A B C E F G H I J L M N O P Q R S T U V

A

actionPerformed(ActionEvent) - Method in class org.limn.render.ui.ViewControlPane
 
addControls(Panel) - Method in interface org.limn.render.LimnViewer
add control panel to the viewer.
addControls(Panel) - Method in class org.limn.render.SimpleViewer
 
addRenderable(LimnRenderable) - Method in interface org.limn.render.LimnViewer
will allow additional objects to augment the display.
addRenderable(LimnRenderable) - Method in class org.limn.render.RecordCanvas
 
addRenderable(LimnRenderable) - Method in class org.limn.render.SimpleViewer
 
addRenderable(LimnRenderable) - Method in interface org.limn.render.LimnRender
a renderable should be able to collect other objects that implement the Limnrednerable interface.
augment(Graphics, int, int, int) - Method in class org.limn.data.ParsingThread
augment is the method required for the Renderable interface.
augment(Graphics, int, int, int) - Method in class org.limn.engine.PPHolesFactory
 
augment(Graphics, int, int, int) - Method in class org.limn.engine.TourEngine
 
augment(Graphics, int, int, int) - Method in interface org.limn.render.LimnRenderable
This method is to be called from within the rendering stage.

B

backward() - Method in class org.limn.render.QuicktimeImageProducer
 
backward() - Method in class org.limn.render.JPEGImageProducer
 
backward() - Method in interface org.limn.render.ui.ViewPane
 

C

checkBasis(double[][], double[][]) - Method in class org.limn.engine.GTBasisFactory
 
checkBasis(double[][], double[][]) - Method in class org.limn.engine.LittleTourFactory
 
checkProx(double[][], double[][]) - Static method in class org.limn.engine.TourUtil
 
clear() - Method in interface org.limn.render.LimnViewer
will deleted the collection of LimnRenderables held by the object.
clear() - Method in class org.limn.render.SimpleViewer
 
clear() - Method in class org.limn.render.QuicktimeImageProducer
 
clear() - Method in class org.limn.render.JPEGImageProducer
 
clear() - Method in interface org.limn.render.ui.ViewPane
 
copyBasis(double[][], double[][]) - Method in class org.limn.engine.TourInterpolate
 
createImage(ImageProducer, int) - Method in interface org.limn.render.LimnViewer
 
createImage(ImageProducer, int) - Method in class org.limn.render.SimpleViewer
 
createSubset(double, double, double, double, int, LimnViewer) - Method in interface org.limn.data.LimnFilter
createSubset needs the x and y corners of the brush rectangle, the index of the animation frame (to sync up the projections) and a LimnViewer (the graphics element) to allow the subset data to be added to the collection of renderable objects
createSubset(double, double, double, double, int, LimnViewer) - Method in class org.limn.data.SimpleFilter
 

E

execute(Movie) - Method in class org.limn.render.QuicktimeImageProducer
 

F

FileBasisFactory - class org.limn.engine.FileBasisFactory.
FileBasisFactory reads projection basis from a text file and cycles through the projects returning the active one each time that the generateBasis method is called.
FileBasisFactory(LimnData) - Constructor for class org.limn.engine.FileBasisFactory
 
finishing() - Method in class org.limn.engine.FileBasisFactory
 
finishing() - Method in class org.limn.engine.RecordingFactory
finishing will close the file and free any resources associated with the file.
finishing() - Method in interface org.limn.engine.LimnBasisFactory
finishing will release resources and finish the animation process.
finishingStep() - Method in class org.limn.engine.TourInterpolate
 
forward() - Method in class org.limn.render.QuicktimeImageProducer
 
forward() - Method in class org.limn.render.JPEGImageProducer
 
forward() - Method in interface org.limn.render.ui.ViewPane
 

G

gen_norm_variates(double[][]) - Method in class org.limn.engine.GTBasisFactory
 
generateBasis(double[][], double[][]) - Method in class org.limn.engine.FileBasisFactory
 
generateBasis(double[][], double[][]) - Method in class org.limn.engine.GTBasisFactory
 
generateBasis(double[][], double[][]) - Method in class org.limn.engine.PPHolesFactory
 
generateBasis(double[][], double[][]) - Method in interface org.limn.engine.LimnBasisFactory
generates a new target basis t, checking that the target is compatible with the base.
generateBasis(double[][], double[][]) - Method in class org.limn.engine.LittleTourFactory
 
generateProjection() - Method in interface org.limn.engine.LimnEngine
generateProjection is used to generate the next projection
generateProjection() - Method in class org.limn.engine.TourEngine
 
generateProjection(int) - Method in interface org.limn.engine.LimnEngine
generateProjection is used to generate the projection for the step indicated by the index number.
generateProjection(int) - Method in class org.limn.engine.TourEngine
 
getHeight() - Method in class org.limn.render.RecordCanvas
 
getHeight() - Method in interface org.limn.render.LimnRender
 
getImage() - Method in class org.limn.render.RecordCanvas
 
getImage() - Method in interface org.limn.render.LimnRender
returns the image handle, this is used by the recorder object.
getName(int) - Method in class org.limn.data.RAFData
 
getNumCol() - Method in class org.limn.data.RAFData
 
getNumCol() - Method in class org.limn.data.SimpleData
 
getNumCol() - Method in interface org.limn.data.LimnData
 
getNumRow() - Method in class org.limn.data.RAFData
 
getNumRow() - Method in class org.limn.data.SimpleData
 
getNumRow() - Method in interface org.limn.data.LimnData
 
getPanel() - Method in class org.limn.render.ui.ViewControlPane
 
getProjection(int, double[]) - Method in interface org.limn.data.LimnBasis
 
getProjection(int, double[]) - Method in class org.limn.data.SimpleBasis
 
getProperties() - Static method in class org.limn.data.LimnProperties
used to return the handle of the one (and only one) active properties object.
getRow(int) - Method in class org.limn.data.RAFData
 
getRow(int) - Method in class org.limn.data.SimpleData
 
getRow(int) - Method in interface org.limn.data.LimnData
 
getValue(int, int) - Method in class org.limn.data.RAFData
 
getValue(int, int) - Method in class org.limn.data.SimpleData
 
getValue(int, int) - Method in interface org.limn.data.LimnData
 
getWidth() - Method in class org.limn.render.RecordCanvas
 
getWidth() - Method in interface org.limn.render.LimnRender
 
gram_schmidt(double[], double[]) - Static method in class org.limn.engine.TourUtil
 
gramSchmidt(double[][]) - Static method in class org.limn.engine.TourUtil
 
GTBasisFactory - class org.limn.engine.GTBasisFactory.
GTBasisFactory is a simple factory that creates random projections.
GTBasisFactory(LimnData) - Constructor for class org.limn.engine.GTBasisFactory
 

H

HistogramPlot - class org.limn.render.HistogramPlot.
HistogramPlot is an alternative plot type.
HistogramPlot(LimnData) - Constructor for class org.limn.render.HistogramPlot
 

I

imageUpdate(Image, int, int, int, int, int) - Method in class org.limn.record.QuickImage
 
init() - Method in class org.limn.data.SimpleFilter
 
init() - Method in class org.limn.record.JPEGRecorder
 
init() - Method in class org.limn.record.QuicktimeRecorder
 
init() - Method in class org.limn.engine.FileBasisFactory
 
init() - Method in class org.limn.engine.GTBasisFactory
 
init() - Method in interface org.limn.engine.LimnBasisFactory
will reseed the basis generator or reset if reading basis from a file this allows the TourEngine to seek to a specific index in a set tour (littletour or filebasistour), and allows a random tour to reset if something has gone strange.
init() - Method in class org.limn.engine.LittleTourFactory
 
initEngine() - Method in class org.limn.engine.TourEngine
 
initRecorder() - Method in class org.limn.engine.TourEngine
 
inner_prod(double[], double[]) - Static method in class org.limn.engine.TourUtil
 

J

JPEGImageProducer - class org.limn.render.JPEGImageProducer.
ImageProducer creates images to be rendered in java from a series of jpeg images.
JPEGImageProducer(LimnViewer) - Constructor for class org.limn.render.JPEGImageProducer
 
JPEGRecorder - class org.limn.record.JPEGRecorder.
This is an alternative method to animation recording.
JPEGRecorder() - Constructor for class org.limn.record.JPEGRecorder
 

L

LimnBasis - interface org.limn.data.LimnBasis.
LimnBasis is a small wrapper class that contains the active projection.
LimnBasisFactory - interface org.limn.engine.LimnBasisFactory.
includes contract methods for generating new projection basis, seeding new basis to begin the process.
LimnData - interface org.limn.data.LimnData.
LimnData provides some basic data access and selection features.
LimnEngine - interface org.limn.engine.LimnEngine.
LimnEngine provides the basic methods that other objects will need to know about to interact with a Engine.
LimnFilter - interface org.limn.data.LimnFilter.
LimnFilter interface is used to specifiy the methods needed for filtering and subsetting operations.
LimnImageProducer - interface org.limn.render.LimnImageProducer.
LimnImageProducer is an Interface that specifies the necessary methods that allow playback of a prerecorded animation.
LimnProperties - class org.limn.data.LimnProperties.
LimnProperties is a singleton object used to store global constants for the recording and playback objects.
LimnRecorder - interface org.limn.record.LimnRecorder.
LimnRecorder interface specifies the method signatures that an object will need to implement to be used as an animation building object in the Limn cycle.
LimnRender - interface org.limn.render.LimnRender.
Contract methods involving aspects of the image rendering stage of the production process.
LimnRenderable - interface org.limn.render.LimnRenderable.
LimnRenderable is intended to use to allow additional objects to provide graphics to the main render object.
LimnViewer - interface org.limn.render.LimnViewer.
LimnViewer interface contrains the set of methods that would concern an object interestested in displaying and interacting with a prerecorded animation.
LittleTourFactory - class org.limn.engine.LittleTourFactory.
LittleTourFactory uses the stanard variable pair projections used for a scatterplot matrix.
LittleTourFactory(LimnData) - Constructor for class org.limn.engine.LittleTourFactory
 
loadProperties(String) - Static method in class org.limn.data.LimnProperties
 

M

measure(double[][]) - Method in class org.limn.engine.GTBasisFactory
 
measure(double[][]) - Method in class org.limn.engine.PPHolesFactory
 
measure(double[][]) - Method in class org.limn.engine.LittleTourFactory
 
mouseClicked(MouseEvent) - Method in class org.limn.render.SimpleViewer
 
mouseDragged(MouseEvent) - Method in class org.limn.render.SimpleViewer
 
mouseEntered(MouseEvent) - Method in class org.limn.render.SimpleViewer
 
mouseExited(MouseEvent) - Method in class org.limn.render.SimpleViewer
 
mouseMoved(MouseEvent) - Method in class org.limn.render.SimpleViewer
 
mousePressed(MouseEvent) - Method in class org.limn.render.SimpleViewer
 
mouseReleased(MouseEvent) - Method in class org.limn.render.SimpleViewer
 

N

newBasis() - Method in class org.limn.engine.FileBasisFactory
 
newBasis() - Method in class org.limn.engine.GTBasisFactory
 
newBasis() - Method in interface org.limn.engine.LimnBasisFactory
seeds a new basis array.
newBasis() - Method in class org.limn.engine.LittleTourFactory
 
newMovie(int, int, int, LimnRender, LimnEngine) - Method in class org.limn.record.JPEGRecorder
 
newMovie(int, int, int, LimnRender, LimnEngine) - Method in class org.limn.record.QuicktimeRecorder
 
newMovie(int, int, int, LimnRender, LimnEngine) - Method in interface org.limn.record.LimnRecorder
 
newSizeNotified(QTImageDrawer, Dimension) - Method in class org.limn.record.QuickImage
 
norm(double[]) - Static method in class org.limn.engine.TourUtil
 

O

org.limn.data - package org.limn.data
 
org.limn.engine - package org.limn.engine
 
org.limn.record - package org.limn.record
 
org.limn.render - package org.limn.render
 
org.limn.render.ui - package org.limn.render.ui
 
output() - Static method in class org.limn.data.SimpleParser
 

P

paint(Graphics) - Method in class org.limn.record.QuickImage
 
paint(Graphics) - Method in class org.limn.render.ParallelCoordinatePlot
 
paint(Graphics) - Method in class org.limn.render.ScatterPlotCanvas
 
paint(Graphics) - Method in class org.limn.render.SimpleViewer
 
paint(Graphics) - Method in class org.limn.render.HistogramPlot
 
ParallelCoordinatePlot - class org.limn.render.ParallelCoordinatePlot.
ParallelCoordinatePlot is an alternative rendering type.
ParallelCoordinatePlot(LimnData) - Constructor for class org.limn.render.ParallelCoordinatePlot
 
parseFile(String) - Static method in class org.limn.data.SimpleParser
 
parseFile(String) - Static method in class org.limn.data.ReaderParser
parseFile will parse the data file and return a SimpleData object
parseFile(String) - Static method in class org.limn.data.RAFParser
file name only will indicate that dataset should be loaded completely.
parseFile(String, int) - Static method in class org.limn.data.RAFParser
file name and buffersize will return a RAFData object with the indicated buffer size
parseFile(String, int, boolean) - Static method in class org.limn.data.RAFParser
 
ParsingThread - class org.limn.data.ParsingThread.
This class is used to subset data in the LimnFilter object.
ParsingThread(LimnEngine, int, double, double, double, double, LimnData, String) - Constructor for class org.limn.data.ParsingThread
Constructor needs a limnengine object and index to determine the proper project to base its subsetting on.
path(double[][], double[][]) - Method in class org.limn.engine.TourInterpolate
 
PPHolesFactory - class org.limn.engine.PPHolesFactory.
PPHolesFactory extends GTBasisFactory to include a calculation of the PPHoles index for each basis created by the factory.
PPHolesFactory(LimnData) - Constructor for class org.limn.engine.PPHolesFactory
 
prep() - Method in class org.limn.record.QuicktimeRecorder
 
prepareImage(Image, ImageObserver) - Method in interface org.limn.render.LimnViewer
 
prepareImage(Image, ImageObserver) - Method in class org.limn.render.SimpleViewer
 
prepImage(LimnBasis, LimnRecorder) - Method in class org.limn.render.RecordCanvas
 
prepImage(LimnBasis, LimnRecorder) - Method in interface org.limn.render.LimnRender
prepare/repaint the image for recording.
printBasis(double[][]) - Method in class org.limn.engine.TourEngine
This is used to seek to a specific projection in the tour process.

Q

QuickImage - class org.limn.record.QuickImage.
QuickImage is a utility class used by the QuicktimeRecorder class it allows the java graphics to be rendered to a quicktime canvas
QuickImage(Dimension, LimnRender) - Constructor for class org.limn.record.QuickImage
 
QuicktimeImageProducer - class org.limn.render.QuicktimeImageProducer.
ImageProducer creates images to be rendered in java from a quicktime movie.
QuicktimeImageProducer(LimnViewer) - Constructor for class org.limn.render.QuicktimeImageProducer
 
QuicktimeRecorder - class org.limn.record.QuicktimeRecorder.
QuicktimeRecorder is the main recording module for the animation building process.
QuicktimeRecorder() - Constructor for class org.limn.record.QuicktimeRecorder
 

R

RAFData - class org.limn.data.RAFData.
RAFData implements the LimnData interface.
RAFData(String, int, long[], double[][], String[], String[]) - Constructor for class org.limn.data.RAFData
constructor takes the file name, buffer size in rows, the long values that represent locations of each buffered section in the file, minmax values, names of variables to exclude and column names
RAFData(String, int, String[]) - Constructor for class org.limn.data.RAFData
constructor takes the file name, the number of rows to use to buffer the data and any names of variables to exclude from the dataset
RAFParser - class org.limn.data.RAFParser.
RAFParser is a class of static methods used for parsing and preparing file information to be used by the RAFDAta object.
RAFParser() - Constructor for class org.limn.data.RAFParser
 
reachedTargetPlane(double) - Method in class org.limn.engine.TourInterpolate
 
ReaderParser - class org.limn.data.ReaderParser.
ReaderParser uses a fileReader to buffer the data object before loading it into a LimnData object.
ReaderParser() - Constructor for class org.limn.data.ReaderParser
 
record(double[][]) - Method in class org.limn.engine.RecordingFactory
record will preserve the basis values to a file.
recordBasis(String) - Method in class org.limn.engine.FileBasisFactory
 
recordBasis(String) - Method in class org.limn.engine.RecordingFactory
 
recordBasis(String) - Method in interface org.limn.engine.LimnBasisFactory
allows the basis projections to be written out to a file, given the name.
RecordCanvas - class org.limn.render.RecordCanvas.
A basic implementation of the LimnRender interface.
RecordCanvas(LimnData) - Constructor for class org.limn.render.RecordCanvas
 
recordImage() - Method in class org.limn.record.JPEGRecorder
 
recordImage() - Method in class org.limn.record.QuicktimeRecorder
 
recordImage() - Method in interface org.limn.record.LimnRecorder
 
RecordingFactory - class org.limn.engine.RecordingFactory.
RecordingFactory is an abstract class that can be extended to provide functionality that allows the basis to be recorde to a file.
RecordingFactory() - Constructor for class org.limn.engine.RecordingFactory
 
rest() - Method in class org.limn.render.QuicktimeImageProducer
 
rest() - Method in class org.limn.render.JPEGImageProducer
 
rest() - Method in interface org.limn.render.ui.ViewPane
 
run() - Method in class org.limn.data.ParsingThread
run method overrides the Thread class run method, it is invoked when the thread is started this method is where the data is subsetted and written to a file
run() - Method in class org.limn.render.QuicktimeImageProducer
 
run() - Method in class org.limn.render.JPEGImageProducer
 

S

saveMovie() - Method in class org.limn.record.JPEGRecorder
 
saveMovie() - Method in class org.limn.record.QuicktimeRecorder
 
saveMovie() - Method in interface org.limn.record.LimnRecorder
 
saveProperties() - Static method in class org.limn.data.LimnProperties
 
scaleX(double) - Method in class org.limn.render.ParallelCoordinatePlot
 
scaleX(double) - Method in class org.limn.render.ScatterPlotCanvas
 
scaleX(double) - Method in class org.limn.render.HistogramPlot
 
scaleY(double) - Method in class org.limn.render.ParallelCoordinatePlot
 
scaleY(double) - Method in class org.limn.render.ScatterPlotCanvas
 
scaleY(double) - Method in class org.limn.render.HistogramPlot
 
ScatterPlotCanvas - class org.limn.render.ScatterPlotCanvas.
ScatterPlotCanvas is the main graphics class used in the animation building process.
ScatterPlotCanvas(LimnData) - Constructor for class org.limn.render.ScatterPlotCanvas
 
seedBasis(double[][]) - Method in class org.limn.engine.GTBasisFactory
 
seedBasis(double[][]) - Method in class org.limn.engine.LittleTourFactory
 
setActive(String[]) - Method in class org.limn.data.RAFData
 
setActive(String[]) - Method in class org.limn.data.SimpleData
 
setActive(String[]) - Method in interface org.limn.data.LimnData
setActive will reduce the data to only the rows named in the string array
setCount(int) - Method in interface org.limn.render.LimnViewer
set the index of the position in the tour, this will then allow renderable objects to know what projections to base their drawing on.
setCount(int) - Method in class org.limn.render.SimpleViewer
 
setImageSource() - Method in class org.limn.record.QuickImage
 
SimpleBasis - class org.limn.data.SimpleBasis.
SimpleBasis is a very basic implementation of the LimnBasis interface.
SimpleBasis(double[][]) - Constructor for class org.limn.data.SimpleBasis
 
SimpleData - class org.limn.data.SimpleData.
SimpleData is a very basic implementation of the LimnData interface.
SimpleData(double[][], double[][], String[]) - Constructor for class org.limn.data.SimpleData
 
SimpleData(double[][], String[]) - Constructor for class org.limn.data.SimpleData
 
SimpleFilter - class org.limn.data.SimpleFilter.
SimpleFilter implements the LimnFilter interface.
SimpleFilter(String, String) - Constructor for class org.limn.data.SimpleFilter
 
SimpleParser - class org.limn.data.SimpleParser.
SimpleParser is a utility class used to parse a plain white space delineated data file into a LimnData object.
SimpleParser() - Constructor for class org.limn.data.SimpleParser
 
SimpleViewer - class org.limn.render.SimpleViewer.
SimpleViewer is used in the Viewing process.
SimpleViewer(LimnFilter) - Constructor for class org.limn.render.SimpleViewer
 
start() - Method in interface org.limn.render.LimnImageProducer
 
step() - Method in interface org.limn.engine.LimnEngine
Step allerts the engine that the animation projection process has finished and the resources are available to begin the next iteration of the cycle.
step() - Method in class org.limn.engine.TourEngine
 
step() - Method in interface org.limn.render.LimnImageProducer
 
stepBack() - Method in interface org.limn.render.LimnImageProducer
 
stepBack() - Method in class org.limn.render.QuicktimeImageProducer
 
stepBack() - Method in class org.limn.render.JPEGImageProducer
 
stepBack() - Method in interface org.limn.render.ui.ViewPane
 
stepForward() - Method in class org.limn.render.QuicktimeImageProducer
 
stepForward() - Method in class org.limn.render.JPEGImageProducer
 
stepForward() - Method in interface org.limn.render.ui.ViewPane
 
stop() - Method in interface org.limn.render.LimnImageProducer
 

T

test() - Method in class org.limn.data.RAFData
 
TourEngine - class org.limn.engine.TourEngine.
Tour engine is the main implementation of the LimnEngine Interface.
TourEngine(LimnBasisFactory) - Constructor for class org.limn.engine.TourEngine
this is type of constructor is used by the viewer class when it needs to create a projection basis for subsetting data
TourEngine(LimnBasisFactory, LimnRecorder, LimnRender) - Constructor for class org.limn.engine.TourEngine
 
TourInterpolate - class org.limn.engine.TourInterpolate.
TourInterpolate provides routines used in interpolation between tour projections.
TourInterpolate() - Constructor for class org.limn.engine.TourInterpolate
 
tourReproject(double[][]) - Method in class org.limn.engine.TourInterpolate
 
TourUtil - class org.limn.engine.TourUtil.
TourUtil contains basis utility routines for any tour method.
TourUtil() - Constructor for class org.limn.engine.TourUtil
 

U

update(Graphics) - Method in class org.limn.render.RecordCanvas
 
updateImage(Image) - Method in interface org.limn.render.LimnViewer
 
updateImage(Image) - Method in class org.limn.render.SimpleViewer
 

V

ViewControlPane - class org.limn.render.ui.ViewControlPane.
GUI panel used by the View program to allow interaction controls for animation playback.
ViewControlPane(ViewPane) - Constructor for class org.limn.render.ui.ViewControlPane
 
ViewPane - interface org.limn.render.ui.ViewPane.
ViewPane interface provides the basic method signatures needed to control playback of an animation.

A B C E F G H I J L M N O P Q R S T U V