A B C D E G H I J L M N P S T U V X Z

A

AChart<T extends org.jfree.chart.plot.Plot> - Class in maltcms.ui.charts

Abstract base class for Charts of Type T extending Plot of JFreeChart.

AChart() - Constructor for class maltcms.ui.charts.AChart

actionPerformed(ActionEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.TabbedPanel

addAnnotation(ChartPanel, JFreeChart, XYItemEntity, int, int) - Method in class maltcms.ui.charts.JFreeChartViewer.XYAnnotationAdder

addChart(JFreeChart, String) - Method in class maltcms.ui.charts.JFreeChartViewer

addSeries(String, Array, Color) - Method in class maltcms.ui.charts.MassSpectrumPlot

Add a new mass spectra to the plot.

AlignmentMapChart - Class in maltcms.ui.charts

Creates a Plot displaying the mapping between two aligned time series.

AlignmentMapChart(List<Tuple2DI>, Array, Array, String, int, int) - Constructor for class maltcms.ui.charts.AlignmentMapChart

B

BHeatMapChart - Class in maltcms.ui.charts

Creates a chart with labeled domain axis, displaying a heatmap as backgroundimage.

BHeatMapChart(String, String, String, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, String) - Constructor for class maltcms.ui.charts.BHeatMapChart

Default constructor.

C

call() - Method in class maltcms.ui.charts.EPlotRunner

call() - Method in class maltcms.ui.charts.PlotRunner

chartMouseClicked(ChartMouseEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener

chartMouseMoved(ChartMouseEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener

CombinedDomainXYChart - Class in maltcms.ui.charts

Combines Different plots (favorably XYPlots) to share a common domain, such that they are vertically stacked (default).

CombinedDomainXYChart(String, String, boolean, List<XYPlot>) - Constructor for class maltcms.ui.charts.CombinedDomainXYChart

configure(Configuration) - Method in class maltcms.ui.charts.AChart

configure(Configuration) - Method in class maltcms.ui.charts.EPlotRunner

configure(Configuration) - Method in class maltcms.ui.charts.GradientPaintScale

configure(Configuration) - Method in class maltcms.ui.charts.PlotRunner

configure(Configuration) - Method in class maltcms.ui.charts.XYChart

create() - Method in class maltcms.ui.charts.AChart

create() - Method in class maltcms.ui.charts.AlignmentMapChart

create() - Method in class maltcms.ui.charts.BHeatMapChart

create() - Method in class maltcms.ui.charts.CombinedDomainXYChart

create() - Method in class maltcms.ui.charts.HeatMapChart

create() - Method in class maltcms.ui.charts.MassSpectrumPlot

create() - Method in class maltcms.ui.charts.SpiderWebChart

create() - Method in class maltcms.ui.charts.XYChart

create() - Method in class maltcms.ui.charts.XYZChart

create2DRidgeCostDS(int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

create2DRidgeNeighborhoodDS(int, QuadTree<Ridge>, int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createAdaptiveColorHeatmap(ArrayDouble.D2) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createCategoryDataset(String[], String[], double[][]) - Static method in class maltcms.ui.charts.SpiderWebChart

createColorHeatmap(ArrayDouble.D2) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createCostHistogramDS(int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createNeighborhoodHistogramDS(int, int, QuadTree<Ridge>, int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createPAIm(BufferedImage) - Method in class maltcms.ui.TabbedPanel

CwtChartFactory - Class in maltcms.commands.fragments2d.peakfinding

CwtChartFactory() - Constructor for class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

D

drawItem(Graphics2D, XYItemRendererState, Rectangle2D, PlotRenderingInfo, XYPlot, ValueAxis, ValueAxis, XYDataset, int, int, CrosshairState, int) - Method in class maltcms.ui.renderer.LineVectorRenderer

E

EPlotRunner - Class in maltcms.ui.charts

This class is an extension of the normal PlotRunner and will generate a serialized file.

EPlotRunner(Plot, String, String, File) - Constructor for class maltcms.ui.charts.EPlotRunner

Old constructor.

EPlotRunner(JFreeChart, String, File) - Constructor for class maltcms.ui.charts.EPlotRunner

Default constructor.

G

getActiveChartPanel() - Method in class maltcms.ui.charts.JFreeChartViewer

getAlpha() - Method in class maltcms.ui.charts.GradientPaintScale

getBarDistance() - Method in class maltcms.ui.charts.MassSpectrumPlot

Getter.

getBarWidth() - Method in class maltcms.ui.charts.MassSpectrumPlot

Getter.

getBeta() - Method in class maltcms.ui.charts.GradientPaintScale

getContent() - Method in class maltcms.ui.TabbedPanel

getFile() - Method in class maltcms.ui.charts.PlotRunner

getFileMenu() - Method in class maltcms.ui.charts.JFreeChartViewer

getFilename() - Method in class maltcms.ui.charts.PlotRunner

getFiletype() - Method in class maltcms.ui.charts.PlotRunner

getFontFamily() - Method in class maltcms.ui.charts.PlotRunner

getImgheight() - Method in class maltcms.ui.charts.PlotRunner

getImgwidth() - Method in class maltcms.ui.charts.PlotRunner

getJfc() - Method in class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

getJmb() - Method in class maltcms.ui.charts.JFreeChartViewer

getJtp() - Method in class maltcms.ui.charts.JFreeChartViewer

getLookupImage() - Method in class maltcms.ui.charts.GradientPaintScale

getLowerBound() - Method in class maltcms.ui.charts.GradientPaintScale

getMaxAnnotations() - Method in class maltcms.ui.charts.MassSpectrumPlot

Getter.

getMaximumSize() - Method in class maltcms.ui.TabbedPanel

getMaxX() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMaxY() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMinX() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMinY() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getPaint(double) - Method in class maltcms.ui.charts.GradientPaintScale

getParent() - Method in class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

getPlot() - Method in class maltcms.ui.charts.PlotRunner

getPreferredSize() - Method in class maltcms.ui.TabbedPanel

getRamp() - Method in class maltcms.ui.charts.GradientPaintScale

getSelectedDomainVariable() - Method in class maltcms.ui.charts.VariableSelectionPanel

getSelectedValuesVariable() - Method in class maltcms.ui.charts.VariableSelectionPanel

getStatus() - Method in class maltcms.ui.charts.JFreeChartViewer

getTargetContainer() - Method in class maltcms.ui.charts.PlotRunner

getTitle() - Method in class maltcms.ui.charts.AChart

getTitle() - Method in class maltcms.ui.charts.AlignmentMapChart

getTitle() - Method in class maltcms.ui.charts.BHeatMapChart

getTitle() - Method in class maltcms.ui.charts.CombinedDomainXYChart

getTitle() - Method in class maltcms.ui.charts.HeatMapChart

getTitle() - Method in class maltcms.ui.charts.MassSpectrumPlot

getTitle() - Method in class maltcms.ui.charts.PlotRunner

getTitle() - Method in class maltcms.ui.charts.SpiderWebChart

getTitle() - Method in class maltcms.ui.charts.XYChart

getTitle() - Method in class maltcms.ui.charts.XYZChart

getUpperBound() - Method in class maltcms.ui.charts.GradientPaintScale

getYaxis_max() - Method in class maltcms.ui.charts.AChart

getYaxis_min() - Method in class maltcms.ui.charts.AChart

GradientPaintScale - Class in maltcms.ui.charts

GradientPaintScale(double[], double, double, Color[]) - Constructor for class maltcms.ui.charts.GradientPaintScale

H

HeatMapChart - Class in maltcms.ui.charts

Creates a chart with labeled domain axis, displaying a heatmap.

HeatMapChart(BufferedImage, String, String, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, String) - Constructor for class maltcms.ui.charts.HeatMapChart

I

isHeadless() - Method in class maltcms.ui.charts.PlotRunner

isSaveGraphics() - Method in class maltcms.ui.charts.PlotRunner

isSerializeJFreeChart() - Method in class maltcms.ui.charts.PlotRunner

isSizeOverride() - Method in class maltcms.ui.charts.PlotRunner

isStop() - Method in class maltcms.ui.charts.PlotRunner

J

JFreeChartViewer - Class in maltcms.ui.charts

JFreeChartViewer() - Constructor for class maltcms.ui.charts.JFreeChartViewer

JFreeChartViewer.ChartPanelMouseListener - Class in maltcms.ui.charts

JFreeChartViewer.ChartPanelMouseListener(ChartPanel) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener

JFreeChartViewer.ChartSerializeAction - Class in maltcms.ui.charts

JFreeChartViewer.ChartSerializeAction() - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

JFreeChartViewer.ChartSerializeAction(String, Icon) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

JFreeChartViewer.ChartSerializeAction(String) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

JFreeChartViewer.ChromatogramOpenAction - Class in maltcms.ui.charts

JFreeChartViewer.ChromatogramOpenAction() - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

JFreeChartViewer.ChromatogramOpenAction(String, Icon) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

JFreeChartViewer.ChromatogramOpenAction(String) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

JFreeChartViewer.FileOpenAction - Class in maltcms.ui.charts

JFreeChartViewer.FileOpenAction() - Constructor for class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

JFreeChartViewer.FileOpenAction(String, Icon) - Constructor for class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

JFreeChartViewer.FileOpenAction(String) - Constructor for class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

JFreeChartViewer.XYAnnotationAdder - Class in maltcms.ui.charts

JFreeChartViewer.XYAnnotationAdder() - Constructor for class maltcms.ui.charts.JFreeChartViewer.XYAnnotationAdder

L

LineVectorRenderer - Class in maltcms.ui.renderer

Extension of default VectorRenderer, omitting heads / tails of vectors.

LineVectorRenderer() - Constructor for class maltcms.ui.renderer.LineVectorRenderer

M

main(String[]) - Static method in class maltcms.ui.charts.GradientPaintScale

main(String[]) - Static method in class maltcms.ui.charts.JFreeChartViewer

maltcms.commands.fragments2d.peakfinding - package maltcms.commands.fragments2d.peakfinding

maltcms.ui - package maltcms.ui

maltcms.ui.charts - package maltcms.ui.charts

maltcms.ui.renderer - package maltcms.ui.renderer

MassSpectrumPlot - Class in maltcms.ui.charts

Will create a XYPlot bar chart.

MassSpectrumPlot(String, boolean, boolean) - Constructor for class maltcms.ui.charts.MassSpectrumPlot

Constructor to create an empty plot.

MassSpectrumPlot(String, String, Array, boolean, boolean) - Constructor for class maltcms.ui.charts.MassSpectrumPlot

Default constructor.

N

normalize(List<Array>, String, boolean) - Method in class maltcms.ui.charts.AChart

P

PlotRunner - Class in maltcms.ui.charts

Callable which returns a JFreeChart object.

PlotRunner(Plot, String, String, File) - Constructor for class maltcms.ui.charts.PlotRunner

S

saveImages(File, String, List<JFreeChart>) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

saveImages(String, String, List<JFreeChart>) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

setAlpha(double) - Method in class maltcms.ui.charts.GradientPaintScale

setAlphaBeta(double, double) - Method in class maltcms.ui.charts.GradientPaintScale

setAvailableVariables(String[]) - Method in class maltcms.ui.charts.VariableSelectionPanel

setBarDistance(double) - Method in class maltcms.ui.charts.MassSpectrumPlot

Setter.

setBarWidth(double) - Method in class maltcms.ui.charts.MassSpectrumPlot

Setter.

setBeta(double) - Method in class maltcms.ui.charts.GradientPaintScale

setFile(File) - Method in class maltcms.ui.charts.PlotRunner

setFileMenu(JMenu) - Method in class maltcms.ui.charts.JFreeChartViewer

setFilename(String) - Method in class maltcms.ui.charts.PlotRunner

setFiletype(String) - Method in class maltcms.ui.charts.PlotRunner

setFontFamily(String) - Method in class maltcms.ui.charts.PlotRunner

setGap(int) - Method in class maltcms.ui.charts.CombinedDomainXYChart

setHeadless(boolean) - Method in class maltcms.ui.charts.PlotRunner

setImgheight(int) - Method in class maltcms.ui.charts.PlotRunner

setImgwidth(int) - Method in class maltcms.ui.charts.PlotRunner

setJfc(JFreeChart) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

setJmb(JMenuBar) - Method in class maltcms.ui.charts.JFreeChartViewer

setJtp(JTabbedPane) - Method in class maltcms.ui.charts.JFreeChartViewer

setLowerBound(double) - Method in class maltcms.ui.charts.GradientPaintScale

setMaxAnnotations(int) - Method in class maltcms.ui.charts.MassSpectrumPlot

Setter.

setParent(Component) - Method in class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

setPlot(Plot) - Method in class maltcms.ui.charts.PlotRunner

setRamp(int[][]) - Method in class maltcms.ui.charts.GradientPaintScale

setSaveGraphics(boolean) - Method in class maltcms.ui.charts.PlotRunner

setSerializeJFreeChart(boolean) - Method in class maltcms.ui.charts.PlotRunner

setSizeOverride(boolean) - Method in class maltcms.ui.charts.PlotRunner

setStatus(JLabel) - Method in class maltcms.ui.charts.JFreeChartViewer

setStop(boolean) - Method in class maltcms.ui.charts.PlotRunner

setTargetContainer(JFrame) - Method in class maltcms.ui.charts.PlotRunner

setTitle(String) - Method in class maltcms.ui.charts.AChart

setTitle(String) - Method in class maltcms.ui.charts.AlignmentMapChart

setTitle(String) - Method in class maltcms.ui.charts.BHeatMapChart

setTitle(String) - Method in class maltcms.ui.charts.CombinedDomainXYChart

setTitle(String) - Method in class maltcms.ui.charts.HeatMapChart

setTitle(String) - Method in class maltcms.ui.charts.MassSpectrumPlot

setTitle(String) - Method in class maltcms.ui.charts.PlotRunner

setTitle(String) - Method in class maltcms.ui.charts.SpiderWebChart

setTitle(String) - Method in class maltcms.ui.charts.XYChart

setTitle(String) - Method in class maltcms.ui.charts.XYZChart

setUpperBound(double) - Method in class maltcms.ui.charts.GradientPaintScale

setYaxis_max(double) - Method in class maltcms.ui.charts.AChart

setYaxis_min(double) - Method in class maltcms.ui.charts.AChart

SpiderWebChart - Class in maltcms.ui.charts

Chart displaying a plot of different variables organized as a spider's web.

SpiderWebChart(String, CategoryDataset) - Constructor for class maltcms.ui.charts.SpiderWebChart

SpiderWebChart(String, String[], String[], double[][]) - Constructor for class maltcms.ui.charts.SpiderWebChart

T

TabbedPanel - Class in maltcms.ui

Visual class displaying the proposed partitioning of an array with a given set of anchors.

TabbedPanel(PartitionedArray, AnchorPairSet) - Constructor for class maltcms.ui.TabbedPanel

translatePointToImageCoord(Point2D, Rectangle2D) - Method in class maltcms.ui.charts.XYBPlot

Translates a given screen point from a mouse event to the coredponding image coordinates.

translatePointToImageCoords(double, double) - Method in class maltcms.ui.charts.XYBPlot

Maps a point from axis coordinates to image coordinates.

U

updateBackground() - Method in class maltcms.ui.charts.XYBPlot

This method will update the background image on the chart.

V

VariableSelectionPanel - Class in maltcms.ui.charts

VariableSelectionPanel() - Constructor for class maltcms.ui.charts.VariableSelectionPanel

Creates new form VariableSelectionPanel

X

XYBPlot - Class in maltcms.ui.charts

This class extends the XYPlot to a Plot with a zoomable background image.

XYBPlot(String, NumberAxis, NumberAxis) - Constructor for class maltcms.ui.charts.XYBPlot

Default constructor.

XYBPlot(String, String, String) - Constructor for class maltcms.ui.charts.XYBPlot

Default constructor.

XYChart - Class in maltcms.ui.charts

Chart to display one Variable's data, or additionally combined with domain values.

XYChart(String, String[], Array[], Array[], Array, Array, String[], String, String) - Constructor for class maltcms.ui.charts.XYChart

XYChart(String, String[], Array[], Array[], String, String, boolean) - Constructor for class maltcms.ui.charts.XYChart

XYChart(String, String[], Array[], Array[], String, String) - Constructor for class maltcms.ui.charts.XYChart

XYChart(String, String[], Array[], String, String) - Constructor for class maltcms.ui.charts.XYChart

XYZChart - Class in maltcms.ui.charts

Heatmap like chart, using to variable's values as indices for a third variable's value.

XYZChart(String, String, String, String, Array, ArrayList<Array>, ArrayList<Array>) - Constructor for class maltcms.ui.charts.XYZChart

Z

zoomDomainAxes(double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

zoomDomainAxes(double, PlotRenderingInfo, Point2D, boolean) - Method in class maltcms.ui.charts.XYBPlot

zoomDomainAxes(double, double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

zoomRangeAxes(double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

zoomRangeAxes(double, PlotRenderingInfo, Point2D, boolean) - Method in class maltcms.ui.charts.XYBPlot

zoomRangeAxes(double, double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

A B C D E G H I J L M N P S T U V X Z