job
Set end to current date and time.
setEnd(Date) - Method in class databionics.modules.Job
Set end to this date and time
setEpochs(int) - Method in class databionics.esom.train.SOM
Set the number of training epochs.
setExt(String) - Method in class databionics.io.FileType
Set the extension of file type
setExtensionListInDescription(boolean) - Method in class databionics.io.FileExtensionFilter
Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
setFailingCondition(String) - Method in class databionics.io.Explanation
Set the failing condition.
setFailingRule(String) - Method in class databionics.io.Explanation
Set the failing rule.
setFavoriteColor(Color) - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Set the favourite color.
setFavoriteColor(Color) - Method in class databionics.esom.tool.AbstractToolRenderer
 
setFgRenderer(ForegroundRenderer) - Method in class databionics.esom.tool.AbstractToolRenderer
 
setFile(BaseFile) - Method in class databionics.project.FileSlot
Set the file object
setFileData(FileType, BaseFile) - Method in class databionics.project.Project
Set data for a filetype
setFilename(String) - Method in class databionics.esom.tool.AbstractTool
 
setFilename(String) - Method in class databionics.io.BaseFile
Change the name of the file.
setFilename(String) - Method in class databionics.io.ColorTable
Change the name of the file.
setFileName(FileType, String) - Method in class databionics.project.Project
Set filename for a filetype and fire ChangeEvent
setFlag(String, String) - Static method in class databionics.project.DataManager
set a flag for specified DataObject in default instance
setFlag(String, String, String) - Static method in class databionics.project.DataManager
set a flag for specified DataObject in
setFontSize(int) - Method in class databionics.esom.renderer.foreground.NamesRenderer
Set the bestmatch size.
setForegroundNames(StringList) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Set the foreground names
setForegroundTool(ForegroundTool) - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
 
setForegroundTool(ForegroundTool) - Method in class databionics.esom.renderer.Renderer
 
setFrame(boolean) - Method in class databionics.esom.renderer.foreground.ForegroundTool
 
setFrame(boolean) - Method in class databionics.esom.renderer.Renderer
Deprecated.  
setFrameColor(Color) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Set frame color
setFrameColor(Color) - Method in class databionics.esom.renderer.foreground.FrameRenderer
Set the frame color
setGradient(String) - Method in class databionics.esom.renderer.RendererTool
Set the gradient
setGrid(Grid) - Method in class databionics.esom.renderer.Renderer
Set the grid of weight vectors.
setGrid(Grid) - Method in class databionics.esom.train.SOM
Set the grid of weight vectors.
setGridChanged(boolean) - Method in class databionics.esom.renderer.Renderer
 
setH(int) - Method in class databionics.esom.train.HybridBatchSOM
 
setHexagonal(boolean) - Method in class databionics.esom.renderer.Renderer
Set the hexagonal flag
setHighlightedBms(IntArrayList) - Method in class databionics.esom.tool.data.DataTool
 
setHighlightedBms(IntArrayList) - Method in class databionics.esom.tool.data.HighlightRenderer
 
setHits(int) - Method in class databionics.esom.train.BestMatchHit
sets the number of hits, only used to set to zero
setIconName(String) - Method in class databionics.modules.Module
Set the icon
setImage(BufferedImage) - Method in class databionics.esom.gui.PicPanel
Set the image which should be displayed
setImage(BufferedImage) - Method in class databionics.esom.renderer.Renderer
 
setIndex(int) - Method in class databionics.io.DataItem
Set the index of data point.
setInfoTool(InfoTool) - Method in class databionics.esom.renderer.Renderer
 
setInit(String) - Method in class databionics.esom.train.SOM
Set the method of initialization for the weights
setIslandMatrix(DoubleMatrix2D) - Method in class databionics.esom.tool.island.IslandRenderer
 
setJobParameters() - Method in class databionics.esom.gui.util.RunDialog
Set the job's parameters from the input fields
setJobParameters() - Method in class databionics.gui.RunDialog
Set the job's parameters from the input fields
setK(int) - Method in class databionics.esom.train.KBatchSOM
 
setKeyColumnName(String) - Method in class databionics.io.LrnFile
Set key column nams.
setKeys(IntArrayList) - Method in class databionics.esom.train.SOM
Set the list of unique keys for the data patterns.
setKeys(IntArrayList) - Method in class databionics.io.ClassmaskFile
Set keys.
setKeys(int[]) - Method in class databionics.io.ClassmaskFile
Set keys.
setKeys() - Method in class databionics.io.ClassmaskFile
Add automatically generated keys.
setKeys(IntArrayList) - Method in class databionics.io.ClsFile
Set keys.
setKeys(int[]) - Method in class databionics.io.ClsFile
Set keys.
setKeys() - Method in class databionics.io.ClsFile
Add automatically generated keys.
setKeys(IntArrayList) - Method in class databionics.io.LrnFile
Set keys.
setKeys(int[]) - Method in class databionics.io.LrnFile
Set keys.
setKeys() - Method in class databionics.io.LrnFile
Add automatically generated keys.
setLegendTool(LegendTool) - Method in class databionics.esom.renderer.Renderer
 
setLineSize(int) - Method in class databionics.esom.renderer.foreground.LineRenderer
Set the bestmatch size.
setLoader(ToolLoader) - Method in class databionics.esom.gui.MainFrame
 
setLoader(ToolLoader) - Method in class databionics.esom.gui.RenderPanel
 
setLoader(ToolLoader) - Method in class databionics.esom.gui.util.RunDialog
 
setLoader(ToolLoader) - Method in class databionics.esom.renderer.background.BackgroundTool
 
setLoader(ToolLoader) - Method in class databionics.esom.tool.AbstractTool
 
setLoader(ToolLoader) - Method in class databionics.esom.train.TrainAction
 
setLoader(ToolLoader) - Method in class databionics.esom.train.TrainCallback
 
setLocale(Locale) - Method in class databionics.io.BaseFile
Change the current locale.
setLogger(Logger) - Method in class databionics.gui.LogPanel
Set the logger to add appender to
setLogger(String) - Method in class databionics.gui.LogPanel
Set the logger to add appender to
setLogger(Class) - Method in class databionics.gui.LogPanel
Set the logger to add appender to
setLogPanel(LogPanel) - Method in class databionics.esom.gui.ToolLoader
 
setLongName(String) - Method in class databionics.modules.Parameter
Set the long name to be used as "--longname"
setLRenderer(LegendRenderer) - Method in class databionics.esom.tool.legend.Legend
 
setLrnChanged(boolean) - Method in class databionics.esom.renderer.Renderer
 
setLrnFile(LrnFile) - Method in class databionics.esom.renderer.Renderer
 
setLrnFile(LrnFile) - Method in class databionics.esom.tool.data.DataTableModel
sets the lrnFile
setLrnFilename(String) - Method in class databionics.esom.renderer.Renderer
 
setLrnIdx(int) - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
setManual(boolean) - Method in class databionics.esom.tool.data.DataTool
 
setManualKeys(IntArrayList) - Method in class databionics.esom.tool.data.DataTool
 
setManualNames(ArrayList) - Method in class databionics.esom.tool.data.DataTool
 
setManualNamesFile(NamesFile) - Method in class databionics.esom.tool.data.DataTool
 
setMap(Map) - Method in class databionics.io.MapFile
Change the data in the map and the list.
setMapspace(int) - Method in class databionics.io.DataClass
 
setMaskForegrounds(ForegroundList) - Method in class databionics.esom.renderer.Renderer
 
setMatrix(DoubleMatrix2D) - Method in class databionics.esom.renderer.Renderer
Set the matrix
setMatrix(DoubleMatrix2D) - Method in class databionics.esom.tool.ProtoPanel
 
setMax(int, double) - Method in class databionics.io.ColorStatistics
 
setMax(float) - Method in class databionics.modules.FloatParameter
Set the maximum value
setMax(Float) - Method in class databionics.modules.FloatParameter
Set the maximum value
setMax(int) - Method in class databionics.modules.IntParameter
Set the maximum value
setMax(Integer) - Method in class databionics.modules.IntParameter
Set the maximum value
setMax(int) - Method in class databionics.project.FileSlot
sets the max number of history elements
setMaximum(Float) - Method in class databionics.io.Condition
Set Max.
setMaximum(Float) - Method in class databionics.io.IntervalCondition
Set Max.
setMessage(String) - Method in class databionics.esom.gui.util.MessagePanel
 
setMethod(String) - Method in class databionics.esom.tool.legend.PictureLegend
 
setMethod(int) - Method in class databionics.esom.tool.slideshow.SlideShow
 
setMin(int, double) - Method in class databionics.io.ColorStatistics
 
setMin(float) - Method in class databionics.modules.FloatParameter
Set the minimum value
setMin(Float) - Method in class databionics.modules.FloatParameter
Set the minimum value
setMin(int) - Method in class databionics.modules.IntParameter
Set the minimum value
setMin(Integer) - Method in class databionics.modules.IntParameter
Set the minimum value
setMinimum(Float) - Method in class databionics.io.Condition
Set Min.
setMinimum(Float) - Method in class databionics.io.IntervalCondition
Set Min.
setModel(TableModel) - Method in class databionics.esom.tool.data.DataTable
 
setModules(Modules) - Method in class databionics.project.Project
Set modules
setMoveCallback(CallBack) - Method in class databionics.esom.tool.AbstractTool
 
setName(String) - Method in class databionics.esom.gui.util.GradientComboBox
Set a color table by name
setName(String) - Method in class databionics.io.DataClass
Set the name of DataClass.
setName(String) - Method in class databionics.io.FileType
Set the name of file type
setName(String) - Method in class databionics.io.KeyName
Set name of key.
setName(String) - Method in class databionics.io.Rule
Set name of rule.
setName(String) - Method in class databionics.modules.Module
Set the name
setName(String) - Method in class databionics.modules.Parameter
Set the name to be used as "-name"
setName(String) - Method in class databionics.modules.Tool
Set the name
setName(String) - Method in class databionics.project.FileSlot
Add a file to this slot
setName(String) - Method in class databionics.project.Project
Set project's name
setNames(NamesFile) - Method in class databionics.esom.renderer.Renderer
 
setNames(StringList) - Method in class databionics.esom.tool.bminfo.BMInfoTool
 
setNames(StringList) - Method in class databionics.io.LrnFile
Set names.
setNames() - Method in class databionics.io.LrnFile
Set automatically generated names.
setNeighborhood(Neighborhood) - Method in class databionics.esom.train.SOM
Set the neighborhood kernel function.
setNoForeground(boolean) - Method in class databionics.esom.renderer.Renderer
 
setNotClassName(String) - Method in class databionics.io.DiffCondition
Set name of class excluded by this rule.
setNotClassName(String) - Method in class databionics.io.DiffRule
Set name of class excluded by this rule.
setNotIn(String) - Method in class databionics.io.Explanation
Set the class not in.
setNumberFormat(NumberFormat) - Method in class databionics.esom.train.SOM
Set the number format
setOffline(boolean) - Method in class databionics.esom.train.HybridBatchSOM
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.search.BmSearch
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.search.LocalBmSearch
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.search.MuchFasterLearning
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.search.MuchFasterLearning2
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.search.NoBmSearch
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.search.SimpleBmSearch
 
setOldBestmatches(IntArrayList) - Method in class databionics.esom.train.SOM
 
setOnline(boolean) - Method in class databionics.esom.train.HybridBatchSOM
 
setOnline(boolean) - Method in class databionics.esom.train.SOM
 
setOnly(boolean) - Method in class databionics.esom.util.actions.LoadUmxFileAction
 
setOnly(boolean) - Method in class databionics.esom.util.actions.LoadWtsFileAction
 
setOperatingSystem(String) - Method in class databionics.modules.Tool
Set the os
setOperator(String) - Method in class databionics.io.Rule
Set Operator.
setOpinionMode(boolean) - Method in class databionics.esom.gui.ToolLoader
 
setOptional(boolean) - Method in class databionics.modules.Parameter
Set flag whether this parameter is optional or required
setOverlapMatrix(DoubleMatrix2D) - Method in class databionics.esom.tool.island.IslandRenderer
 
setOverlapMode(boolean) - Method in class databionics.esom.tool.island.IslandRenderer
 
setOverlapMode(boolean) - Method in class databionics.esom.tool.island.IslandTool
 
setParetoRadius() - Method in class databionics.math.ParetoDensity
Calculate and set Pareto radius.
setPartCls(ClsFile) - Method in class databionics.esom.tool.data.DataTool
 
setPartLrn(LrnFile) - Method in class databionics.esom.tool.data.DataTool
 
setPath(String) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setPercentile(int) - Method in class databionics.esom.renderer.background.PMatrixRenderer
Set the percentile parameter
setPermute(boolean) - Method in class databionics.esom.train.SOM
Set the flag whether to permute data vectors before each epoch.
setPictures(PicturesFile) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setPicturesFilename(String) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setPnlFGColor(JPanel) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Set the fg color panel
setPolygonMode(boolean) - Method in class databionics.esom.tool.AbstractTool
 
setPosition(int) - Method in class databionics.esom.tool.slideshow.SlideShow
 
setPosttileForegrounds(ForegroundList) - Method in class databionics.esom.renderer.Renderer
 
setPrefix(String) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setPretileForegrounds(ForegroundList) - Method in class databionics.esom.renderer.Renderer
 
setProject(Project) - Method in class databionics.Application
Sets the current poject holding filename of different types and optionally the data from the files.
setProject(Project) - Method in class databionics.esom.gui.ToolLoader
 
setPromapspace(double) - Method in class databionics.io.DataClass
 
setRadius(int) - Method in class databionics.esom.neighborhood.Neighborhood
Set the maximum distance from bestmatch on grid to be considered
setRadius(double) - Method in class databionics.esom.renderer.background.PMatrixRenderer
Set the radius parameter.
setRadius() - Method in class databionics.esom.renderer.background.PMatrixRenderer
Set the radius parameter to the pareto radius
setRadius(double) - Method in class databionics.math.ParetoDensity
Set radius directly
setRadius(int) - Method in class databionics.math.ParetoDensity
Set radius to distance percentile
setRadiusCooling(Cooling) - Method in class databionics.esom.train.SOM
Set the cooling strategy of the neighborhood radius.
setRateCooling(Cooling) - Method in class databionics.esom.train.SOM
Set the cooling strategy of learning rate.
setReDraw(boolean) - Method in class databionics.esom.renderer.Renderer
 
setRelation(String) - Method in class databionics.io.ArffFile
Set relation name
setReMask(boolean) - Method in class databionics.esom.renderer.Renderer
 
setRenderer(Renderer) - Method in class databionics.esom.gui.MainFrame
 
setRenderer(Renderer) - Method in class databionics.esom.gui.RenderPanel
Sets the renderer
setRenderer(Renderer) - Method in class databionics.esom.gui.ToolLoader
 
setRenderer(Renderer) - Method in class databionics.esom.renderer.background.BackgroundRenderer
Set reference to the main renderer.
setRenderer(Renderer) - Method in class databionics.esom.renderer.foreground.ForegroundRenderer
Set the renderer
setRenderer(Renderer) - Method in class databionics.esom.tool.AbstractTool
 
setRenderer(Renderer) - Method in class databionics.esom.tool.legend.Legend
 
setRenderer(int, int) - Method in class databionics.esom.tool.legend.LegendRenderer
 
setRenderer(Renderer) - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
setRenderer(Renderer) - Method in class databionics.esom.tool.ProtoPanel
 
setRenderer(Renderer) - Method in class databionics.esom.train.TrainCallback
 
setRenderPanel(RenderPanel) - Method in class databionics.esom.gui.ToolLoader
 
setRenderPanel(RenderPanel) - Method in class databionics.esom.tool.ProtoPanel
 
setRenderPosition(int) - Method in class databionics.esom.renderer.foreground.ForegroundList
Set the RenderPosition.
setRePostFore(boolean) - Method in class databionics.esom.renderer.Renderer
 
setRePreFore(boolean) - Method in class databionics.esom.renderer.Renderer
 
setReRender(boolean) - Method in class databionics.esom.renderer.Renderer
 
setReTile(boolean) - Method in class databionics.esom.renderer.Renderer
 
setReZoom(boolean) - Method in class databionics.esom.renderer.Renderer
 
setRow(int) - Method in class databionics.io.Bestmatch
Set row of best match.
setRows(int) - Method in class databionics.esom.grid.RectangularGrid
Set number of rows
setRows(int) - Method in class databionics.io.BMFile
Set the number of rows in the map
setSameHits(int) - Method in class databionics.esom.train.BestMatchHit
sets the number of hits, only used to set to zero
setSaved(boolean) - Method in class databionics.project.Project
Set if project has changed after last saving
setSaveEpoch(int) - Method in class databionics.esom.train.SOM
Set number of epochs after which a *.bm and a *.wts are saved
setSaveEpochBoolean() - Method in class databionics.esom.train.SOM
sets the boolean flag true, because we are saving during epochs
setSavePrefix(String) - Method in class databionics.esom.train.SOM
Set the prefix for the filename used to regularily save *.bm, *.wts and *.umx files
setSaveUMatrix(boolean) - Method in class databionics.esom.train.SOM
set the flag for saving a U-Matrix every nth epoch
setScaling(double) - Method in class databionics.esom.neighborhood.Neighborhood
Set the scaling factor for all weights
setSelected(boolean) - Method in class databionics.esom.tool.data.DataTool
 
setSelectedTool(AbstractTool) - Method in interface databionics.esom.gui.AbstractGuiComponent
 
setSelectedTool(AbstractTool) - Method in class databionics.esom.gui.BottomBar
selects the given Tool
setSelectedTool(AbstractTool) - Method in class databionics.esom.gui.MainFrame
 
setSelectedTool(AbstractTool) - Method in class databionics.esom.gui.RenderPanel
 
setSelection(IntArrayList) - Method in class databionics.esom.tool.data.SelectedDataTableModel
sets the selected data in selectedLrn
setShow(SlideShow) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setShowProgress(boolean) - Method in class databionics.gui.LogPanel
Set flag whether progress bar is visible or not
setShowProgress(boolean) - Method in class databionics.modules.Tool
Set flag whether show progress when running this tool
setSignificance(Float) - Method in class databionics.io.Condition
Set significance.
setSignificance(Float) - Method in class databionics.io.IntervalCondition
Set significance.
setSize(int) - Method in class databionics.esom.grid.Grid
Set the value of size.
setSize(int) - Method in class databionics.esom.grid.MatrixGrid
Set the value of size.
setSlideCacheBm(BMFile) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSlideList(Vector) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSlideListBm(Vector) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSlideLoaded(boolean) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSlidePictures(Vector) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSlideShow(boolean) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSlideWts(Vector) - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
setSmoothFactor(int) - Method in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
Set the smooth parameter
setSOM(SOM) - Method in class databionics.esom.train.search.BmSearch
 
setSpeed(int) - Method in class databionics.esom.tool.slideshow.SlideShow
 
setStandAlone(boolean) - Method in class databionics.Application
Set flag whether app is run from main
setStart() - Method in class databionics.modules.Job
Set start to current date and time
setStart(Date) - Method in class databionics.modules.Job
Set start to this date and time
setStopped(boolean) - Method in class databionics.esom.tool.slideshow.SlideShow
 
setTemplate(String) - Method in class databionics.modules.OutputFileParameter
Set the filename template
setThread(PlayThread) - Method in class databionics.esom.tool.slideshow.SlideShow
 
setTiled(boolean) - Method in class databionics.esom.renderer.Renderer
Set the tiled flag
setTiled(boolean) - Method in class databionics.esom.renderer.RendererTool
Set tiled mode.
setTiledMode(boolean) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Set tiled flag
setToolBar(JToolBar) - Method in class databionics.esom.tool.AbstractTool
 
setToroid(boolean) - Method in class databionics.esom.renderer.Renderer
 
setToroidLayout(String) - Method in class databionics.esom.renderer.Renderer
Set the toroid layout
setTransparency(boolean) - Method in class databionics.esom.tool.island.IslandRenderer
 
setTransparency(boolean) - Method in class databionics.esom.tool.island.IslandToolRenderer
 
setType(String) - Method in class databionics.esom.gui.util.MessagePanel
 
setType(FileType) - Method in class databionics.modules.AbstractFileParameter
Set the file type
setType(FileType) - Method in class databionics.project.FileSlot
Set filetype
setUmxLoaded(boolean) - Method in class databionics.esom.renderer.background.BackgroundTool
Set the flag if a height matrix (*.umx) but no Grid (*.wts) is loaded.
setUmxLoaded(boolean) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Set flag whether umx instead of wts is loaded With umx no opinion foreground can be used.
setUmxLoaded(boolean) - Method in class databionics.esom.renderer.RendererTool
 
setValue(String) - Method in class databionics.modules.AbstractStringParameter
Set the value
setValue(float) - Method in class databionics.modules.FloatParameter
Set the value.
setValue(Float) - Method in class databionics.modules.FloatParameter
Set the value.
setValue(String) - Method in class databionics.modules.FloatParameter
Set the value as a string If var is less than the minimum, set the minimum instead and throw LessThanMinException to issue a warning.
setValue(String) - Method in class databionics.modules.InputFileParameter
Set the value.
setValue(int) - Method in class databionics.modules.IntParameter
Set the value.
setValue(Integer) - Method in class databionics.modules.IntParameter
Set the value.
setValue(String) - Method in class databionics.modules.IntParameter
Set the value as a string.
setValue(String) - Method in class databionics.modules.MultipleChoiceElement
Set the value
setValue(MultipleChoiceElement) - Method in class databionics.modules.MultipleChoiceParameter
Set the value if it is in the list of allowed values.
setValue(String) - Method in class databionics.modules.OutputFileParameter
Set the value.
setValue(Boolean) - Method in class databionics.modules.SwitchParameter
Set the value
setValue(boolean) - Method in class databionics.modules.SwitchParameter
Set the value
setValueAt(Object, int, int) - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
manages values, given to the table
setValueAt(Object, int, int) - Method in class databionics.esom.tool.component.ComponentTableModel
handles value, which is set to one cell
setValueAt(Object, int, int) - Method in class databionics.esom.tool.data.DataTableModel
handles value, which is set to one cell
setValueAt(Object, int, int) - Method in class databionics.esom.tool.data.SelectedDataTableModel
handles value, which is set to one cell
setValueAt(Object, int, int) - Method in class databionics.esom.tool.dataclass.DataclassTableModel
manages given values
setValueAt(Object, int, int) - Method in class databionics.esom.tool.info.InfoToolTableModel
 
setValueAt(Object, int, int) - Method in class databionics.esom.tool.island.IslandTableModel
manages values, given to the table
setValueAt(Object, int, int) - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
setView(int) - Method in class databionics.esom.tool.legend.Legend
Selects one of the LegendRenderers given in the renderList
setWorkDir(String) - Method in class databionics.Application
Sets the curent working directory.
setWorkdirFromFilename(String) - Method in class databionics.esom.Analyze
 
setWtsFilename(String) - Method in class databionics.esom.renderer.Renderer
 
setX(int) - Method in class databionics.esom.tool.bminfo.BMInfoPanel
 
setX(int) - Method in class databionics.esom.tool.ProtoPanel
 
setY(int) - Method in class databionics.esom.tool.bminfo.BMInfoPanel
 
setY(int) - Method in class databionics.esom.tool.ProtoPanel
 
setZoom(int) - Method in class databionics.esom.renderer.Renderer
Set the zoom factor
shift(int, int) - Method in class databionics.esom.grid.ToroidRectangularGrid
shift grid by relative coordinates
shiftX - Variable in class databionics.esom.renderer.Renderer
Horizontal shift of original matrix (only in toroid mode)
shiftY - Variable in class databionics.esom.renderer.Renderer
Vertical shift of original matrix (only in toroid mode)
show() - Method in class databionics.esom.gui.util.RunDialog
Overridden show method.
show - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
show() - Method in class databionics.gui.RunDialog
Overridden show method.
ShowAboutAction - Class in databionics.esom.util.actions
Creates a window with the about information
ShowAboutAction() - Constructor for class databionics.esom.util.actions.ShowAboutAction
Default Constructor
showBackground(String) - Method in class databionics.esom.renderer.background.BackgroundTool
 
ShowHelpAction - Class in databionics.esom.util.actions
Evokes the help documentation
ShowHelpAction() - Constructor for class databionics.esom.util.actions.ShowHelpAction
 
showImage() - Method in class databionics.esom.gui.RenderPanel
Displays the actual Image
showImage(BufferedImage) - Method in class databionics.esom.gui.RenderPanel
Displays the actual Image
showPopup(MouseEvent) - Method in class databionics.esom.tool.AbstractToolTable
shows the pop up menu after a mouse event
showPopup(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTable
shows the pop up menu after a mouse event
showPopup(MouseEvent) - Method in class databionics.esom.tool.component.ComponentTable
 
showPopup(MouseEvent) - Method in class databionics.esom.tool.data.DataTable
shows the popUp menue
showPopup(MouseEvent) - Method in class databionics.esom.tool.dataclass.DataclassTable
shows the pop up menu after a mouse event
showPopup(MouseEvent) - Method in class databionics.esom.tool.info.InfoToolTable
 
showPopup(MouseEvent) - Method in class databionics.esom.tool.island.IslandTable
 
showPopup(MouseEvent) - Method in class databionics.esom.tool.legend.Legend
 
showPopup(MouseEvent) - Method in class databionics.esom.tool.slideshow.SlideShowInfoTable
 
showProgress - Variable in class databionics.gui.LogPanel
flag whether to show progress bar
showProgress - Variable in class databionics.modules.Tool
boolean: true, if there is a parameter, which shows the progress while running tool
showProgress() - Method in class databionics.modules.Tool
Get flag whether show progress when running this tool
showTool(String) - Method in class databionics.esom.gui.ToolLoader
 
significance - Variable in class databionics.io.Condition
The significance value of the rule.
significance - Variable in class databionics.io.IntervalCondition
The significance value of the rule.
similar(String, String) - Static method in class databionics.text.SimilarString
Check whether the Strings are similar As similar qualifies: 1) equal 2) both not empty and contained int one another 3) trigram metric greater than 0.5
similarIndexOf(String) - Method in class databionics.text.StringList
Get index of string similar to value.
SimilarityTool - Class in databionics.esom.tool.similarity
tool for getting bestmatches from one district
SimilarityTool(boolean, Application) - Constructor for class databionics.esom.tool.similarity.SimilarityTool
 
SimilarString - Class in databionics.text
A Strings that can be compared to other strings byte common metrics.
SimilarString() - Constructor for class databionics.text.SimilarString
Standard constructor without arguments.
SimilarString(String) - Constructor for class databionics.text.SimilarString
 
SimpleBmSearch - Class in databionics.esom.train.search
brut force bm search
SimpleBmSearch() - Constructor for class databionics.esom.train.search.SimpleBmSearch
 
size - Variable in class databionics.esom.grid.Grid
number of grid points
size() - Method in class databionics.esom.grid.Grid
Get the value of size.
size(int) - Method in class databionics.io.ClassmaskFile
Get size of a class
size(DataClass) - Method in class databionics.io.ClassmaskFile
Get size of a class
size(int) - Method in class databionics.io.ClsFile
Get size of a class
size(DataClass) - Method in class databionics.io.ClsFile
Get size of a class
sldTool - Variable in class databionics.esom.train.TrainCallback
 
sldTreshold - Variable in class databionics.esom.tool.classmask.ClassmaskTool
This slider is used to determine the treshold for not automated floodfill
sleep(long) - Method in class databionics.Application
Call sleep on current thread and handle interruptions
sleepAndExit() - Method in class databionics.GraphicalApplication
Things to be done after main window is displayed.
slideBar - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
slideCache - Variable in class databionics.esom.tool.slideshow.SlideshowTool
matrix for caching during slideShow
slideCacheBm - Variable in class databionics.esom.tool.slideshow.SlideshowTool
BMFile for caching during slideShow
slideList - Variable in class databionics.esom.tool.slideshow.SlideshowTool
List with umxfile locations for slide show
slideListBm - Variable in class databionics.esom.tool.slideshow.SlideshowTool
List with bmfile locations for slide show
slideLoaded - Variable in class databionics.esom.tool.slideshow.SlideshowTool
Flag for differ between two kinds of slide show
slidePictures - Variable in class databionics.esom.tool.slideshow.SlideshowTool
List with DoubleMatrix for slideShow
SlideShow - Class in databionics.esom
Tool for generating images for the slide show
SlideShow() - Constructor for class databionics.esom.SlideShow
standard constructor.
SlideShow - Class in databionics.esom.tool.slideshow
frame that shows pictures, saved during training, in a slide show
SlideShow(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.SlideShow
 
slideShow - Variable in class databionics.esom.tool.slideshow.SlideshowTool
Flag for slide show
SlideShowAction - Class in databionics.esom.tool.slideshow
starts the slide show, if there are enough generated pictures
SlideShowAction(SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.SlideShowAction
standard constructor
SlideShowAction(boolean, SlideshowTool) - Constructor for class databionics.esom.tool.slideshow.SlideShowAction
constructor with flag for generating new slide show
SlideShowCallback - Class in databionics.esom.tool.slideshow
callback for project run dialog
SlideShowCallback(ToolLoader) - Constructor for class databionics.esom.tool.slideshow.SlideShowCallback
constructor
SlideShowInfoTable - Class in databionics.esom.tool.slideshow
table with information about actual slide show
SlideShowInfoTable(AbstractTool) - Constructor for class databionics.esom.tool.slideshow.SlideShowInfoTable
 
SlideShowInfoTableModel - Class in databionics.esom.tool.slideshow
model for slide show info table
SlideShowInfoTableModel(AbstractTool) - Constructor for class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
slideshowTool - Variable in class databionics.esom.gui.ToolLoader
 
SlideshowTool - Class in databionics.esom.tool.slideshow
tool for slide show
SlideshowTool(boolean, Application) - Constructor for class databionics.esom.tool.slideshow.SlideshowTool
 
slideTool - Variable in class databionics.esom.SlideShow
the Renderer
slideWts - Variable in class databionics.esom.tool.slideshow.SlideshowTool
list with wts files after training
SlowBatchSOM - Class in databionics.esom.train
batch version of SOM Training, without counting more hits, just update everything after whole epoche
SlowBatchSOM() - Constructor for class databionics.esom.train.SlowBatchSOM
Standard constructor
SmoothedDataHistoRenderer - Class in databionics.esom.renderer.background
Smoothed Data Histogram (SDH) background renderer as proposed by Pampalk.
SmoothedDataHistoRenderer() - Constructor for class databionics.esom.renderer.background.SmoothedDataHistoRenderer
Standard constructor
smoothFactor - Variable in class databionics.esom.renderer.background.SmoothedDataHistoRenderer
the smooth parameter
som - Variable in class databionics.esom.train.search.BmSearch
 
SOM - Class in databionics.esom.train
Abstract base class for a self organizing map training algorithm.
SOM() - Constructor for class databionics.esom.train.SOM
Standard constructor.
sort() - Method in class databionics.io.ClassmaskFile
Sort classifications by key number.
sort() - Method in class databionics.io.ClsFile
Sort classifications by key number.
sortedHeights - Variable in class databionics.esom.renderer.HeightStatistics
 
south - Variable in class databionics.esom.tool.slideshow.SlideShow
 
space - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
speed - Variable in class databionics.esom.tool.slideshow.SlideShow
 
squaredEuclideanGridDistance(int, int, int, int) - Static method in class databionics.esom.grid.RectangularGrid
Squared Euclidean distance on rectangular grids.
standalone - Variable in class databionics.Application
flag whether app is run in stand alone mode from own main method
start() - Method in class databionics.Application
Start app thread
start - Variable in class databionics.esom.cooling.Cooling
initial value of the parameter
start - Variable in class databionics.modules.Job
date and time when job was started
start() - Method in class databionics.modules.Job
Start the job
startButton - Variable in class databionics.esom.gui.util.RunDialog
Buttons.
startButton - Variable in class databionics.gui.RunDialog
Buttons.
stateChanged(ChangeEvent) - Method in class databionics.esom.gui.BottomBar
 
stateChanged(ChangeEvent) - Method in class databionics.esom.tool.component.ComponentTool
 
stateChanged(ChangeEvent) - Method in class databionics.esom.tool.info.InfoTool
 
stddevs - Variable in class databionics.esom.neighborhood.GaussNeighborhood
number of standard deviations corresponding to radius
stepBackward - Variable in class databionics.esom.tool.slideshow.SlideShow
 
stepForward - Variable in class databionics.esom.tool.slideshow.SlideShow
 
stepList - Variable in class databionics.io.ColorMapping
 
steps - Variable in class databionics.esom.cooling.Cooling
number of steps toward the final value of the parameter
steps - Variable in class databionics.esom.tool.legend.Legend
 
steps - Variable in class databionics.io.ColorMapping
 
stepSlideShowBack() - Method in class databionics.esom.tool.slideshow.SlideShow
 
stop - Variable in class databionics.esom.tool.slideshow.SlideShow
 
stop() - Method in class databionics.esom.train.SOM
Stopping criterion
stopButton - Variable in class databionics.esom.gui.util.RunDialog
 
stopButton - Variable in class databionics.gui.RunDialog
 
stopped - Variable in class databionics.esom.tool.slideshow.SlideShow
 
StringCounter - Class in databionics.text
A HashMap to count occurences of Strings.
StringCounter() - Constructor for class databionics.text.StringCounter
Standard constructor without arguments.
StringCounter(StringCounter) - Constructor for class databionics.text.StringCounter
 
StringCounter(StringList) - Constructor for class databionics.text.StringCounter
 
StringList - Class in databionics.text
A LinkedList of Strings.
StringList() - Constructor for class databionics.text.StringList
Standard constructor without arguments.
StringList(StringList) - Constructor for class databionics.text.StringList
 
StringList(Collection) - Constructor for class databionics.text.StringList
Constructor with a collection of objects.
StringList(String) - Constructor for class databionics.text.StringList
Constructor with a single string.
StringParameter - Class in databionics.modules
Parameter with string argument.
StringParameter() - Constructor for class databionics.modules.StringParameter
 
stringToLocale(String) - Static method in class databionics.util.Utils
Convert string to locale
StringUtils - Class in databionics.text
Utility methods for Strings.
StringUtils() - Constructor for class databionics.text.StringUtils
 
subCursor - Variable in class databionics.esom.gui.RenderPanel
 
substract - Variable in class databionics.esom.tool.ProtoPanel
 
subtract(String) - Method in class databionics.text.StringCounter
 
sum - Variable in class databionics.esom.train.BestMatchHit
sum of prjected data vectors
SwitchParameter - Class in databionics.modules
Switch parameter without an argument.
SwitchParameter() - Constructor for class databionics.modules.SwitchParameter
Default constructor

T

tableChanged(TableModelEvent) - Method in class databionics.esom.tool.classmask.ClassmaskTable
manages table changes
tableChanged(TableModelEvent) - Method in class databionics.esom.tool.data.DataTable
manages table changes
template - Variable in class databionics.modules.OutputFileParameter
template for filename
test(int, int) - Method in class databionics.esom.train.search.BmSearchStat
 
testIntersection(Rectangle2D, Rectangle2D) - Method in class databionics.esom.renderer.foreground.BoundaryList
 
text - Variable in class databionics.esom.gui.util.MessagePanel
 
text - Variable in class databionics.gui.LogPanel.ClearAction
 
textArea - Variable in class databionics.gui.LogPanel
text area for messages
thread - Variable in class databionics.Application
corresponding thread
thread - Variable in class databionics.esom.tool.slideshow.SlideShow
 
threetimes - Variable in class databionics.esom.tool.island.IslandTool
 
tileBackground() - Method in class databionics.esom.renderer.Renderer
Tile the background image for toroid projection.
tiled - Variable in class databionics.esom.renderer.Renderer
Flag for tiled projection
tiledImage - Variable in class databionics.esom.renderer.Renderer
The possibly tiled background image
tiledMode(boolean) - Method in class databionics.esom.gui.ToolLoader
 
toArray() - Method in class databionics.modules.Job
Build an array holding the parameters and values
toExtNGrams(int) - Method in class databionics.text.SimilarString
Build extended n-grams of string by adding _ at start and end.
toExtNGrams(int, String) - Static method in class databionics.text.StringUtils
Build extended n-grams of string by adding _ at start and end.
toggleIndex(int) - Method in class databionics.esom.tool.data.DataTable
toggles index i
toNGrams(int) - Method in class databionics.text.SimilarString
Build n-grams of string.
toNGrams(int, String) - Static method in class databionics.text.StringUtils
Build n-grams of string.
tool - Variable in class databionics.esom.gui.util.RunDialog
Tool to run with this dialog
tool - Variable in class databionics.esom.tool.AbstractLoadAction
 
tool - Variable in class databionics.esom.tool.AbstractSaveAction
 
tool - Variable in class databionics.esom.tool.AbstractToolRenderer
 
tool - Variable in class databionics.esom.tool.AbstractToolTable
 
tool - Variable in class databionics.esom.tool.BottomTab
 
tool - Variable in class databionics.esom.tool.classmask.ClassmaskTableModel
 
tool - Variable in class databionics.esom.tool.component.ComponentTableModel
this tool
tool - Variable in class databionics.esom.tool.data.DataTableModel
 
tool - Variable in class databionics.esom.tool.data.SelectedDataTableModel
 
tool - Variable in class databionics.esom.tool.dataclass.DataclassTableModel
 
tool - Variable in class databionics.esom.tool.info.InfoToolTableModel
 
tool - Variable in class databionics.esom.tool.island.IslandTableModel
 
tool - Variable in class databionics.esom.tool.island.LoadImxFileAction
 
tool - Variable in class databionics.esom.tool.island.SaveImxFileAction
 
tool - Variable in class databionics.esom.tool.ProtoPanel
 
tool - Variable in class databionics.esom.tool.slideshow.LoadPicturesAction
 
tool - Variable in class databionics.esom.tool.slideshow.SlideShow
 
tool - Variable in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
tool - Variable in class databionics.gui.RunDialog
Tool to run with this dialog
Tool - Class in databionics.modules
A program that processes data.
Tool() - Constructor for class databionics.modules.Tool
Default constructor
toolBar - Variable in class databionics.esom.tool.AbstractTool
ToolBar for the BottomTAb.
toolBar - Variable in class databionics.esom.tool.BottomTab
 
toolbar - Variable in class databionics.esom.tool.slideshow.SlideShow
 
toolHash - Variable in class databionics.esom.gui.ToolLoader
Hashtable containing the Tools.
ToolLoader - Class in databionics.esom.gui
 
ToolLoader(boolean) - Constructor for class databionics.esom.gui.ToolLoader
 
toolRenderer - Variable in class databionics.esom.tool.AbstractTool
If the Tool has a foreground-rendering function it is handled there.
tools - Variable in class databionics.modules.Module
list of tools
toroid - Variable in class databionics.esom.renderer.Renderer
Flag for toroid renderering
ToroidEuclideanGrid - Class in databionics.esom.grid
Toroid grid with euclidean distance.
ToroidEuclideanGrid() - Constructor for class databionics.esom.grid.ToroidEuclideanGrid
Standard constructor
ToroidEuclideanGrid(int, int, int) - Constructor for class databionics.esom.grid.ToroidEuclideanGrid
Constructor with sizes
ToroidGrid - Class in databionics.esom.grid
Toroid grid.
ToroidGrid() - Constructor for class databionics.esom.grid.ToroidGrid
Standard constructor
ToroidGrid(int, int, int) - Constructor for class databionics.esom.grid.ToroidGrid
Constructor with sizes
toroidLayout - Variable in class databionics.esom.renderer.Renderer
Layout for toroid projection
ToroidManhattanGrid - Class in databionics.esom.grid
Toroid grid with manhattan distance.
ToroidManhattanGrid() - Constructor for class databionics.esom.grid.ToroidManhattanGrid
Standard constructor
ToroidManhattanGrid(int, int, int) - Constructor for class databionics.esom.grid.ToroidManhattanGrid
Constructor with sizes
ToroidMaxGrid - Class in databionics.esom.grid
Toroid grid with maximum distance.
ToroidMaxGrid() - Constructor for class databionics.esom.grid.ToroidMaxGrid
Standard constructor
ToroidMaxGrid(int, int, int) - Constructor for class databionics.esom.grid.ToroidMaxGrid
Constructor with sizes
toroidPolygons - Variable in class databionics.esom.gui.util.DoublePolygon
 
ToroidRectangularGrid - Class in databionics.esom.grid
Abstract base class for all toroid grid structures with a rectangular shaped grid.
ToroidRectangularGrid() - Constructor for class databionics.esom.grid.ToroidRectangularGrid
Standard constructor
ToroidRectangularGrid(int, int, int) - Constructor for class databionics.esom.grid.ToroidRectangularGrid
Constructor with sizes
toString(String) - Method in class databionics.io.Bestmatch
String representation with custom delimiter.
toString() - Method in class databionics.io.ColorStatistics
 
toString(String) - Method in class databionics.io.Condition
String representation.
toString(String) - Method in class databionics.io.DataClass
String representation with custom delimiter.
toString() - Method in class databionics.io.DataItem
String representation with default delimiter (tab).
toString(String) - Method in class databionics.io.DataItem
String representation with custom delimiter.
toString(String) - Method in class databionics.io.DiffCondition
String representation.
toString(String) - Method in class databionics.io.Explanation
String representation.
toString(String) - Method in class databionics.io.IntervalCondition
String representation.
toString(String) - Method in class databionics.io.KeyName
String representation
toString(String) - Method in class databionics.io.Rule
String representation.
toString() - Method in class databionics.modules.AbstractStringParameter
String representation with name and value as needed for starting a tool.
toString() - Method in class databionics.modules.FloatParameter
String representation with name and value as needed for starting a tool.
toString() - Method in class databionics.modules.IntParameter
String representation with name and value as needed for starting a tool.
toString() - Method in class databionics.modules.Job
String representation of job
toString() - Method in class databionics.modules.MultipleChoiceElement
String representation
toString() - Method in class databionics.modules.MultipleChoiceParameter
String representation with name and value as needed for starting a tool.
toString() - Method in class databionics.modules.Parameter
String representation.
toString() - Method in class databionics.modules.SwitchParameter
String representation with name and value as needed for starting a tool.
toString() - Method in class databionics.project.DataManager
String of workspace variables
toString() - Method in class databionics.text.SimilarString
String representation
toString(String) - Method in class databionics.text.StringList
Get string representation, items seperated with given separator.
toString() - Method in class databionics.text.StringList
Get string representation, items seperated with space.
toString() - Method in class databionics.util.IntegerList
Get string representation, numbers seperated with space.
toStringArray() - Method in class databionics.text.StringList
Return string list as array
toStringList() - Method in class databionics.util.IntegerList
Get list of numbers as strings.
toXml() - Method in class databionics.modules.FileParameter
XML representation
toXml() - Method in class databionics.modules.FloatParameter
XML representation
toXml() - Method in class databionics.modules.FolderParameter
XML representation
toXml() - Method in class databionics.modules.InputFileParameter
XML representation
toXml() - Method in class databionics.modules.IntParameter
XML representation
toXml() - Method in class databionics.modules.Job
write a job in a string in xml-format
toXml() - Method in class databionics.modules.MultipleChoiceElement
XML representation
toXml() - Method in class databionics.modules.MultipleChoiceParameter
XML representation
toXml() - Method in class databionics.modules.OutputFileParameter
XML representation
toXml() - Method in class databionics.modules.Parameter
XML representation
toXml() - Method in class databionics.modules.StringParameter
XML representation
toXml() - Method in class databionics.modules.SwitchParameter
XML representation
toXml(String) - Method in class databionics.project.FileSlot
write a fileSlot in a string in xml-format
toXml() - Method in class databionics.project.Project
XML representation of this project
Train - Class in databionics.esom
Command line tool for SOM training
Train() - Constructor for class databionics.esom.Train
standard constructor.
train() - Method in class databionics.esom.train.SOM
General training algorithm for the SOM.
TrainAction - Class in databionics.esom.train
calls the dialog for training
TrainAction() - Constructor for class databionics.esom.train.TrainAction
Default Constructor
TrainCallback - Class in databionics.esom.train
callback for trainig run dialog
TrainCallback() - Constructor for class databionics.esom.train.TrainCallback
 
transformRadius(int) - Method in class databionics.esom.grid.Grid
How to transform an official radius into the internal format.
transformRadius(int) - Method in class databionics.esom.grid.PlanarEuclideanGrid
How to transform an official radius into the squared internal format.
transformRadius(int) - Method in class databionics.esom.grid.ToroidEuclideanGrid
How to transform an official radius into the squared internal format.
transparentMode - Variable in class databionics.esom.tool.island.IslandTool
 
treshold - Variable in class databionics.esom.tool.classmask.ClassmaskTool
The treshold for floodfill.
twice - Variable in class databionics.esom.tool.island.IslandTool
 
TwoMatchRenderer - Class in databionics.esom.renderer.background
TwoMatch background renderer.
TwoMatchRenderer() - Constructor for class databionics.esom.renderer.background.TwoMatchRenderer
Standard constructor
TxtFile - Class in databionics.io
Dummy class to provide this FileType for plain text files.
TxtFile() - Constructor for class databionics.io.TxtFile
 
txtPath - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
txtPrefix - Variable in class databionics.esom.tool.slideshow.SlideshowTool
 
type - Variable in class databionics.esom.gui.util.MessagePanel
kind of error
type - Variable in class databionics.modules.AbstractFileParameter
filetype
type - Variable in class databionics.project.FileSlot
this slot contains filenames of this type

U

UMatrixRenderer - Class in databionics.esom.renderer.background
U-Matrix background renderer.
UMatrixRenderer() - Constructor for class databionics.esom.renderer.background.UMatrixRenderer
Standard constructor
UmxFile - Class in databionics.io
File that stores an U-Matrix in a 2D array.
UmxFile() - Constructor for class databionics.io.UmxFile
Standard constructor
UmxFile(String) - Constructor for class databionics.io.UmxFile
Constructor with a filename
UmxFile(int, int) - Constructor for class databionics.io.UmxFile
Constructor with size for an empty array.
umxFilename - Variable in class databionics.esom.renderer.Renderer
 
umxLoaded(boolean) - Method in class databionics.esom.gui.ToolLoader
 
undisplayForeground(ForegroundRenderer) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Hide a foreground.
undisplayForeground(String) - Method in class databionics.esom.renderer.foreground.ForegroundTool
Hide a foreground by name.
update() - Method in class databionics.esom.renderer.background.BackgroundTool
Updates the GUI elements dependent on the flag umxLoaded.
update() - Method in class databionics.esom.renderer.foreground.ForegroundTool
Update enabled status of GUI elements.
update() - Method in class databionics.esom.renderer.RendererTool
 
update() - Method in class databionics.esom.tool.AbstractTool
Updates all gui elements, if not null.
update() - Method in class databionics.esom.tool.classmask.ClassmaskTable
 
update() - Method in class databionics.esom.tool.classmask.ClassmaskTableModel
 
update() - Method in class databionics.esom.tool.classmask.ClassmaskTool
 
update() - Method in class databionics.esom.tool.component.ComponentTableModel
 
update() - Method in class databionics.esom.tool.data.DataTable
update the table with tableModel
update() - Method in class databionics.esom.tool.data.DataTool
update the table and set the DataTab active
update() - Method in class databionics.esom.tool.dataclass.DataclassTool
 
update() - Method in class databionics.esom.tool.info.InfoToolTableModel
 
update() - Method in class databionics.esom.tool.island.IslandTool
 
update() - Method in class databionics.esom.tool.legend.Legend
Reset the panel using the given renderer
update(int) - Method in class databionics.esom.tool.legend.Legend
 
update() - Method in class databionics.esom.tool.legend.LegendRenderer
 
update(int) - Method in class databionics.esom.tool.legend.LegendRenderer
 
update() - Method in class databionics.esom.tool.legend.LegendTool
 
update() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
update() - Method in class databionics.esom.tool.slideshow.SlideShowInfoTableModel
 
update() - Method in class databionics.esom.tool.slideshow.SlideshowTool
 
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.Batch2SOM
Empty implementation.
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.BatchSOM
Empty implementation.
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.HybridBatchSOM
if threshold is reached, go online
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.KBatchSOM
Empty implementation.
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.OnlineSOM
Update the current neuron and the neighborhood
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.SlowBatchSOM
Empty implementation.
update(DoubleMatrix1D, int, int) - Method in class databionics.esom.train.SOM
Things to be done, after finding a bestmatch, e.g.
updateContent() - Method in class databionics.esom.tool.legend.ColorLegend
 
updateContent() - Method in class databionics.esom.tool.legend.HeightsLegend
 
updateContent() - Method in class databionics.esom.tool.legend.LegendRenderer
 
updateContent() - Method in class databionics.esom.tool.legend.PictureLegend
 
updateContent() - Method in class databionics.esom.tool.pointinfo.GlobalNInfoRenderer
 
updateContent() - Method in class databionics.esom.tool.pointinfo.LocalNInfoRenderer
 
updateContent() - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
updateContent() - Method in class databionics.esom.tool.pointinfo.ValueInfoRenderer
 
updateData(MouseEvent) - Method in class databionics.esom.tool.bminfo.BMInfoPanel
updates the data
updateData(MouseEvent) - Method in class databionics.esom.tool.classmask.ClassmaskCreatorPanel
 
updateData(MouseEvent) - Method in class databionics.esom.tool.data.SelectionPanel
 
updateData(MouseEvent) - Method in class databionics.esom.tool.dataclass.DataclassCreatorPanel
 
updateData(MouseEvent) - Method in class databionics.esom.tool.island.IslandCreatorPanel
 
updateData(MouseEvent) - Method in class databionics.esom.tool.ProtoPanel
 
updateNeighborhood(DoubleMatrix1D, int) - Method in class databionics.esom.train.BatchSOM
Update a neuron and its neighborhood.
updateNeighborhood(DoubleMatrix1D, int) - Method in class databionics.esom.train.HybridBatchSOM
Update a neuron and its neighborhood.
updateNeighborhood(DoubleMatrix1D, int) - Method in class databionics.esom.train.KBatchSOM
Update a neuron and its neighborhood.
updateNeighborhood(DoubleMatrix1D, int) - Method in class databionics.esom.train.SOM
Update a neuron and its neighborhood.
updateNeuron(int, DoubleMatrix1D, double) - Method in class databionics.esom.train.SOM
Update a single weight vector.
updatePointInfo(int, int) - Method in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
updatePolygon() - Method in class databionics.esom.tool.ProtoPanel
 
updatePopMenu() - Method in class databionics.esom.tool.data.DataTool
 
useForAll(FileType) - Method in class databionics.project.Project
Use filename in slot with FileType type for all slots
useRadius - Variable in class databionics.esom.renderer.background.PMatrixRenderer
flag whether to use radius instead of percentile
Utils - Class in databionics.util
Some static utility functions
Utils() - Constructor for class databionics.util.Utils
 

V

value - Variable in class databionics.modules.AbstractStringParameter
parameter value
value - Variable in class databionics.modules.FloatParameter
parameter value
value - Variable in class databionics.modules.IntParameter
parameter value
value - Variable in class databionics.modules.MultipleChoiceElement
parameter value
value - Variable in class databionics.modules.MultipleChoiceParameter
parameter value
value - Variable in class databionics.modules.SwitchParameter
parameter value
ValueInfoRenderer - Class in databionics.esom.tool.pointinfo
Shows the wts-/lrn-data of the actual MousePosition as Values
ValueInfoRenderer() - Constructor for class databionics.esom.tool.pointinfo.ValueInfoRenderer
Basic constructor
valueOf(Element) - Static method in class databionics.modules.FileParameter
Create a FileParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.FloatParameter
Create a FloatParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.FolderParameter
Create a FolderParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.InputFileParameter
Create a FileParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.IntParameter
Create a IntParameter from an XML tag
valueOf(Element, Modules) - Static method in class databionics.modules.Job
load a job out of the xml-tag "el"
valueOf(Element) - Static method in class databionics.modules.Module
Create a Module from an XML tag
valueOf(Element) - Static method in class databionics.modules.MultipleChoiceElement
Create a MultipleChoiceElement from an XML tag
valueOf(Element) - Static method in class databionics.modules.MultipleChoiceParameter
Create a MultipleChoiceParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.OutputFileParameter
Create a FileParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.StringParameter
Create a StringParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.SwitchParameter
Create a IntParameter from an XML tag
valueOf(Element) - Static method in class databionics.modules.Tool
Create a Tool from an XML tag
valueOf(Element, String) - Static method in class databionics.project.FileSlot
load a slot out of the xml-tag
view - Variable in class databionics.esom.train.SOM
possibly permuted view on training data, only used internally

W

w - Variable in class databionics.esom.tool.ProtoPanel
 
WARN - Static variable in class databionics.esom.gui.util.MessagePanel
 
watch - Variable in class databionics.gui.RunDialog
Thread for the buttons
water - Variable in class databionics.esom.tool.island.IslandTool
 
weights - Variable in class databionics.esom.grid.MatrixGrid
matrix to store weights
weights - Variable in class databionics.esom.neighborhood.CachedNeighborhood
cache with precalculated values of the weights
width - Variable in class databionics.esom.renderer.Renderer
The original width of the display in 2D
windowActivated(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
handle event
windowActivated(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
handle event
windowActivated(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
windowClosed(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
handle event
windowClosed(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
handle event
windowClosed(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
windowClosing(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
exit and manage exit
windowClosing(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
exit somana
windowClosing(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
windowDeactivated(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
handle event
windowDeactivated(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
handle event
windowDeactivated(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
windowDeiconified(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
handle event
windowDeiconified(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
handle event
windowDeiconified(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
windowIconified(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
handle event
windowIconified(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
handle event
windowIconified(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
windowOpened(WindowEvent) - Method in class databionics.esom.tool.slideshow.ExitSlideShowAction
handle event
windowOpened(WindowEvent) - Method in class databionics.esom.util.actions.ExitAction
handle event
windowOpened(WindowEvent) - Method in class databionics.gui.BaseMainFrame
 
workdir - Variable in class databionics.Application
current working directory
workspaceToString() - Method in class databionics.project.DataManager
 
write(char[], int, int) - Method in class databionics.gui.LogPanelWriter
Write an array of chars to the panel
writeStringList(BufferedWriter, StringList, String) - Static method in class databionics.io.BaseFile
Write a StringList to a writer.
writeStringList(BufferedWriter, StringList) - Static method in class databionics.io.BaseFile
Write a StringList to a writer.
wtsChanged - Variable in class databionics.esom.renderer.background.BackgroundRenderer
flag wether Grid changed.
wtsChanged() - Method in class databionics.esom.renderer.background.BackgroundRenderer
Called when the ESOM Grid changed.
wtsChanged() - Method in interface databionics.esom.util.WtsChangeListener
Called when the grid weights have changed.
WtsChangeListener - Interface in databionics.esom.util
Listener for changes of grid weights.
WtsFile - Class in databionics.io
File that stores weights for a SOM grid
WtsFile() - Constructor for class databionics.io.WtsFile
Standard constructor
WtsFile(String) - Constructor for class databionics.io.WtsFile
Constructor with a filename
WtsFile(int, int, int) - Constructor for class databionics.io.WtsFile
Constructor with size for an empty array.
wtsFilename - Variable in class databionics.esom.renderer.Renderer
 
wtsListeners - Variable in class databionics.esom.renderer.Renderer
 

X

x - Variable in class databionics.esom.gui.util.MessagePanel
 
x - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
x - Variable in class databionics.esom.tool.ProtoPanel
 

Y

y - Variable in class databionics.esom.gui.util.MessagePanel
 
y - Variable in class databionics.esom.tool.pointinfo.PointInfoRenderer
 
y - Variable in class databionics.esom.tool.ProtoPanel
 

Z

zeros - Variable in class databionics.esom.tool.island.IslandTool
 
zoom - Variable in class databionics.esom.renderer.Renderer
The scaling factor
zoomBackground() - Method in class databionics.esom.renderer.Renderer
 
zoomColorMatrix(DoubleMatrix2D) - Method in class databionics.esom.renderer.Renderer
 
zoomColorMatrix(int, DoubleMatrix2D) - Static method in class databionics.esom.renderer.RendererTools
 
zoomedMatrix - Variable in class databionics.esom.renderer.Renderer
The interpolated height above each pixal
zoomedOpn - Variable in class databionics.esom.renderer.Renderer
 

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