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A

a95 - Variable in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
α95, the 95% confidence interval, in degrees
about - Variable in class net.talvi.puffinplot.PuffinActions
Opens the application's ‘About’ dialog box.
about() - Method in class net.talvi.puffinplot.PuffinApp
Shows the application's ‘About’ dialog box, giving brief information about PuffinPlot.
AboutBox - Class in net.talvi.puffinplot.window
An ‘about this program’ dialog box giving brief information about PuffinPlot.
AboutBox(PuffinApp) - Constructor for class net.talvi.puffinplot.window.AboutBox
Creates a new about box.
actionPerformed(ActionEvent) - Method in class net.talvi.puffinplot.window.ControlPanel
Handles action events.
actionPerformed(ActionEvent) - Method in class net.talvi.puffinplot.window.ProgressDialog
 
actionPerformed(ActionEvent) - Method in class net.talvi.puffinplot.window.TreatmentWindow
Handle an action event.
add(int, T) - Method in class net.talvi.puffinplot.data.CustomFields
Adds a new value to this custom field list.
add(TreatmentStep) - Method in class net.talvi.puffinplot.data.Line
Associates a TreatmentStep with this line.
add(List<File>) - Method in class net.talvi.puffinplot.RecentFileList
Adds a new file-set to the top of the list.
add(RenderingHints) - Method in class net.talvi.puffinplot.window.PuffinRenderingHints
addCurrentTreatmentStepListener(CurrentTreatmentStepListener) - Method in class net.talvi.puffinplot.window.GraphDisplay
Add a listener for changes to the current datum (i.e.
addDecRad(double) - Method in class net.talvi.puffinplot.data.Vec3
Returns a new vector equal to this vector with the specified angle added to the declination.
addExtraLine(String) - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
Add a line to the internal extra line cache
addIncRad(double) - Method in class net.talvi.puffinplot.data.Vec3
Returns a new vector equal to this vector with the specified angle added to the inclination.
addMessage(String, Object...) - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
Add a formatted message to the internal message cache.
addPath(Path2D, boolean) - Method in class net.talvi.puffinplot.plots.LineCache
Adds a path to this cache.
addPoint(TreatmentStep, Point2D, boolean, boolean, boolean) - Method in class net.talvi.puffinplot.plots.Plot
Adds a point to this plot's internal buffer.
addSampleClickListener(SampleClickListener) - Method in class net.talvi.puffinplot.plots.Plot
Adds a listener for sample clicks to this plot.
addSavedListener(Suite.SavedListener) - Method in class net.talvi.puffinplot.data.Suite
Add a listener for the Suite's save state
addTreatmentStep(TreatmentStep) - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
Add a treatment step to the internal cache.
addTreatmentStep(TreatmentStep) - Method in class net.talvi.puffinplot.data.Sample
Adds a treatment step to this sample.
addTreatmentStep(TreatmentStep) - Method in class net.talvi.puffinplot.data.Suite
Adds a datum to the suite.
addVisibilityChangedListener(Consumer<Boolean>) - Method in class net.talvi.puffinplot.plots.Plot
Adds a listener for visibility changes to this plot.
AlignDeclinationsDialog - Class in net.talvi.puffinplot.window
A dialog allowing the user to perform declination alignment between core sections.
AlignDeclinationsDialog(PuffinApp) - Constructor for class net.talvi.puffinplot.window.AlignDeclinationsDialog
Create a new declination alignment dialog.
alignSectionDeclinations(int, double, CoreSections.TargetDeclinationType) - Method in class net.talvi.puffinplot.data.Suite
Align the declinations of core sections in this suite.It is assumed that the suite is continuous; the discrete IDs of samples are interpreted as core section identifiers.
alignSectionDeclinations - Variable in class net.talvi.puffinplot.PuffinActions
Automatically aligns declinations between core sections.
alignSections(int, double, CoreSections.TargetDeclinationType) - Method in class net.talvi.puffinplot.data.CoreSections
Aligns the declinations of these core sections from the top down.
AmsCalculationType - Enum in net.talvi.puffinplot.data
The type of a statistical calculation on AMS tensors.
AmsData - Class in net.talvi.puffinplot.data
This class holds AMS (anisotropy of magnetic susceptibility) data for a named sample.
AmsData(String, OrientationParameters, double[], double, double, double, double, double) - Constructor for class net.talvi.puffinplot.data.AmsData
Creates a new AMS data set with the data provided.
AmsLoader - Class in net.talvi.puffinplot.data.file
Turns an AGICO .ASC AMS file into a list of AmsData objects.
AmsLoader(File) - Constructor for class net.talvi.puffinplot.data.file.AmsLoader
Creates a new AMS loader for a specified file.
AmsPlot - Class in net.talvi.puffinplot.plots
A plot which shows the principal axes of anisotropy of magnetic susceptibility (AMS) tensors, and statistical means and confidence regions for groups of tensors.
AmsPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.AmsPlot
Creates an AMS plot with the supplied parameters.
angleFromLast(Vec3) - Method in class net.talvi.puffinplot.data.GreatCircle
Returns the angle between the supplied direction and the last point on the great-circle fit.
angleTo(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Returns the signed angle between this vector and another vector.
appendFiles - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to choose one or more files to append to the current data suite.
AppleEventHandler - Class in net.talvi.puffinplot
AppleEventHandler handles the user actions About, Open, Preferences, and Quit on Mac OS X systems, passing them on to the appropriate methods of a PuffinApp instance specified on initialization.
apply(TreatmentStep) - Method in enum net.talvi.puffinplot.data.TreatmentStepOperation
Apply this operation to a treatment step.
applyTextAttributes(AttributedString) - Method in class net.talvi.puffinplot.plots.Plot
Applies this plot's standard text attributes to an attributed string.
ArasonLevi - Class in net.talvi.puffinplot.data
Calculate and store Arason-Levi Maximum Likelihood Estimates (MLE) for inclination-only data.
ArasonLevi.ArithMean - Class in net.talvi.puffinplot.data
Calculate and store mean inclination estimates based on a simple arithmetic mean.
areSectionEndDirectionsDefined(int) - Method in class net.talvi.puffinplot.data.CoreSections
Reports whether all samples within section ends have a defined direction.
areSectionEndDirectionsDefined(int) - Method in class net.talvi.puffinplot.data.Suite
Report whether samples near the ends of core sections have an associated direction, e.g.
areTreatmentStepsLabelled() - Method in class net.talvi.puffinplot.plots.Plot
Determines whether the points should be labelled.
areTreatmentStepsLabelled() - Method in class net.talvi.puffinplot.plots.SampleEqualAreaPlot
 
areTreatmentStepsLabelled() - Method in class net.talvi.puffinplot.plots.ZPlot
 
ArmAxis - Enum in net.talvi.puffinplot.data
ArmAxis represents the axis along which an ARM (anhysteretic remanent magnetization) field has been applied.

B

bootAmsNaive - Variable in class net.talvi.puffinplot.PuffinActions
Calculates bootstrap AMS statistics on the selected samples.
bootAmsParam - Variable in class net.talvi.puffinplot.PuffinActions
Calculates parametric bootstrap AMS statistics on the selected samples.
Bundle - Class in net.talvi.puffinplot
Provides a static method for saving a PuffinPlot suite as a self-contained bundle comprising data, calculation results, scripts for automated processing, and optionally the PuffinPlot jar itself.
Bundle() - Constructor for class net.talvi.puffinplot.Bundle
 

C

cachedGraphics - Variable in class net.talvi.puffinplot.plots.EqualAreaPlot
The graphics object to which the plot is currently being drawn.
calculate(Collection<Double>) - Static method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
Calculate the arithmetic mean of a collection of inclinations.
calculate(Collection<Double>) - Static method in class net.talvi.puffinplot.data.ArasonLevi
Calculate Arason-Levi parameters for a collection of inclinations.
calculate(Collection<Vec3>) - Static method in class net.talvi.puffinplot.data.FisherValues
Returns a set of Fisherian statistics, calculated using the Fisher (1953) method, for a collection of vectors.
calculate(List<TreatmentStep>) - Static method in class net.talvi.puffinplot.data.MedianDestructiveField
Calculate and create a median destructive field (or temperature) value for the supplied data.
calculate(Sample, Correction) - Static method in class net.talvi.puffinplot.data.PcaAnnotated
Performs principal component analysis (PCA) on the specified sample.
calculate(List<Vec3>, boolean) - Static method in class net.talvi.puffinplot.data.PcaValues
Performs principal component analysis (PCA) on the supplied vectors and returns an object containing the results of the analysis.
calculate(Collection<Vec3>) - Static method in class net.talvi.puffinplot.data.SuiteCalcs.Means
Calculate Fisher statistics on a set of directions.
calculate(FisherParams, Location) - Static method in class net.talvi.puffinplot.data.VGP
Calculate a VGP for the given direction and location.
calculateAmsStatistics(List<Sample>, AmsCalculationType, String) - Method in class net.talvi.puffinplot.data.Suite
Calculates and stores AMS statistics using an external script.
calculateBootstrap(List<Tensor>, boolean, String) - Static method in class net.talvi.puffinplot.data.KentParams
Calculates 95% Kent confidence ellipses from the supplied tensors by running the bootams.py script from Lisa Tauxe's pmagpy suite.
calculateFisher(Correction) - Method in class net.talvi.puffinplot.data.Sample
Calculates a Fisherian mean for the selected demagnetization steps.
calculateFisherStats(Correction) - Method in class net.talvi.puffinplot.data.Site
Calculate Fisherian statistics on the PCA directions of samples within this site.
calculateGreatCirclesDirection(Correction, String) - Method in class net.talvi.puffinplot.data.Site
Calculate a mean direction for the site using best-fit great circles.
calculateGreatCirclesDirections() - Method in class net.talvi.puffinplot.PuffinApp
For all selected sites, calculates the site mean direction by best-fit intersection of great circles fitted to that site's samples.
calculateHext(List<Tensor>, String) - Static method in class net.talvi.puffinplot.data.KentParams
Calculates 95% Kent confidence ellipses from the supplied tensors by running the s_hext.py script from Lisa Tauxe's pmagpy suite.
calculateMagSusJump() - Method in class net.talvi.puffinplot.data.Sample
Finds the first jump in magnetic susceptibility in the sample's demagnetization data.
calculateMdf() - Method in class net.talvi.puffinplot.data.Sample
Calculates the median destructive field using the visible treatmentSteps points of this sample and stores the results within this sample.
calculateMultiSuiteMeans(List<Suite>) - Static method in class net.talvi.puffinplot.data.Suite
Calculates and returns Fisher statistics on all the calculated PCA directions for samples within supplied suites.
calculateMultiSuiteMeans() - Method in class net.talvi.puffinplot.PuffinApp
Calculate means across all currently loaded suites.
calculateRpi - Variable in class net.talvi.puffinplot.PuffinActions
Performs an RPI calculation.
calculateSHA1(File) - Static method in class net.talvi.puffinplot.Util
Calculate the SHA-1 digest of a file and return it as an upper-case hexadecimal string.
calculateSiteFishers(Correction) - Method in class net.talvi.puffinplot.data.Suite
For each site in this suite, calculates Fisher statistics on the sample PCA directions.
calculateSuiteMeans(List<Sample>, List<Site>) - Method in class net.talvi.puffinplot.data.Suite
Calculates Fisher statistics on all the calculated PCA directions for samples within the suite.
calculateVgp() - Method in class net.talvi.puffinplot.data.Site
Calculates a virtual geomagnetic pole for the site, if possible.
calculateWithMagSus(Suite, Suite) - Static method in class net.talvi.puffinplot.data.SuiteRpiEstimate
Estimate RPI by normalizing NRM to MS.
calculateWithStepwiseAF(Suite, Suite, double, double) - Static method in class net.talvi.puffinplot.data.SuiteRpiEstimate
Estimate RPI by normalizing a stepwise demagnetized NRM to another stepwise demagnetized remanence (ARM or IRM).
calculateWithStepwiseARM(Suite, Suite, double, double) - Static method in class net.talvi.puffinplot.data.SuiteRpiEstimate
Estimate RPI by normalizing a stepwise demagnetized NRM to a stepwise imparted ARM.
CaltechLoader - Class in net.talvi.puffinplot.data.file
A file loader for CIT (Caltech) data files.
CaltechLoader() - Constructor for class net.talvi.puffinplot.data.file.CaltechLoader
 
checkInstalled(boolean) - Static method in class net.talvi.puffinplot.JythonJarManager
Checks whether the Jython jar file is installed locally and has the correct size.
checkOptions(Map<String, Object>) - Method in interface net.talvi.puffinplot.data.file.FileLoader
Checks that a set of options is valid for this file loader.
checkSha1Digest(boolean) - Static method in class net.talvi.puffinplot.JythonJarManager
Calculates the SHA-1 digest of the Jython jar file and verifies it against a hard-coded reference value.
circleFit - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, fits a great circle to the selected points.
CiteWindow - Class in net.talvi.puffinplot.window
A window which displays information on how to cite PuffinPlot.
CiteWindow(PuffinApp) - Constructor for class net.talvi.puffinplot.window.CiteWindow
Creates a new CiteWindow.
clear() - Method in class net.talvi.puffinplot.window.PuffinRenderingHints
clearAmsCalcs - Variable in class net.talvi.puffinplot.PuffinActions
Clears AMS calculations for the current suite.
clearAmsCalcs() - Method in class net.talvi.puffinplot.PuffinApp
Clears the results of any AMS calculations for the current suite.
clearAmsCalculations() - Method in class net.talvi.puffinplot.data.Suite
Clears any AMS calculations on this suite
clearCalculations() - Method in class net.talvi.puffinplot.data.Sample
Clears all calculations for this sample (PCA, MDF, and great-circle fit) and deselects all treatment steps.
clearFisherStats() - Method in class net.talvi.puffinplot.data.Site
Clears the stored Fisher statistics, if any.
clearGcFit() - Method in class net.talvi.puffinplot.data.Site
Clears the stored great-circle fit parameters, if any
clearGreatCircle() - Method in class net.talvi.puffinplot.data.Sample
Clears great-circle fit for this sample.
clearPca() - Method in class net.talvi.puffinplot.data.Sample
Clears PCA calculations for this sample.
clearPoints() - Method in class net.talvi.puffinplot.plots.Plot
Clear this plot's internal buffer of points.
clearPreferences - Variable in class net.talvi.puffinplot.PuffinActions
Clears the current user preferences, resetting them to their default values.
clearPreferences() - Method in class net.talvi.puffinplot.PuffinApp
Shows a confirmation dialog.
clearSampleCalcs - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, clears all calculations and deselects all points.
clearSampleGreatCircle - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, clears great circle fit.
clearSamplePca - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, clears PCA calculation.
clearSelection - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, deselects all the points.
clearSiteCalcs - Variable in class net.talvi.puffinplot.PuffinActions
Clears any previously calculated Fisherian or great-circle site directions.
clearSiteCalculations() - Method in class net.talvi.puffinplot.PuffinApp
Clears any previously calculated Fisherian or great-circle site directions.
clearSites(Collection<Sample>) - Method in class net.talvi.puffinplot.data.Suite
Clears sites for specified samples within this suite.
clearSites - Variable in class net.talvi.puffinplot.PuffinActions
Clears site definitions for selected samples.
clipLineToRectangle(Line2D, Rectangle2D) - Static method in class net.talvi.puffinplot.Util
Clips a line to a supplied rectangle.
close() - Method in class net.talvi.puffinplot.data.CsvWriter
Closes the underlying writer supplied to this CSV writer's constructor.
close - Variable in class net.talvi.puffinplot.PuffinActions
Closes the current data suite.
closeCurrentSuite() - Method in class net.talvi.puffinplot.PuffinApp
Closes the suite whose data is currently being displayed.
collectMeasurementTypes(Collection<TreatmentStep>) - Static method in class net.talvi.puffinplot.data.TreatmentStep
Returns a set of all the measurement types of the supplied treatment steps.
compare(TreatmentStep, TreatmentStep) - Method in class net.talvi.puffinplot.data.TreatmentLevelComparator
Compare treatment steps according to their treatment level.
compare(TreatmentStep, TreatmentStep) - Method in class net.talvi.puffinplot.data.TreatmentStepMomentComparator
Compares the magnetic moments of the supplied datum objects using the criteria specified in the constructor.
contains(double) - Method in class net.talvi.puffinplot.data.MultiRange
Determine if a value is within one of the ranges of this multirange.
containsSample(String) - Method in class net.talvi.puffinplot.data.Suite
Determine whether this suite contain a same with a specified identifier (name).
ControlPanel - Class in net.talvi.puffinplot.window
The control panel provides a user interface for common operations.
ControlPanel(PuffinApp) - Constructor for class net.talvi.puffinplot.window.ControlPanel
Creates a new control panel
convertDiscreteToContinuous(Map<String, String>) - Method in class net.talvi.puffinplot.data.Suite
Converts this suite from a discrete suite to a continuous suite using a supplied mapping from sample names to depths.
convertDiscreteToContinuous(File) - Method in class net.talvi.puffinplot.data.Suite
Converts a discrete suite to a continuous suite, using a file to provide the mapping from sample names to depths.
convertDiscreteToContinuous - Variable in class net.talvi.puffinplot.PuffinActions
Converts a discrete suite into a continuous one.
convertStringToColumnWidths(String) - Static method in class net.talvi.puffinplot.data.file.FileFormat
Turns a string containing comma-separated decimal integers into a List of Integers.
convertToPuffinPlotConvention(VectorAndOrientations) - Method in class net.talvi.puffinplot.data.file.OrientationParameters
This method takes a VectorAndOrientations object and interprets its contents according to the settings in this OrientationParameters object.
copyStepSelection - Variable in class net.talvi.puffinplot.PuffinActions
Copies the range of selected points from the current sample onto a clipboard.
copyStepSelection() - Method in class net.talvi.puffinplot.PuffinApp
Copies the current pattern of selected treatment steps to a clipboard.
CoreSection - Class in net.talvi.puffinplot.data
A representation of a section of core, comprising a contiguous sequence of Samples.
CoreSection.End - Enum in net.talvi.puffinplot.data
A representation of the end of a core section -- top or bottom.
CoreSections - Class in net.talvi.puffinplot.data
A collection of CoreSections, stored as a linked hash map indexed by a string identifier.
CoreSections.TargetDeclinationType - Enum in net.talvi.puffinplot.data
The declination which should be aligned with a reference alignment passed to CoreSections.alignSections(int, double, net.talvi.puffinplot.data.CoreSections.TargetDeclinationType).
correctForm(double, double) - Method in class net.talvi.puffinplot.data.Vec3
Applies a sample correction to this vector.
correctFormationDipDirectionForP4(double) - Method in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
Taking this parameter as P4, converts a formation dip direction to the "P4=0" convention.
Correction - Class in net.talvi.puffinplot.data
This class represents the corrections which may be applied to the measured remanence to estimate the true remanence.
Correction(boolean, boolean, Correction.Rotation, boolean) - Constructor for class net.talvi.puffinplot.data.Correction
Creates a new set of corrections
Correction.Rotation - Enum in net.talvi.puffinplot.data
An enumeration of the types of rotation correction which may be applied to a sample's data.
correctSample(double, double) - Method in class net.talvi.puffinplot.data.Vec3
Applies a sample correction to this vector.
correctSampleDipForP2(double) - Method in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
Taking this parameter as P2, converts a dip to the "P2=90" convention.
create() - Static method in class net.talvi.puffinplot.PuffinApp
Create and return a new PuffinApp object.
createBundle(Suite, Path, Correction, List<Sample>, List<Site>, boolean) - Static method in class net.talvi.puffinplot.Bundle
Create and save a PuffinPlot data bundle.
createBundle - Variable in class net.talvi.puffinplot.PuffinActions
Creates a bundle.
createNewSuite() - Method in class net.talvi.puffinplot.PuffinApp
Creates a new, empty suite and adds it to the suite list.
cropRectangle(Rectangle2D, double, double, double, double) - Method in class net.talvi.puffinplot.plots.Plot
Returns a cropped version of a specified rectangle.
cross(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Returns the cross product of this vector and another vector.
CsvWriter - Class in net.talvi.puffinplot.data
This class provides a wrapper around a supplied Writer to allow easy writing of lines of data with fields separated by a particular string.
CsvWriter(Writer, String) - Constructor for class net.talvi.puffinplot.data.CsvWriter
Creates a new CSV writer which will write to the specified writer and separate fields with the specified string.
CsvWriter(Writer) - Constructor for class net.talvi.puffinplot.data.CsvWriter
Creates a new CSV writer which will write to the specified writer using a comma as the field separator.
CurrentTreatmentStepListener - Interface in net.talvi.puffinplot.window
A listener for changes in the current treatment step.
CustomFieldEditor - Class in net.talvi.puffinplot.window
An editing window for custom field headings.
CustomFieldEditor(CustomFields<String>, String, PuffinApp) - Constructor for class net.talvi.puffinplot.window.CustomFieldEditor
Creates a new custom field editor window.
CustomFields<T> - Class in net.talvi.puffinplot.data
Represents a set of custom fields for sample annotation.
CustomFields(List<T>) - Constructor for class net.talvi.puffinplot.data.CustomFields
Creates a set of custom fields with the specified values.
CustomFields() - Constructor for class net.talvi.puffinplot.data.CustomFields
Creates an empty set of custom fields.

D

dataChanged() - Method in class net.talvi.puffinplot.window.TableWindow
Forces the data table to update its display.
DEFAULT_PLOT_POSITIONS - Static variable in class net.talvi.puffinplot.plots.Plot
the default sizes and positions of the plots
DemagPlot - Class in net.talvi.puffinplot.plots
Demagnetization plot.
DemagPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.DemagPlot
Creates a demagnetization plot with the supplied parameters
DemagTable - Class in net.talvi.puffinplot.plots
A table showing some of the data from individual treatment steps of a single sample.
DemagTable(PlotParams) - Constructor for class net.talvi.puffinplot.plots.DemagTable
Creates a demagnetization table with the supplied parameters
DepthPlot - Class in net.talvi.puffinplot.plots
A simple x/y plot for the entire suite with depth on the x axis and a sample parameter on the y axis.
DepthPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.DepthPlot
Creates a depth plot with the supplied parameters
dimensions - Variable in class net.talvi.puffinplot.plots.Plot
the plot's dimensions
Direction - Enum in net.talvi.puffinplot.plots
A representation of a two-dimensional perpendicular direction.
distance(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Returns the distance between two vectors.
divideBy(double) - Method in class net.talvi.puffinplot.data.Vec3
Divides this vector by a scalar value.
divideBy(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Divides the components of this vector individually by the corresponding components of another vector.
doAllCalculations(Correction, String) - Method in class net.talvi.puffinplot.data.Suite
Performs all possible sample and site calculations.
doAmsCalc(AmsCalculationType, String) - Method in class net.talvi.puffinplot.PuffinApp
Performs statistical calculations on AMS data using a script from Lisa Tauxe's pmagpy software suite.
doInBackground() - Method in class net.talvi.puffinplot.DownloadWorker
 
doPca(Correction) - Method in class net.talvi.puffinplot.data.Sample
Performs principal component analysis on a subset of the magnetic moment data of this sample.
doPcaOnSelection() - Method in class net.talvi.puffinplot.PuffinApp
For all selected samples, determine a best-fit line to the selected treatment steps by principal component analysis.
doReversalTest(List<Suite>) - Static method in class net.talvi.puffinplot.data.Suite
Performs a reversal test on a list of suites.
doSampleCalculations(Correction) - Method in class net.talvi.puffinplot.data.Suite
Performs calculations for each sample in this suite.
doSiteCalculations(Correction, String) - Method in class net.talvi.puffinplot.data.Suite
Calculates mean directions for all suitable sites in the suite.
dot(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Returns the dot product of this vector and another vector.
DOWN - Static variable in class net.talvi.puffinplot.data.Vec3
a unit vector pointing down
download() - Static method in class net.talvi.puffinplot.JythonJarManager
Downloads the Jython jar from a hard-coded URL and saves it in the application data directory.
downloadUrlToFile(String, Path) - Static method in class net.talvi.puffinplot.Util
Downloads data from a URL and saves it to a file.
DownloadWorker - Class in net.talvi.puffinplot
A SwingWorker which downloads a file from a specified URL and saves it to a specified path.
DownloadWorker(URL, Path) - Constructor for class net.talvi.puffinplot.DownloadWorker
Create a worker which will download a a file from a given URL to a given path.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.AmsPlot
Draws this plot.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.DemagPlot
Draws this plot.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.DemagTable
Draws the table.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.DepthPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.LineCache
Draws the paths in this cache.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.NrmHistogram
Draws this plot.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.Plot
Draws this plot.
draw(Graphics2D) - Method in interface net.talvi.puffinplot.plots.PlotPoint
Draws this point in a supplied graphics context.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.PlotTitle
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.RpiPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SampleEqualAreaPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SampleParamsLegend
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SampleParamsTable
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SeparateSuiteEqualAreaPlot
Draws this plot.
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SiteEqualAreaPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SiteParamsLegend
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SiteParamsTable
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SuiteEqualAreaPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.SuiteParamsTable
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.TernaryPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.VgpMap
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.VgpTable
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.ZPlot
 
draw(Graphics2D) - Method in class net.talvi.puffinplot.plots.ZPlot.ZplotLegend
 
drawAxes() - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Draws the axes of the plot.
drawGreatCircle(Vec3, boolean) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Projects and draws a great circle
drawGreatCircleSegment(Vec3, Vec3) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Draws the projection of a specified great-circle segment.
drawGreatCircleSegment(Vec3, Vec3, Vec3) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Draws the projection of a specified great-circle segment.
drawLineSegments(List<Vec3>) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Projects and draws the supplied vectors.
drawPoints(Graphics2D) - Method in class net.talvi.puffinplot.plots.Plot
Draws the points in this plot's internal buffer.
drawWithPossibleLine(Graphics2D, PlotPoint, boolean) - Method in interface net.talvi.puffinplot.plots.PlotPoint
Draws this point in a specified graphics context, possibly drawing a line from a supplied previous point to this one.

E

EAST - Static variable in class net.talvi.puffinplot.data.Vec3
a unit vector pointing east
EditSampleParametersWindow - Class in net.talvi.puffinplot.window
A window allowing the user to edit orientation corrections.
EditSampleParametersWindow(PuffinApp) - Constructor for class net.talvi.puffinplot.window.EditSampleParametersWindow
Creates a new correction window.
Eigens - Class in net.talvi.puffinplot.data
A class to calculate and store the eigenvalues and eigenvectors of a matrix.
Eigens(Matrix) - Constructor for class net.talvi.puffinplot.data.Eigens
Create an object holding the eigenvectors and eigenvalues of the supplied matrix.
EmptyLoadedData - Class in net.talvi.puffinplot.data.file
A trivial implementation of the LoadedData interface, which contains no data, only an optional single message.
EmptyLoadedData(String) - Constructor for class net.talvi.puffinplot.data.file.EmptyLoadedData
Instantiate an EmptyLoadedData object with a single message.
EmptyLoadedData() - Constructor for class net.talvi.puffinplot.data.file.EmptyLoadedData
Instantiate an EmptyLoadedData object with no message.
envelope(Collection<Point2D>) - Static method in class net.talvi.puffinplot.Util
Returns the rectangular envelope for the supplied points.
EqualAreaPlot - Class in net.talvi.puffinplot.plots
An abstract superclass for Lambert azimuthal equal-area plots.
EqualAreaPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.EqualAreaPlot
Creates a new equal-area plot with the supplies parameters.
equals(Object) - Method in class net.talvi.puffinplot.data.file.OrientationParameters
Compares equality of two orientation parameter sets.
equals(Object) - Method in class net.talvi.puffinplot.data.Vec3
 
equals(Vec3, double) - Method in class net.talvi.puffinplot.data.Vec3
Compares vectors for equality to a specified precision.
equatorPoint(Vec3, Vec3) - Static method in class net.talvi.puffinplot.data.Vec3
Returns the unit vector on the intersection of the equator (z=0 line) and the great circle between the supplied points.
errorDialog(String, String, Component) - Static method in class net.talvi.puffinplot.PuffinApp
Displays a dialog box reporting an error.
errorDialog(String, String) - Method in class net.talvi.puffinplot.PuffinApp
Displays a dialog box reporting an error over this PuffinApp's main window.
exportAsString() - Method in class net.talvi.puffinplot.data.CustomFields
Returns a string representation of the list of values.
exportCalcsMultiSuite - Variable in class net.talvi.puffinplot.PuffinActions
Opens a ‘Save’ dialog box; suite calculations are saved to the chosen file (if any).
exportCalcsSample - Variable in class net.talvi.puffinplot.PuffinActions
Opens a ‘Save’ dialog box; sample calculations are saved to the chosen file (if any).
exportCalcsSite - Variable in class net.talvi.puffinplot.PuffinActions
Opens a ‘Save’ dialog box; site calculations are saved to the chosen file (if any).
exportCalcsSuite - Variable in class net.talvi.puffinplot.PuffinActions
Opens a ‘Save’ dialog box; suite calculations are saved to the chosen file (if any).
exportFields(List<TreatmentParameter>) - Method in class net.talvi.puffinplot.data.Sample
Returns a specified subset of demagnetization treatmentSteps as strings.
exportFieldValues(Collection<TreatmentParameter>, String) - Method in class net.talvi.puffinplot.data.TreatmentStep
Produces a string containing string representations of the contents of selected data fields.
exportIrm - Variable in class net.talvi.puffinplot.PuffinActions
Opens a save dialog allowing the export of the current suite's IRM data as a tab-delimited text file.
exportPdfFreehep - Variable in class net.talvi.puffinplot.PuffinActions
Opens a save dialog allowing the current main display to be saved as a PDF file.
exportPdfFreehep(File) - Method in class net.talvi.puffinplot.PuffinApp
Writes a PDF file containing data plots with the current layout for all selected samples.
exportPdfItext - Variable in class net.talvi.puffinplot.PuffinActions
Opens a save dialog allowing the current main display to be saved as a PDF file.
exportPdfItext(File) - Method in class net.talvi.puffinplot.PuffinApp
Writes a PDF file containing data plots with the current layout for all selected samples.
exportPrefs - Variable in class net.talvi.puffinplot.PuffinActions
Exports the current user preferences to an XML file.
exportSvgBatik - Variable in class net.talvi.puffinplot.PuffinActions
Opens a save dialog allowing the current main display to be saved as an SVG file using the Batik library.
exportSvgFreehep - Variable in class net.talvi.puffinplot.PuffinActions
Opens a save dialog allowing the current main display to be saved as an SVG file using the FreeHEP library.
exportToFile(File) - Method in class net.talvi.puffinplot.PuffinPrefs
Exports the current preferences to a specified file.
exportToFiles(File, List<TreatmentParameter>) - Method in class net.talvi.puffinplot.data.Suite
Exports a subset of this suite's data to multiple files, one file per sample.

F

FieldUnit - Enum in net.talvi.puffinplot.data
This enum represents a unit in which magnetic field strength can be measured.
FileFormat - Class in net.talvi.puffinplot.data.file
This class represents an ASCII-based file format with one row per measurement.
FileFormat(Map<Integer, TreatmentParameter>, int, MeasurementType, TreatmentType, String, boolean, List<Integer>, MomentUnit, FieldUnit) - Constructor for class net.talvi.puffinplot.data.file.FileFormat
Creates a new file format with the specified parameters.
FileLoader - Interface in net.talvi.puffinplot.data.file
An interface implemented by PuffinPlot file loaders.
FileType - Enum in net.talvi.puffinplot.data
The fields of this enum represent the types of file that PuffinPlot can read.
FiletypeDialog - Class in net.talvi.puffinplot.window
A dialog allowing the user to select a file type.
FiletypeDialog(Frame) - Constructor for class net.talvi.puffinplot.window.FiletypeDialog
Creates a new FiletypeDialog.
fisherBySite - Variable in class net.talvi.puffinplot.PuffinActions
Calculates Fisherian statistics on PCA directions from the current site.
fisherOnSample - Variable in class net.talvi.puffinplot.PuffinActions
Calculates Fisherian statistics on selected demagnetization steps of the selected samples.
FisherParams - Interface in net.talvi.puffinplot.data
This interface provides access to the standard parameters for Fisherian spherical statistics: mean direction, alpha-95, and k.
FisherValues - Class in net.talvi.puffinplot.data
This class calculates Fisher (1953) spherical statistics on sets of vectors.
fitGreatCircle(Correction) - Method in class net.talvi.puffinplot.data.Sample
Fits a great circle to a subset of the magnetic moment vectors in this sample.
fitGreatCirclesToSelection() - Method in class net.talvi.puffinplot.PuffinApp
For all selected samples, fit a great circle to the selected treatment steps.
flip(MeasurementAxis) - Method in class net.talvi.puffinplot.data.Sample
Rotates all magnetic moment data (as stored in treatment steps) 180 degrees about the specified axis.
flipSampleX - Variable in class net.talvi.puffinplot.PuffinActions
Rotates the currently selected samples 180° about the X axis.
flipSampleY - Variable in class net.talvi.puffinplot.PuffinActions
Rotates the currently selected samples 180° about the Y axis.
flipSampleZ - Variable in class net.talvi.puffinplot.PuffinActions
Rotates the currently selected samples 180° about the Z axis.
flipSelectedSamples(MeasurementAxis) - Method in class net.talvi.puffinplot.PuffinApp
For all selected samples, rotates magnetization data 180° around the specified axis.
formationAzimuth - Variable in class net.talvi.puffinplot.data.file.VectorAndOrientations
A formation azimuth value in degrees.
formationDip - Variable in class net.talvi.puffinplot.data.file.VectorAndOrientations
A formation dip value in degrees, measured downward from the horizontal plane.
fromBestFit(List<Vec3>) - Static method in class net.talvi.puffinplot.data.GreatCircle
Constructs a best-fitting great circle for the supplied vectors.
fromDegrees(double, double) - Static method in class net.talvi.puffinplot.data.Location
Returns a Location representing the supplied degree co-ordinates.
fromDirections(Vec3, Vec3, Vec3) - Static method in class net.talvi.puffinplot.data.Tensor
Creates a tensor with the specified axes.
fromGitFiles(Class, String, String, String, String, String) - Static method in class net.talvi.puffinplot.Version
Provides a version object from resources containing git command output.
fromGitOutput(String, String, String, String, String) - Static method in class net.talvi.puffinplot.Version
Provides a version object corresponding to the output of git commands.
fromGitProperties(UnaryOperator<String>) - Static method in class net.talvi.puffinplot.Version
Provides a version object corresponding to some supplied git build properties.
fromMercurialProperties(UnaryOperator<String>) - Static method in class net.talvi.puffinplot.Version
Provides a version object corresponding to some supplied Mercurial build properties.
fromPolarDegrees(double, double, double) - Static method in class net.talvi.puffinplot.data.Vec3
Creates a vector from a polar specification in degrees.
fromPolarRadians(double, double, double) - Static method in class net.talvi.puffinplot.data.Vec3
Creates a vector from a polar specification in radians.
fromPole(Vec3) - Static method in class net.talvi.puffinplot.data.GreatCircle
Create a great circle with the given pole.
fromPrefs(Preferences) - Static method in class net.talvi.puffinplot.data.SensorLengths
Creates a sensor lengths object from a string representation in a Preferences object.
fromPresetName(String) - Static method in class net.talvi.puffinplot.data.SensorLengths
Creates a sensor lengths object with lengths determined by a named preset.
fromRadians(double, double) - Static method in class net.talvi.puffinplot.data.Location
Returns a Location representing the supplied radian co-ordinates.
fromSampleListByDiscreteId(List<Sample>) - Static method in class net.talvi.puffinplot.data.CoreSections
Split a sample list into core sections according to the discrete IDs of the samples.
fromSamples(List<Sample>) - Static method in class net.talvi.puffinplot.data.CoreSection
Returns a core section containing the specified samples in the specified order.
fromString(String) - Static method in enum net.talvi.puffinplot.data.ArmAxis
Creates an ArmAxis from the supplied string.
fromString(String) - Static method in class net.talvi.puffinplot.data.Correction
Creates a correction from the supplied string.
fromString(String) - Static method in enum net.talvi.puffinplot.data.MeasurementType
Creates a measurement type from a string representation.
fromString(String) - Static method in class net.talvi.puffinplot.data.MultiRange
Initialize a multirange from a string specification, e.g.
fromString(String) - Method in class net.talvi.puffinplot.data.Sample
Sets some of sample's fields based on a supplied string.
fromString(String) - Static method in class net.talvi.puffinplot.data.SensorLengths
Creates a new sensor lengths object from a string definition.
fromString(String) - Method in class net.talvi.puffinplot.data.Site
Sets site data from information in a string.
fromString(String) - Method in class net.talvi.puffinplot.data.Suite
Sets suite data from a string.
fromStrings(String, String, String) - Static method in class net.talvi.puffinplot.data.SensorLengths
Creates a new sensor lengths object from three strings specifying the individual sensor lengths.
fromStrings(List<String>) - Method in class net.talvi.puffinplot.data.TreatmentStep.Reader
Creates a a datum object using the supplied strings to populate the data fields.
fromVec3(Vec3) - Static method in class net.talvi.puffinplot.data.Location
 
fromVectors(Collection<Vec3>, boolean) - Static method in class net.talvi.puffinplot.data.Eigens
Create an orientation tensor from the supplied vectors, then return the results of eigen analysis upon the constructed matrix.

G

get(int) - Method in class net.talvi.puffinplot.data.CustomFields
Gets the value of a specified custom field.
get(String) - Method in class net.talvi.puffinplot.IdToFileMap
Return the directory associated with an identifier.
get2gProtocol() - Method in class net.talvi.puffinplot.PuffinPrefs
Returns the measurement protocol used when opening 2G data files.
getA95() - Method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
 
getA95() - Method in class net.talvi.puffinplot.data.ArasonLevi
 
getA95() - Method in interface net.talvi.puffinplot.data.FisherParams
Returns the alpha-95 value denoting the 95% confidence interval.
getA95() - Method in class net.talvi.puffinplot.data.FisherValues
 
getA95() - Method in class net.talvi.puffinplot.data.GreatCircles
 
getActions() - Method in class net.talvi.puffinplot.PuffinApp
Returns the actions associated with this PuffinApp.
getAfX() - Method in class net.talvi.puffinplot.data.TreatmentStep
For AF or ARM treatment, returns the x-axis AF field strength in tesla.
getAfY() - Method in class net.talvi.puffinplot.data.TreatmentStep
For AF or ARM treatment, returns the y-axis AF field strength in tesla.
getAfZ() - Method in class net.talvi.puffinplot.data.TreatmentStep
For AF or ARM treatment, returns the z-axis AF field strength in tesla.
getAll() - Method in class net.talvi.puffinplot.data.SuiteCalcs.Means
 
getAllSamplesInSelectedSites() - Method in interface net.talvi.puffinplot.plots.PlotParams
 
getAllSamplesInSelectedSites() - Method in class net.talvi.puffinplot.PuffinApp
Gets all the samples in all the sites having at least one selected sample.
getAms() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's AMS tensor.
getAmsBootstrapParams() - Method in class net.talvi.puffinplot.data.Suite
Returns the parameters of the last AMS bootstrap statistics (if any) calculated on this suite's data.
getAmsHextParams() - Method in class net.talvi.puffinplot.data.Suite
Returns the parameters of the last AMS Hext statistics (if any) calculated on this suite's data.
getAntiZoom() - Method in class net.talvi.puffinplot.window.GraphDisplay
Returns the inverse transform of the zoom transform.
getAppDataDirectory() - Static method in class net.talvi.puffinplot.Util
Return a directory where PuffinPlot can store files for "internal" use.
getArea() - Method in class net.talvi.puffinplot.data.TreatmentStep
For continuous measurements, returns the cross-sectional area of the core.
getArmAxis() - Method in class net.talvi.puffinplot.data.TreatmentStep
For ARM treatment, returns the axis of the ARM field.
getArmField() - Method in class net.talvi.puffinplot.data.TreatmentStep
For ARM treatment, returns the ARM bias field strength.
getAxis(int) - Method in class net.talvi.puffinplot.data.Tensor
Returns one of the tensor's three principal axes as a vector.
getAxisLabel() - Method in enum net.talvi.puffinplot.data.TreatmentType
Returns the axis label to use when plotting a graph involving this treatment.
getBuildProperty(String) - Method in class net.talvi.puffinplot.PuffinApp
Reads values from the build.properties file.
getByHeading(String) - Static method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns the field whose heading string is the specified string, or null if no such field exists.
getCentre() - Method in interface net.talvi.puffinplot.plots.PlotPoint
 
getCirclePoints(Correction) - Method in class net.talvi.puffinplot.data.Sample
Returns the magnetic moment vectors used for the current great-circle fit.
getCircles() - Method in class net.talvi.puffinplot.data.GreatCircles
Returns the great circles which were originally supplied to the constructor.
getColumnHeader() - Method in enum net.talvi.puffinplot.data.MeasurementType
Returns a suitable column header for sample identifiers.
getColumnMap() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getColumnWidthsAsString() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getCommaSeparatedHeader() - Method in class net.talvi.puffinplot.data.MagSusSampleRpiEstimate
 
getCommaSeparatedHeader() - Method in interface net.talvi.puffinplot.data.SampleRpiEstimate
 
getCommaSeparatedHeader() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getCompassDir() - Method in enum net.talvi.puffinplot.plots.Direction
 
getComponent(MeasurementAxis) - Method in class net.talvi.puffinplot.data.Vec3
Returns a specified component of this vector.
getControlPanel() - Method in class net.talvi.puffinplot.window.MainWindow
Returns the control panel for the plots displayed in this window.
getCorrection() - Method in interface net.talvi.puffinplot.plots.PlotParams
Returns the correction to be applied to magnetic moment data.
getCorrection() - Method in class net.talvi.puffinplot.PuffinApp
Returns the correction currently being applied to the data displayed by this PuffinApp.
getCorrection() - Method in class net.talvi.puffinplot.window.ControlPanel
Returns the correction to apply to magnetic moment data.
getCreator() - Method in class net.talvi.puffinplot.data.Suite
Returns a string identifying the program and version which created this suite.
getCurrentlyPrintingSample() - Method in class net.talvi.puffinplot.window.MainGraphDisplay
If printing is in progress, return the sample which is currently being printed.
getCurrentPageFormat() - Method in class net.talvi.puffinplot.PuffinApp
Returns the current page format.
getCurrentSample() - Method in class net.talvi.puffinplot.data.Suite
Returns the current sample
getCurrentSample() - Method in class net.talvi.puffinplot.PuffinApp
Gets the currently displayed Sample
getCurrentSampleIndex() - Method in class net.talvi.puffinplot.data.Suite
Returns the index defining the current sample.
getCurrentSite() - Method in class net.talvi.puffinplot.PuffinApp
Returns the site for which data is currently being displayed.
getCurrentSuite() - Method in class net.talvi.puffinplot.PuffinApp
Returns the currently displayed Suite.
getCustomFlagNames() - Method in class net.talvi.puffinplot.data.Suite
Returns the names (titles) of the custom flags for this suite.
getCustomFlags() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's custom flags.
getCustomNoteNames() - Method in class net.talvi.puffinplot.data.Suite
Returns the names (titles) of the custom notes for this suite.
getCustomNotes() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's custom notes.
getDashedStroke() - Method in class net.talvi.puffinplot.plots.Plot
Returns the default dashed stroke style.
getDateString() - Method in class net.talvi.puffinplot.Version
 
getDecDeg() - Method in class net.talvi.puffinplot.data.Vec3
Returns this vector's declination in degrees.
getDecimalFormatSymbols() - Static method in class net.talvi.puffinplot.Util
Return symbols for formatting decimal numbers for on-screen display.
getDecRad() - Method in class net.talvi.puffinplot.data.Vec3
Returns this vector's declination in radians.
getDefaultArea() - Static method in class net.talvi.puffinplot.data.TreatmentStep
 
getDefaultValue() - Method in interface net.talvi.puffinplot.data.file.OptionDefinition
Returns a default value for the option.
getDefaultValue() - Method in class net.talvi.puffinplot.data.file.SimpleOptionDefinition
 
getDefaultValue() - Method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns this field's default value.
getDefaultVolume() - Static method in class net.talvi.puffinplot.data.TreatmentStep
 
getDemagLevel() - Method in class net.talvi.puffinplot.data.MedianDestructiveField
Returns the treatment level at which the intensity of the sample's magnetic moment reached half of its initial value.
getDepth() - Method in class net.talvi.puffinplot.data.Sample
Returns the depth of a this sample within a continuous long core, where applicable.
getDepth() - Method in class net.talvi.puffinplot.data.TreatmentStep
For continuous measurements, returns the depth of this measurement within the core.
getDepthIndex() - Method in class net.talvi.puffinplot.window.SampleChooser
For long core suites, returns the current depth index.
getDescription() - Method in class net.talvi.puffinplot.data.Correction
Returns a user-friendly string describing this correction.
getDescription() - Method in interface net.talvi.puffinplot.data.file.OptionDefinition
 
getDescription() - Method in class net.talvi.puffinplot.data.file.SimpleOptionDefinition
 
getDimensions() - Method in class net.talvi.puffinplot.plots.Plot
Returns the dimensions of this plot.
getDimensionsAsString() - Method in class net.talvi.puffinplot.plots.Plot
Returns a string representation of this plot's dimensions.
getDipDeg() - Method in class net.talvi.puffinplot.data.Vec3
Returns the strike of the plane normal this vector
getDirection() - Method in enum net.talvi.puffinplot.data.MeasurementAxis
Returns a compass (field) direction corresponding to this axis.
getDirection() - Method in class net.talvi.puffinplot.data.PcaValues
Returns the direction of the principal PCA axis.
getDirection() - Method in class net.talvi.puffinplot.data.Sample
Returns the sample direction.
getDirectionNearEnd(CoreSection.End, int) - Method in class net.talvi.puffinplot.data.CoreSection
Calculates and returns the Fisherian mean direction of the topmost or bottommost samples in this section.
getDirections() - Method in class net.talvi.puffinplot.data.FisherValues
Returns a list of unit vectors representing the directions of the vectors on which these statistics were calculated.
getDirsBySample() - Method in class net.talvi.puffinplot.data.SuiteCalcs
 
getDirsBySite() - Method in class net.talvi.puffinplot.data.SuiteCalcs
 
getDiscreteId() - Method in class net.talvi.puffinplot.data.Sample
Returns the discrete ID of this sample, as determined by the discrete ID of the first TreatmentStep within the sample.
getDiscreteId() - Method in class net.talvi.puffinplot.data.TreatmentStep
For discrete samples, returns the sample identifier (name).
getDisplayName() - Method in enum net.talvi.puffinplot.data.TreatmentStepOperation
Return this operation's human-readable name
getDm() - Method in class net.talvi.puffinplot.data.VGP
 
getDp() - Method in class net.talvi.puffinplot.data.VGP
 
getEmptyFields() - Static method in class net.talvi.puffinplot.data.FisherValues
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.GreatCircle
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.GreatCircles
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.Location
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.MedianDestructiveField
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.PcaAnnotated
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.Tensor
Returns a list of empty strings equal in length to the number of parameters.
getEmptyFields() - Static method in class net.talvi.puffinplot.data.VGP
Returns a list of empty strings equal in length to the number of parameters.
getEmptySlot() - Method in class net.talvi.puffinplot.data.Line
Returns the first TreatmentStep associated with this line which was a measurement of an empty tray slot, not an actual sample.
getEndSamples(int) - Method in class net.talvi.puffinplot.data.CoreSections
Returns a set containing all the samples which are near the end of any section within this group of sections.
getEquation() - Method in class net.talvi.puffinplot.data.PcaValues
Return a Cartesian equation describing the PCA line.
getErrorCode() - Method in class net.talvi.puffinplot.data.ArasonLevi
Error codes: 0: no problem 1: convergence problem of selected solution 2: failed robustness check 3: convergence and robustness problems
getEstimate() - Method in class net.talvi.puffinplot.data.MagSusSampleRpiEstimate
 
getEstimate() - Method in interface net.talvi.puffinplot.data.SampleRpiEstimate
 
getEstimate() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getEstimateType() - Method in class net.talvi.puffinplot.window.RpiDialog
 
getEtaDir() - Method in class net.talvi.puffinplot.data.KentParams
Returns the direction of the confidence ellipse's first axis
getEtaMag() - Method in class net.talvi.puffinplot.data.KentParams
Returns the semiangle of the confidence ellipse's first axis
getExpectedDownloadSize() - Static method in class net.talvi.puffinplot.JythonJarManager
 
getExtraLines() - Method in class net.talvi.puffinplot.data.file.EmptyLoadedData
 
getExtraLines() - Method in interface net.talvi.puffinplot.data.file.LoadedData
Returns a list of non-processed raw lines from the file.
getExtraLines() - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
 
getFactorForAm() - Method in enum net.talvi.puffinplot.data.MomentUnit
 
getFactorForTesla() - Method in enum net.talvi.puffinplot.data.FieldUnit
 
getFieldUnit() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getFilesAndReorder(int) - Method in class net.talvi.puffinplot.RecentFileList
Returns a specified file-set and moves it to the top of the list.
getFilesetLongNames() - Method in class net.talvi.puffinplot.RecentFileList
Gets a list containing a long name for each fileset, intended for use in the tooltips of the recent files menu.
getFilesetNames() - Method in class net.talvi.puffinplot.RecentFileList
Gets a list containing the names of the file-sets in the file list.
getFirstGcStepLevel() - Method in class net.talvi.puffinplot.data.Sample
Returns the treatment level for the first point used in the great-circle fit.
getFirstRunNumber() - Method in class net.talvi.puffinplot.data.Sample
Returns the run number for the first treatment step in this sample.
getFisherParams() - Method in class net.talvi.puffinplot.data.Site
Returns the Fisherian parameters of the site mean direction, as calculated by Fisher statistics or great-circle analysis.
getFisherValues() - Method in class net.talvi.puffinplot.data.Sample
Returns the results of the last Fisher calculation.
getFisherValues() - Method in class net.talvi.puffinplot.data.Site
Returns the Fisher statistics (if any) calculated for this site.
getFontSize() - Method in class net.talvi.puffinplot.plots.Plot
Returns the standard font size in plot units.
getFormat() - Method in class net.talvi.puffinplot.window.TabularImportWindow
Returns the chosen format.
getFormationCorrectionMatrix(double, double) - Static method in class net.talvi.puffinplot.data.Vec3
Returns a matrix to correct a vector for a given formation orientation.
getFormattedTreatmentLevel() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the treatment level formatted as a string.
getFormAz() - Method in class net.talvi.puffinplot.data.AmsData
Returns the formation dip azimuth in degrees.
getFormAz() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's formation dip azimuth in degrees.
getFormAz() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the formation dip azimuth.
getFormDip() - Method in class net.talvi.puffinplot.data.AmsData
Returns the formation dip in degrees.
getFormDip() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's formation dip angle in degrees.
getFormDip() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the formation dip angle.
getFormStrike() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's formation strike in degrees.
getFormStrike() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the formation strike for this treatment step.
getfTest() - Method in class net.talvi.puffinplot.data.AmsData
Returns the F-test value for the sample's anisotropy measurement.
getGraphDisplay() - Method in class net.talvi.puffinplot.window.MainWindow
Returns this window's graph display.
getGreatCircle() - Method in class net.talvi.puffinplot.data.Sample
Returns the current great-circle fit for this sample, if any.
getGreatCircleLimitHeader() - Static method in class net.talvi.puffinplot.data.Site
Returns headers for information on the treatment steps used for the great-circle analysis.
getGreatCircleLimitStrings() - Method in class net.talvi.puffinplot.data.Site
Returns information on the treatment steps used for the great-circle analysis.
getGreatCircles() - Method in class net.talvi.puffinplot.data.Site
Returns the great-circle parameters (if any) calculated for this site.
getHeaderLines() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getHeaders() - Static method in class net.talvi.puffinplot.data.FisherValues
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.GreatCircle
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.GreatCircles
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.Location
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.MedianDestructiveField
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.PcaAnnotated
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.PcaValues
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.SuiteCalcs
 
getHeaders() - Static method in class net.talvi.puffinplot.data.Tensor
Returns the headers describing the parameters as a list of strings.
getHeaders() - Static method in class net.talvi.puffinplot.data.VGP
Returns the headers describing the parameters as a list of strings.
getHeading() - Method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns the heading string for this field.
getHprojXaxis() - Method in interface net.talvi.puffinplot.plots.PlotParams
Returns the X axis of the Zijderveld plot's horizontal projection.
getHprojXaxis() - Method in class net.talvi.puffinplot.window.ControlPanel
Returns the X-axis of the horizontal Zijderveld plot.
getHprojYaxis() - Method in interface net.talvi.puffinplot.plots.PlotParams
Returns the Y axis of the Zijderveld plot's horizontal projection.
getHprojYaxis() - Method in class net.talvi.puffinplot.window.ControlPanel
Returns the Y-axis of the horizontal Zijderveld plot.
getIdentifier() - Method in interface net.talvi.puffinplot.data.file.OptionDefinition
 
getIdentifier() - Method in class net.talvi.puffinplot.data.file.SimpleOptionDefinition
 
getIdOrDepth() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns sample identifier or measurement depth.
getImportedDirection() - Method in class net.talvi.puffinplot.data.Sample
Returns the imported sample direction, if any.
getIncDeg() - Method in class net.talvi.puffinplot.data.Vec3
Returns this vector's inclination in degrees.
getIncRad() - Method in class net.talvi.puffinplot.data.Vec3
Returns this vector's inclination in radians.
getIndexBySample(Sample) - Method in class net.talvi.puffinplot.data.Suite
Returns the index of a specified sample within this suite.
getInstance(PuffinApp) - Static method in class net.talvi.puffinplot.window.MainWindow
Creates and returns a new main window object.
getInstance() - Static method in class net.talvi.puffinplot.window.PuffinRenderingHints
Return a clean instance of this class.
getIntensities() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getIntensity() - Method in class net.talvi.puffinplot.data.MedianDestructiveField
Returns half of the intensity of the sample's initial magnetic moment.
getIntensity() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the magnitude of the magnetic dipole moment per unit volume in A/m.
getIrmField() - Method in class net.talvi.puffinplot.data.TreatmentStep
For IRM treatment, returns the IRM field strength in tesla.
getK() - Method in interface net.talvi.puffinplot.data.FisherParams
Returns the k-value, an estimate of the precision parameter κ.
getK() - Method in class net.talvi.puffinplot.data.FisherValues
 
getK() - Method in class net.talvi.puffinplot.data.GreatCircles
 
getKappa() - Method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
The inverse variance is returned as an estimate of κ.
getKappa() - Method in class net.talvi.puffinplot.data.ArasonLevi
 
getLastGcStepLevel() - Method in class net.talvi.puffinplot.data.Sample
Returns the treatment level for the last point used in the great-circle fit.
getLastRunNumber() - Method in class net.talvi.puffinplot.data.Sample
Returns the run number for the last treatment step in this sample.
getLatDeg() - Method in class net.talvi.puffinplot.data.Location
 
getLatRad() - Method in class net.talvi.puffinplot.data.Location
 
getLegend() - Method in class net.talvi.puffinplot.plots.ZPlot
Returns the legend for this plot.
getLengths() - Method in class net.talvi.puffinplot.data.SensorLengths
Returns a list of string representations of the sensor lengths in the order x, y, z.
getLetter() - Method in enum net.talvi.puffinplot.plots.Direction
 
getLine() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the measurement's data-file line.
getLocation() - Method in class net.talvi.puffinplot.data.Site
 
getLocation() - Method in class net.talvi.puffinplot.data.VGP
 
getLongDeg() - Method in class net.talvi.puffinplot.data.Location
 
getLongRad() - Method in class net.talvi.puffinplot.data.Location
 
getLower() - Method in class net.talvi.puffinplot.data.SuiteCalcs.Means
 
getM() - Method in class net.talvi.puffinplot.data.GreatCircles
Returns the number of stable endpoints used in the calculation.
getMad1() - Method in class net.talvi.puffinplot.data.Eigens
 
getMad1() - Method in class net.talvi.puffinplot.data.GreatCircle
Returns the MAD1 (planar maximum angular deviation) value for the great-circle fit.
getMad1() - Method in class net.talvi.puffinplot.data.PcaValues
Returns the maximum angle of planar deviation.
getMad3() - Method in class net.talvi.puffinplot.data.Eigens
 
getMad3() - Method in class net.talvi.puffinplot.data.PcaValues
Returns the maximum angle of linear deviation.
getMagDev() - Method in class net.talvi.puffinplot.data.Sample
Returns the geomagnetic field declination at the sampling site.
getMagDev() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the local geomagnetic field declination for the sampling site.
getMagSus() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the magnetic susceptibility of the sample at this stage of treatment
getMagSusJump() - Method in class net.talvi.puffinplot.data.Sample
Returns the results of the magnetic susceptibility jump calculation, if it has been performed.
getMainMenuBar() - Method in class net.talvi.puffinplot.window.MainWindow
Returns this window's menu bar.
getMainWindow() - Method in class net.talvi.puffinplot.PuffinApp
Returns this PuffinApp's main window
getMargin() - Method in class net.talvi.puffinplot.plots.Plot
Returns the size of the margin displayed when resizing the plot.
getMargin() - Method in class net.talvi.puffinplot.plots.PlotTitle
 
getMargin() - Method in class net.talvi.puffinplot.plots.SampleParamsLegend
 
getMargin() - Method in class net.talvi.puffinplot.plots.SiteParamsLegend
 
getMargin() - Method in class net.talvi.puffinplot.plots.ZPlot.ZplotLegend
 
getMaxDepth() - Method in class net.talvi.puffinplot.data.Suite
For a continuous suite, returns the maximum depth of a sample within the suite.
getMdf() - Method in class net.talvi.puffinplot.data.Sample
Returns the results of the MDF calculation if it has been performed, or null if not.
getMean() - Method in class net.talvi.puffinplot.data.KentParams
Returns the mean direction
getMeanDirection() - Method in interface net.talvi.puffinplot.data.FisherParams
Returns the mean direction.
getMeanDirection() - Method in class net.talvi.puffinplot.data.FisherValues
 
getMeanDirection() - Method in class net.talvi.puffinplot.data.GreatCircles
Returns the best-fit mean direction for the supplied circles and directions.
getMeanDirection() - Method in class net.talvi.puffinplot.data.Site
Returns the site mean direction.
getMeanInc() - Method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
 
getMeanInc() - Method in class net.talvi.puffinplot.data.ArasonLevi
 
getMeanRatio() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getMeasurementType() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getMeasurementType() - Method in class net.talvi.puffinplot.data.Sample
Returns the measurement type of this sample (discrete or continuous).
getMeasurementType() - Method in class net.talvi.puffinplot.data.Suite
Returns the measurement type of this suite (discrete or continuous)
getMeasurementType() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the type of this measurement (discrete or continuous).
getMeasurementType() - Method in class net.talvi.puffinplot.window.IapdImportDialog
 
getMessages() - Method in class net.talvi.puffinplot.data.file.EmptyLoadedData
 
getMessages() - Method in interface net.talvi.puffinplot.data.file.LoadedData
Returns a list of messages produced during file reading, intended for presentation to the user.
getMessages() - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
 
getMinDepth() - Method in class net.talvi.puffinplot.data.Suite
For a continuous suite, returns the minimum depth of a sample within the suite.
getMoment() - Method in class net.talvi.puffinplot.data.TreatmentStep
Strictly speaking, the name is not quite accurate: we do not deal with magnetic moment (which would be in Am2) but in magnetic dipole moment per unit volume (in A/m).
getMoment(Correction) - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the measured magnetic dipole moment per unit volume, as modified by the supplied correction.
getMomentUnit() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getN() - Method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
 
getN() - Method in class net.talvi.puffinplot.data.ArasonLevi
 
getN() - Method in interface net.talvi.puffinplot.data.FisherParams
Returns N, the number of directions analysed.
getN() - Method in class net.talvi.puffinplot.data.FisherValues
 
getN() - Method in class net.talvi.puffinplot.data.GreatCircles
Returns the number of great circles used in the calculation.
getName() - Method in class net.talvi.puffinplot.data.AmsData
Returns the sample's name.
getName() - Method in class net.talvi.puffinplot.data.Site
 
getName() - Method in class net.talvi.puffinplot.data.Suite
Returns the name of this suite.
getName() - Method in class net.talvi.puffinplot.plots.AmsPlot
 
getName() - Method in class net.talvi.puffinplot.plots.DemagPlot
Returns this plot's internal name.
getName() - Method in class net.talvi.puffinplot.plots.DemagTable
Returns the internal plot name for this table.
getName() - Method in class net.talvi.puffinplot.plots.DepthPlot
 
getName() - Method in class net.talvi.puffinplot.plots.NrmHistogram
Returns this plot's internal name.
getName() - Method in class net.talvi.puffinplot.plots.Plot
Returns an internal name for this plot.
getName() - Method in class net.talvi.puffinplot.plots.PlotTitle
 
getName() - Method in class net.talvi.puffinplot.plots.RpiPlot
 
getName() - Method in class net.talvi.puffinplot.plots.SampleEqualAreaPlot
 
getName() - Method in class net.talvi.puffinplot.plots.SampleParamsLegend
 
getName() - Method in class net.talvi.puffinplot.plots.SampleParamsTable
 
getName() - Method in class net.talvi.puffinplot.plots.SeparateSuiteEqualAreaPlot
Returns this plot's internal name.
getName() - Method in class net.talvi.puffinplot.plots.SiteEqualAreaPlot
 
getName() - Method in class net.talvi.puffinplot.plots.SiteParamsLegend
 
getName() - Method in class net.talvi.puffinplot.plots.SiteParamsTable
 
getName() - Method in class net.talvi.puffinplot.plots.SuiteEqualAreaPlot
 
getName() - Method in class net.talvi.puffinplot.plots.SuiteParamsTable
 
getName() - Method in class net.talvi.puffinplot.plots.TernaryPlot
 
getName() - Method in class net.talvi.puffinplot.plots.VgpMap
 
getName() - Method in class net.talvi.puffinplot.plots.VgpTable
 
getName() - Method in class net.talvi.puffinplot.plots.ZPlot
 
getName() - Method in class net.talvi.puffinplot.plots.ZPlot.ZplotLegend
 
getNameOrDepth() - Method in class net.talvi.puffinplot.data.Sample
Returns the sample identifier or depth.
getNiceName() - Method in enum net.talvi.puffinplot.data.CoreSections.TargetDeclinationType
 
getNiceName() - Method in enum net.talvi.puffinplot.data.Correction.Rotation
Returns a user-friendly name for this rotation correction.
getNiceName() - Method in enum net.talvi.puffinplot.data.FileType
Returns a user-friendly name for this filetype.
getNiceName() - Method in enum net.talvi.puffinplot.data.MeasurementType
 
getNiceName() - Method in enum net.talvi.puffinplot.data.RpiEstimateType
 
getNiceName() - Method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns this field's ‘nice name’ (string representation for display to user)
getNiceName() - Method in enum net.talvi.puffinplot.data.TreatmentType
Returns a user-friendly name for this treatment.
getNiceName() - Method in class net.talvi.puffinplot.plots.AmsPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.DemagPlot
Returns this plot's user-friendly name.
getNiceName() - Method in class net.talvi.puffinplot.plots.DemagTable
Returns the user-friendly plot name for this table.
getNiceName() - Method in class net.talvi.puffinplot.plots.DepthPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.NrmHistogram
Returns this plot's user-friendly name.
getNiceName() - Method in class net.talvi.puffinplot.plots.Plot
Returns a user-friendly name for this plot.
getNiceName() - Method in class net.talvi.puffinplot.plots.PlotTitle
 
getNiceName() - Method in class net.talvi.puffinplot.plots.RpiPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SampleEqualAreaPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SampleParamsLegend
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SampleParamsTable
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SiteEqualAreaPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SiteParamsLegend
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SiteParamsTable
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SuiteEqualAreaPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.SuiteParamsTable
 
getNiceName() - Method in class net.talvi.puffinplot.plots.TernaryPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.VgpMap
 
getNiceName() - Method in class net.talvi.puffinplot.plots.VgpTable
 
getNiceName() - Method in class net.talvi.puffinplot.plots.ZPlot
 
getNiceName() - Method in class net.talvi.puffinplot.plots.ZPlot.ZplotLegend
 
getNormalizer() - Method in class net.talvi.puffinplot.data.MagSusSampleRpiEstimate
 
getNormalizer() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getNormalizer() - Method in class net.talvi.puffinplot.window.RpiDialog
 
getNpoints() - Method in class net.talvi.puffinplot.data.PcaValues
Returns the number of points used in this PCA.
getNrm() - Method in class net.talvi.puffinplot.data.Sample
Returns the intensity of the sample's natural remanent magnetization (NRM).
getNrm() - Method in class net.talvi.puffinplot.window.RpiDialog
 
getNrmSample() - Method in class net.talvi.puffinplot.data.MagSusSampleRpiEstimate
 
getNrmSample() - Method in interface net.talvi.puffinplot.data.SampleRpiEstimate
 
getNrmSample() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getNrmSuite() - Method in class net.talvi.puffinplot.data.SuiteRpiEstimate
 
getNumberOfSteps() - Method in class net.talvi.puffinplot.data.Sample
Returns the number of treatment steps within this sample.
getNumSamples() - Method in class net.talvi.puffinplot.data.Suite
Returns the number of samples in this suite.
getOptionDefinitions() - Method in interface net.talvi.puffinplot.data.file.FileLoader
 
getOptionDefinitions() - Method in class net.talvi.puffinplot.data.file.IapdLoader
 
getOptionDefinitions() - Method in class net.talvi.puffinplot.data.file.Jr6Loader
 
getOptionDefinitions() - Method in class net.talvi.puffinplot.data.file.TabularFileLoader
 
getOptionDefinitions() - Method in class net.talvi.puffinplot.data.file.TwoGeeLoader
 
getOrigin() - Method in class net.talvi.puffinplot.data.PcaValues
Returns the origin for the PCA fit.
getPath() - Static method in class net.talvi.puffinplot.JythonJarManager
Returns the local path for the Jython jar file with the application data directory.
getPcaAnnotated() - Method in class net.talvi.puffinplot.data.Sample
Returns the annotated results of the last PCA calculation.
getPcaValues() - Method in class net.talvi.puffinplot.data.PcaAnnotated
Returns the results of the principal component analysis.
getPcaValues() - Method in class net.talvi.puffinplot.data.Sample
Returns the results of the last PCA calculation.
getPlot() - Method in class net.talvi.puffinplot.window.SuiteEqAreaWindow
Returns the single equal-area plot contained in this window's graph display.
getPlotByClass(Class) - Method in class net.talvi.puffinplot.window.GraphDisplay
Returns the plot with a specified class.
getPlotParams() - Method in class net.talvi.puffinplot.PuffinApp
 
getPlots() - Method in class net.talvi.puffinplot.window.GraphDisplay
Returns a collection of all the plots in this graph display.
getPlotSize(String) - Method in class net.talvi.puffinplot.PuffinPrefs
Gives the configured size and position for a specified plot.
getPlotSizeString() - Method in class net.talvi.puffinplot.window.GraphDisplay
Returns a string representation of all this display's plot sizes and positions.
getPoints() - Method in class net.talvi.puffinplot.data.GreatCircle
Returns the normalized points to which the great circle was fitted, if any.
getPole() - Method in class net.talvi.puffinplot.data.GreatCircle
Returns a pole to the fitted great circle.
getPrefs() - Method in class net.talvi.puffinplot.PuffinApp
Returns the preferences for this PuffinApp.
getPrefs() - Method in class net.talvi.puffinplot.PuffinPrefs
Returns the underlying Preferences object which holds the preferences.
getPreset() - Method in class net.talvi.puffinplot.data.SensorLengths
Returns the name of the preset sensor lengths, if any.
getPresetNames() - Static method in class net.talvi.puffinplot.data.SensorLengths
Returns the names of the hard-coded preset sensor lengths.
getPuffinFile() - Method in class net.talvi.puffinplot.data.Suite
Returns the name of the PuffinPlot file associated with this suite, if any.
getR() - Method in interface net.talvi.puffinplot.data.FisherParams
Returns R, the total unit vector path length.
getR() - Method in class net.talvi.puffinplot.data.FisherValues
 
getR() - Method in class net.talvi.puffinplot.data.GreatCircles
 
getR() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getRatio() - Method in class net.talvi.puffinplot.data.MagSusSampleRpiEstimate
 
getRealFields() - Static method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns an unmodifiable list of the real fields.
getRealFieldStrings() - Static method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns an unmodifiable list of the string representations of the real fields.
getRecentFiles() - Method in class net.talvi.puffinplot.PuffinApp
Returns the list of recently used files.
getRotation() - Method in class net.talvi.puffinplot.data.Correction
Returns the rotation correction.
getRpis() - Method in class net.talvi.puffinplot.data.SuiteRpiEstimate
 
getrSquared() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getRunNumber() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the number of the machine run during which this measurement was made.
getSampAz() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's dip azimuth in degrees.
getSampAz() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the sample's dip azimuth.
getSampDip() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's dip angle in degrees.
getSampDip() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the sample's dip angle.
getSampHade() - Method in class net.talvi.puffinplot.data.Sample
Returns this sample's hade in degrees.
getSampHade() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the sample hade for this treatment step.
getSample() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the sample of which this measurement was made.
getSample() - Method in interface net.talvi.puffinplot.plots.PlotParams
Returns the sample to plot.
getSample() - Method in interface net.talvi.puffinplot.plots.PlotPoint
 
getSampleAz() - Method in class net.talvi.puffinplot.data.AmsData
Returns the sample's dip azimuth in degrees.
getSampleByIndex(int) - Method in class net.talvi.puffinplot.data.Suite
Returns the sample with the specified index.
getSampleByName(String) - Method in class net.talvi.puffinplot.data.Suite
Returns a sample from this suite with the specified name, or null if no such sample exists.
getSampleChooser() - Method in class net.talvi.puffinplot.window.MainWindow
Returns this window's sample chooser.
getSampleCorrectionMatrix(double, double) - Static method in class net.talvi.puffinplot.data.Vec3
Returns a matrix to correct a vector for a given sample orientation.
getSampleDip() - Method in class net.talvi.puffinplot.data.AmsData
Returns the sample's dip in degrees.
getSamples() - Method in class net.talvi.puffinplot.data.CoreSection
 
getSamples() - Method in interface net.talvi.puffinplot.data.SampleGroup
 
getSamples() - Method in class net.talvi.puffinplot.data.Site
Returns the samples in this site
getSamples() - Method in class net.talvi.puffinplot.data.Suite
Returns all the samples in this suite.
getSamplesByDiscreteId(String) - Method in class net.talvi.puffinplot.data.Suite
Return the samples with a given discrete ID.
getSamplesNearEnd(CoreSection.End, int) - Method in class net.talvi.puffinplot.data.CoreSection
Returns the topmost or bottommost samples in this core section.
getSections() - Method in class net.talvi.puffinplot.data.CoreSections
Get a linked map of core sections.
getSelectedFileType() - Method in class net.talvi.puffinplot.window.FiletypeDialog
 
getSelectedSamples() - Method in interface net.talvi.puffinplot.plots.PlotParams
 
getSelectedSamples() - Method in class net.talvi.puffinplot.PuffinApp
Gets all the currently selected samples.
getSelectedSamples() - Method in class net.talvi.puffinplot.window.SampleChooser
Returns all the currently selected samples.
getSelectedSites() - Method in class net.talvi.puffinplot.PuffinApp
Gets all the sites containing any of the currently selected samples.
getSelectedTreatmentSteps() - Method in class net.talvi.puffinplot.data.Sample
Returns all the selected treatment steps within this sample.
getSelectionBitSet() - Method in class net.talvi.puffinplot.data.Sample
Returns the selected treatment step indices as a bit set.
getSensorLengths() - Method in class net.talvi.puffinplot.PuffinPrefs
Returns the effective sensor lengths for opening 2G data files.
getSeparator() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getSetting(String, String) - Method in interface net.talvi.puffinplot.plots.PlotParams
Gets the string value of a named setting.
getSettingBoolean(String, boolean) - Method in interface net.talvi.puffinplot.plots.PlotParams
Gets the boolean value of a named setting.
getShape() - Method in interface net.talvi.puffinplot.plots.PlotPoint
 
getShortcut() - Method in enum net.talvi.puffinplot.data.FileType
 
getShortName() - Method in class net.talvi.puffinplot.plots.AmsPlot
 
getShortName() - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Returns a short, human-readable name for this plot.
getShortName() - Method in class net.talvi.puffinplot.plots.SampleEqualAreaPlot
 
getShortName() - Method in class net.talvi.puffinplot.plots.SeparateSuiteEqualAreaPlot
 
getShortName() - Method in class net.talvi.puffinplot.plots.SiteEqualAreaPlot
 
getShortName() - Method in class net.talvi.puffinplot.plots.SuiteEqualAreaPlot
 
getSite() - Method in class net.talvi.puffinplot.data.Sample
Returns the site for this sample.
getSiteByName(String) - Method in class net.talvi.puffinplot.data.Suite
Returns a site with the given name, or null if this suite contains no such site.
getSiteEqAreaWindow() - Method in class net.talvi.puffinplot.PuffinApp
Returns the great-circle statistics window.
getSiteFishers() - Method in class net.talvi.puffinplot.data.Suite
Returns the results of the per-site Fisher statistics calculated by Suite.calculateSiteFishers(net.talvi.puffinplot.data.Correction).
getSites() - Method in class net.talvi.puffinplot.data.Suite
Returns the sites within this suite.
getSlope() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
getSlotNumber() - Method in class net.talvi.puffinplot.data.Sample
Returns the tray slot number for discrete samples.
getSlotNumber() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the number of the measurement tray slot in which the sample was measured.
getStepsInRanges(MultiRange) - Method in class net.talvi.puffinplot.data.Sample
 
getStoredException() - Method in class net.talvi.puffinplot.DownloadWorker
If an exception was thrown during the download process, this method will return it.
getStrikeDeg() - Method in class net.talvi.puffinplot.data.Vec3
Returns the strike of the plane normal to this vector
getString(String) - Method in class net.talvi.puffinplot.IdToFileMap
Return the directory associated with an identifier, as a string.
getStroke() - Method in class net.talvi.puffinplot.plots.Plot
Returns the default solid stroke style.
getSuite() - Method in class net.talvi.puffinplot.data.Sample
Returns the suite containing this sample.
getSuite() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the data suite containing this measurement.
getSuiteEqAreaWindow() - Method in class net.talvi.puffinplot.PuffinApp
Returns the suite equal-area plot window.
getSuiteMeans() - Method in class net.talvi.puffinplot.data.Suite
Returns the Fisher parameters calculated on the entire suite.
getSuiteRpiEstimate() - Method in interface net.talvi.puffinplot.plots.PlotParams
 
getSuites() - Method in class net.talvi.puffinplot.PuffinApp
Returns all the Suites currently open within this PuffinApp.
getT63() - Method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
 
getT63() - Method in class net.talvi.puffinplot.data.ArasonLevi
 
getTableWindow() - Method in class net.talvi.puffinplot.PuffinApp
Returns the data table window.
getTau() - Method in class net.talvi.puffinplot.data.KentParams
Returns the tau value (eigenvalue of normalized mean susceptibility tensor).
getTauSigma() - Method in class net.talvi.puffinplot.data.KentParams
Returns (95% confidence region for tau)
getTemperature() - Method in class net.talvi.puffinplot.data.TreatmentStep
For thermal treatment, returns the temperature in degrees Celsius.
getTensor() - Method in class net.talvi.puffinplot.data.AmsData
Returns the sample's susceptibility tensor.
getTextAttributes() - Method in class net.talvi.puffinplot.plots.Plot
Returns this plot's standard text attributes.
getTickLength() - Method in class net.talvi.puffinplot.plots.Plot
Returns the standard length of an axis tick in plot units.
getTimestamp() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the timestamp of this measurement.
getTreatmentLevel() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns a numerical representation of the intensity of the treatment which was applied immediately before this measurement.
getTreatmentLevels() - Method in class net.talvi.puffinplot.data.Sample
Returns an array of the treatment levels in this sample.
getTreatmentLevels() - Method in class net.talvi.puffinplot.data.SuiteRpiEstimate
 
getTreatmentStep() - Method in interface net.talvi.puffinplot.plots.PlotPoint
 
getTreatmentStepByIndex(int) - Method in class net.talvi.puffinplot.data.Sample
Returns a specified treatment step from this sample.
getTreatmentStepByLevel(double) - Method in class net.talvi.puffinplot.data.Sample
Returns the first TreatmentStep in this Sample with the given treatment level.
getTreatmentStepByRunNumber(int) - Method in class net.talvi.puffinplot.data.Sample
Returns the datum with the highest run number which is less than the supplied run number.
getTreatmentStepByTypeAndLevel(Set<TreatmentType>, double) - Method in class net.talvi.puffinplot.data.Sample
Returns a TreatmentStep with a specified treatment type and level.
getTreatmentStepForPosition(Point2D) - Method in class net.talvi.puffinplot.plots.Plot
Returns the datum associated with the point at the given position, or null if no such datum exists.
getTreatmentSteps() - Method in class net.talvi.puffinplot.data.file.EmptyLoadedData
 
getTreatmentSteps() - Method in interface net.talvi.puffinplot.data.file.LoadedData
Returns the treatment steps read from the file.
getTreatmentSteps() - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
 
getTreatmentSteps() - Method in class net.talvi.puffinplot.data.Sample
Returns all the treatment steps within this sample.
getTreatmentType() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
getTreatmentType() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the treatment applied before this measurement (AF, thermal, etc.).
getTreatmentType() - Method in class net.talvi.puffinplot.window.IapdImportDialog
 
getType() - Method in interface net.talvi.puffinplot.data.file.OptionDefinition
 
getType() - Method in class net.talvi.puffinplot.data.file.SimpleOptionDefinition
 
getType() - Method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns the type of this field (double, String, etc.).
getUnit() - Method in enum net.talvi.puffinplot.data.TreatmentType
The units in which this treatment is quantified.
getUnitSize() - Method in class net.talvi.puffinplot.plots.Plot
Returns the size of a plot unit in Java 2D units.
getUnitSize() - Method in interface net.talvi.puffinplot.plots.PlotParams
 
getUpper() - Method in class net.talvi.puffinplot.data.SuiteCalcs.Means
 
getValue(Map<String, Object>) - Method in interface net.talvi.puffinplot.data.file.OptionDefinition
Returns the value of this option in a supplied option map.
getValue(TreatmentParameter) - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns a String representation of a value from a specified data field.
getValues() - Method in class net.talvi.puffinplot.data.Eigens
Returns the eigenvalues in decreasing order.
getVectors() - Method in class net.talvi.puffinplot.data.Eigens
Returns the eigenvectors in order of decreasing eigenvalue.
getVersion() - Method in class net.talvi.puffinplot.PuffinApp
Returns the version of this PuffinPlot build.
getVersionString() - Method in class net.talvi.puffinplot.Version
 
getVgp() - Method in class net.talvi.puffinplot.data.Site
 
getVgpsBySample() - Method in class net.talvi.puffinplot.data.SuiteCalcs
 
getVgpsBySite() - Method in class net.talvi.puffinplot.data.SuiteCalcs
 
getVisiblePlots() - Method in class net.talvi.puffinplot.window.GraphDisplay
Returns a list of the plots which are currently visible.
getVisibleTreatmentSteps() - Method in class net.talvi.puffinplot.data.Sample
Returns all the visible (non-hidden) treatment steps within this sample.
getVolume() - Method in class net.talvi.puffinplot.data.TreatmentStep
For discrete measurements, returns the volume of the sample.
getVprojXaxis() - Method in interface net.talvi.puffinplot.plots.PlotParams
Returns the X axis of the Zijderveld plot's vertical projection.
getVprojXaxis() - Method in class net.talvi.puffinplot.window.ControlPanel
Returns the X-axis of the vertical Zijderveld plot.
getXDrift() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the x drift correction value.
getYDrift() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the y drift correction value.
getYearRange() - Method in class net.talvi.puffinplot.Version
 
getZDrift() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns the z drift correction value.
getZetaDir() - Method in class net.talvi.puffinplot.data.KentParams
Returns the direction of the confidence ellipse's second axis
getZetaMag() - Method in class net.talvi.puffinplot.data.KentParams
Returns the semiangle of the confidence ellipse's second axis
getZRotationMatrix(double) - Static method in class net.talvi.puffinplot.data.Vec3
Returns a matrix for a rotation about the z axis.
GraphDisplay - Class in net.talvi.puffinplot.window
A graphical UI component which lays out and draws one or more plots.
GreatCircle - Class in net.talvi.puffinplot.data
This class represents a great circle, created either directly by specifying a pole direction or indirectly by giving a list of vectors.
greatCircleAnalysis - Variable in class net.talvi.puffinplot.PuffinActions
Determines a site mean through McFadden and McElhinny great-circle intersection.
greatCirclePoints(int, boolean) - Method in class net.talvi.puffinplot.data.Vec3
Returns a list of equally spaced points around a great circle having this vector as its pole.
GreatCircles - Class in net.talvi.puffinplot.data
This class represents a set of great circles and a set of directions.
guess(File) - Static method in enum net.talvi.puffinplot.data.FileType
Attempts to guess the type of a file from its name and contents.

H

handleAbout(AppEvent.AboutEvent) - Method in class net.talvi.puffinplot.AppleEventHandler
Handles an Apple About action by calling PuffinApp.about()
handlePreferences(AppEvent.PreferencesEvent) - Method in class net.talvi.puffinplot.AppleEventHandler
Handles an Apple Preferences action by calling PuffinApp.preferences()
handleQuitRequestWith(AppEvent.QuitEvent, QuitResponse) - Method in class net.talvi.puffinplot.AppleEventHandler
Handles an Apple Quit action by calling PuffinApp.quit()
hashCode() - Method in class net.talvi.puffinplot.data.file.OrientationParameters
Returns a hash code for this parameter set.
hashCode() - Method in class net.talvi.puffinplot.data.Vec3
 
hasMagMoment() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether the treatment step contains a magnetic moment measurement.
hasMagSus() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether this treatment step has any magnetic susceptibility data.
hasMagSusData() - Method in class net.talvi.puffinplot.data.Sample
Reports whether this sample has any magnetic susceptibility data.
hasTreatmentSteps() - Method in class net.talvi.puffinplot.data.Sample
Reports whether this sample contains any treatmentSteps.
hextAms - Variable in class net.talvi.puffinplot.PuffinActions
Calculates Hext AMS statistics on the selected samples.
hideAndDeselectSelectedPoints() - Method in class net.talvi.puffinplot.data.Sample
Sets all the selected treatment steps within this sample to be hidden, so they will not be shown on plots.
hideSelectedSteps - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, makes the selected points invisible.

I

IapdImportDialog - Class in net.talvi.puffinplot.window
Lets the user select options for IAPD file import.
IapdImportDialog(Frame) - Constructor for class net.talvi.puffinplot.window.IapdImportDialog
Creates a new IapdImportDialog.
IapdLoader - Class in net.talvi.puffinplot.data.file
Loader for IAPD files.
IapdLoader() - Constructor for class net.talvi.puffinplot.data.file.IapdLoader
 
IdToFileMap - Class in net.talvi.puffinplot
A class to maintain a mapping between identifier strings and files.
IdToFileMap(UnaryOperator<String>, BiConsumer<String, String>) - Constructor for class net.talvi.puffinplot.IdToFileMap
Creates a new IdToFileMap, which wwill store and retrieve mappings using the supplied getter and putter.
ignoreOnLoading() - Method in class net.talvi.puffinplot.data.TreatmentStep
Returns true if this treatment step should be ignored (thrown away) when loading a data file.
importAms - Variable in class net.talvi.puffinplot.PuffinActions
Opens a file dialog allowing the user to choose an Agico ASC file from which to import AMS data.
ImportAmsDialog - Class in net.talvi.puffinplot.window
A dialog for importing AMS data from files.
ImportAmsDialog(PuffinApp) - Constructor for class net.talvi.puffinplot.window.ImportAmsDialog
Creates a new AMS import dialog.
importAmsFromAsc(List<File>, boolean, boolean, boolean) - Method in class net.talvi.puffinplot.data.Suite
Imports AMS data from ASC files in the format produced by Agico's SAFYR and SUSAR programs.
importAmsFromDelimitedFile(List<File>, boolean) - Method in class net.talvi.puffinplot.data.Suite
Imports AMS data from a whitespace-delimited file.
importFromFile(File) - Method in class net.talvi.puffinplot.PuffinPrefs
Imports preferences from a specified file.
importLocations(File) - Method in class net.talvi.puffinplot.data.Suite
Imports site locations from a CSV file.
importLocations - Variable in class net.talvi.puffinplot.PuffinActions
Imports site location data.
importPrefs - Variable in class net.talvi.puffinplot.PuffinActions
Imports user preferences from an XML file.
inc - Variable in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
mean inclination estimate in degrees
includesEmpty() - Method in class net.talvi.puffinplot.data.Correction
Returns true if this correction includes an empty-slot correction.
includesFormation() - Method in class net.talvi.puffinplot.data.Correction
Returns true if this correction includes a rotation for formation orientation.
includesSample() - Method in class net.talvi.puffinplot.data.Correction
Returns true if this correction includes a rotation for sample orientation.
includesTray() - Method in class net.talvi.puffinplot.data.Correction
Returns true if this correction includes a correction for tray remanence.
index - Variable in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
An index for an azimuthal parameter value (3, 6, 9, or 12), corresponding to an angle on a clock face.
index - Variable in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
An index for a possible orientation parameter value (valid values are 0 and 90).
initialize(PuffinApp) - Static method in class net.talvi.puffinplot.AppleEventHandler
Instantiates a new AppleEventHandler, which will send events to the supplied PuffinApp instance.
instance(List<Vec3>, List<GreatCircle>, String) - Static method in class net.talvi.puffinplot.data.GreatCircles
Calculates a mean direction from the supplied great circle and directions.
interpolateEquatorPoints(List<Vec3>) - Static method in class net.talvi.puffinplot.data.Vec3
Given a list of points, return a list of lists containing the same points plus possible extras.
invert() - Method in class net.talvi.puffinplot.data.Vec3
Returns the inverse of this vector.
invertMoments() - Method in class net.talvi.puffinplot.data.Sample
Inverts all magnetic moment data.
invertSamples - Variable in class net.talvi.puffinplot.PuffinActions
Inverts every vector in the currently selected samples.
isA95Valid() - Method in interface net.talvi.puffinplot.data.FisherParams
Reports whether the alpha-95 value represents a real number.
isActualMeasurement() - Method in enum net.talvi.puffinplot.data.MeasurementType
Returns true if this field corresponds to an actual measurement.
isAnchored() - Method in class net.talvi.puffinplot.data.PcaValues
Reports whether the PCA calculation was anchored.
isAxisScaleLocked() - Method in class net.talvi.puffinplot.PuffinPrefs
Reports whether the axis scale is locked across all samples in the current suite.
isCompatibleValue(Object) - Method in class net.talvi.puffinplot.window.PuffinRenderingHints.Key
isContinuous() - Method in enum net.talvi.puffinplot.data.MeasurementType
Returns true if this field is CONTINUOUS.
isDiscrete() - Method in enum net.talvi.puffinplot.data.MeasurementType
Returns true if this field is DISCRETE.
isDragPlotMode() - Method in class net.talvi.puffinplot.window.GraphDisplay
Reports whether the plots are currently draggable by the user.
isEmpty() - Method in class net.talvi.puffinplot.data.Site
Reports whether there are any samples in this site.
isEmpty() - Method in class net.talvi.puffinplot.data.Suite
Determines whether this suite is empty.
isEmptySlot() - Method in class net.talvi.puffinplot.data.Sample
Reports whether this sample is an empty slot on the measurement tray.
isExcludedFromMenu() - Method in class net.talvi.puffinplot.PuffinAction
Determines whether the Action should be excluded from the normal application menus (on the grounds that it already exists in a special Mac OS X menu and the application is being run on Mac OS X).
isFilenameSet() - Method in class net.talvi.puffinplot.data.Suite
Reports whether a default PuffinPlot file is set for this suite.
isFinite() - Method in class net.talvi.puffinplot.data.Vec3
Checks that this vector contains no NaN or infinite values.
isGroupedBySite() - Method in class net.talvi.puffinplot.plots.SeparateSuiteEqualAreaPlot
Reports whether the Fisher means are grouped by site.
isHalfIntReached() - Method in class net.talvi.puffinplot.data.MedianDestructiveField
Reports whether this sample reached half its initial intensity.
isHidden() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether this treatment step should be hidden on plots.
isImportable() - Method in enum net.talvi.puffinplot.data.TreatmentParameter
Reports whether this field is importable.
isInPca() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether this measurement is used for a PCA fit.
isMagDevAppliedToFormation() - Method in class net.talvi.puffinplot.data.Correction
 
isMagneticField() - Method in enum net.talvi.puffinplot.data.TreatmentType
 
isMagSusOnly() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether this treatment step has magnetic susceptibility but not magnetic moment data.
isNear(Point2D, double) - Method in interface net.talvi.puffinplot.plots.PlotPoint
Report whether this point is near to a supplied Point2D.
isOnCircle() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether this measurement is used for a great-circle fit.
isPcaAnchored() - Method in class net.talvi.puffinplot.data.Sample
Reports whether principal component analysis should be anchored for this sample.
isPcaAnchored() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether PCA fits for this point should be anchored.
isPcaAnchored() - Method in class net.talvi.puffinplot.PuffinPrefs
Reports whether PCA fits should be anchored to the origin.
isPrintingInProgress() - Method in class net.talvi.puffinplot.window.MainGraphDisplay
Report whether printing is currently in progress.
isRequired() - Method in interface net.talvi.puffinplot.data.file.OptionDefinition
Returns true if and only if this option is required.
isRequired() - Method in class net.talvi.puffinplot.data.file.SimpleOptionDefinition
 
isSaved() - Method in class net.talvi.puffinplot.data.Suite
 
isSelected() - Method in class net.talvi.puffinplot.data.TreatmentStep
Reports whether this treatment step is selected.
isSelectionContiguous() - Method in class net.talvi.puffinplot.data.Sample
Returns true if the selected treatment steps are contiguous.
isValid() - Method in class net.talvi.puffinplot.data.GreatCircles
Returns true if this great-circle fit is valid according to the condition specified in the preferences.
isVirtual() - Method in enum net.talvi.puffinplot.data.TreatmentParameter
Reports whether this field is virtual.
isVisible() - Method in class net.talvi.puffinplot.plots.Plot
Reports whether this plot is visible.
itemStateChanged(ItemEvent) - Method in class net.talvi.puffinplot.window.ControlPanel
Handles changes in the state of user interface components.

J

Jr6Loader - Class in net.talvi.puffinplot.data.file
A loader for the JR6 format developed by Agico and used by the REMA6W program.
Jr6Loader() - Constructor for class net.talvi.puffinplot.data.file.Jr6Loader
 
JythonJarManager - Class in net.talvi.puffinplot
A collection of static methods for managing the Jython jar.
JythonJarManager() - Constructor for class net.talvi.puffinplot.JythonJarManager
 

K

kappa - Variable in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
kappa value associated with the estimate
KentParams - Class in net.talvi.puffinplot.data
A class representing the parameters of a Kent confidence ellipse.
KentParams(double, double, double, double, double, double, double, double, double, double) - Constructor for class net.talvi.puffinplot.data.KentParams
Creates an object representing a Kent confidence ellipse defined by the supplied parameters.
KentParams(String) - Constructor for class net.talvi.puffinplot.data.KentParams
Creates an object representing a Kent confidence ellipse defined by the parameters listed in the supplied string.
Key(int) - Constructor for class net.talvi.puffinplot.window.PuffinRenderingHints.Key
Construct a key using the indicated private key.
KEY_E_NOTATION - Static variable in class net.talvi.puffinplot.window.PuffinRenderingHints
Use E notation rather than superscript notation for orders of magnitude.

L

lastPoint() - Method in class net.talvi.puffinplot.data.GreatCircle
Returns the normalized final point used in the great-circle fit, if any.
Line - Class in net.talvi.puffinplot.data
A container class holding all the data within a suite from a particular line number of their respective files.
Line(int) - Constructor for class net.talvi.puffinplot.data.Line
Creates a new Line with the specified line number.
LineCache - Class in net.talvi.puffinplot.plots
A container class to collect Path2D objects for cached plotting.
LineCache(Stroke, Stroke) - Constructor for class net.talvi.puffinplot.plots.LineCache
Creates a new LineCache.
load() - Method in class net.talvi.puffinplot.PuffinPrefs
Loads the preferences from the preferences backing store.
LoadedData - Interface in net.talvi.puffinplot.data.file
A dataset loaded from a file.
Location - Class in net.talvi.puffinplot.data
Represents a location on the Earth's surface (latitude/longitude).

M

mag() - Method in class net.talvi.puffinplot.data.Vec3
Returns the magnitude of this vector.
MagSusSampleRpiEstimate - Class in net.talvi.puffinplot.data
An estimate of relative palaeointensity for a single sample, normalized by magnetic susceptibility.
Main - Class in net.talvi.puffinplot
This class contains the initial entry point for starting PuffinPlot.
Main() - Constructor for class net.talvi.puffinplot.Main
 
main(String[]) - Static method in class net.talvi.puffinplot.Main
Instantiates and starts a new PuffinApp.
MainGraphDisplay - Class in net.talvi.puffinplot.window
A graph display which can show multiple plots.
MainGraphDisplay(PuffinApp) - Constructor for class net.talvi.puffinplot.window.MainGraphDisplay
Create a new main graph display for a given PuffinPlot application.
MainMenuBar - Class in net.talvi.puffinplot.window
The menu bar and attached hierarchy of menus for PuffinPlot's main window.
MainMenuBar(PuffinApp) - Constructor for class net.talvi.puffinplot.window.MainMenuBar
Creates a new menu bar and menu tree.
MainWindow - Class in net.talvi.puffinplot.window
The main window of the PuffinPlot application.
makeEllipse(KentParams) - Static method in class net.talvi.puffinplot.data.Vec3
Returns a list of points outlining the confidence ellipse for a supplied set of Kent statistical parameters.
makeSmallCircle(double) - Method in class net.talvi.puffinplot.data.Vec3
Returns a list of vectors defining a small circle around this vector's direction.
MalformedFileException - Exception in net.talvi.puffinplot.data.file
This exception is thrown when a file format does not conform to the expectations of a file loader.
MalformedFileException(String) - Constructor for exception net.talvi.puffinplot.data.file.MalformedFileException
Creates a new malformed file exception with a specified message.
maxIntensity(Collection<TreatmentStep>) - Static method in class net.talvi.puffinplot.data.TreatmentStep
Returns the maximum magnitude of magnetic dipole moment per unit volume within the supplied group of treatment step objects.
maxMagSus(Collection<TreatmentStep>) - Static method in class net.talvi.puffinplot.data.TreatmentStep
Returns the maximum magnetic susceptibility within the supplied group of treatment step objects.
maxTreatmentLevel(Collection<TreatmentStep>) - Static method in class net.talvi.puffinplot.data.TreatmentStep
Returns the maximum treatment level within the supplied group of treatment step objects.
mdf - Variable in class net.talvi.puffinplot.PuffinActions
Calculates the median destructive field or temperature of the selected samples.
mean(Collection<Vec3>) - Static method in class net.talvi.puffinplot.data.Vec3
Returns the mean of a collection of vectors.
meanDirection(Collection<Vec3>) - Static method in class net.talvi.puffinplot.data.Vec3
Returns the mean direction of a collection of unit vectors.
MeasurementAxis - Enum in net.talvi.puffinplot.data
An axis along which a magnetic moment measurement was made.
MeasurementType - Enum in net.talvi.puffinplot.data
The type of measurement which was performed on a sample or set of samples.
MedianDestructiveField - Class in net.talvi.puffinplot.data
This class calculates and stores the median destructive field (MDF) for a set of TreatmentStep objects.
mergeDuplicateSamples(Collection<Sample>) - Method in class net.talvi.puffinplot.data.Suite
Within the supplied collection of samples, any two or more samples which have the same depth or discrete ID will be merged into a single sample.
mergeDuplicateSamples - Variable in class net.talvi.puffinplot.PuffinActions
Merges samples with the same name or depth, and treatment steps with the same treatment type and level within samples.
mergeDuplicateTreatmentSteps() - Method in class net.talvi.puffinplot.data.Sample
Merges duplicate measurements within this Sample.
mergeDuplicateTreatmentSteps(Collection<Sample>) - Method in class net.talvi.puffinplot.data.Suite
Within each of the supplied samples, merges any TreatmentStep objects which have the same treatment type and treatment level.
mergeDuplicateTreatmentSteps - Variable in class net.talvi.puffinplot.PuffinActions
Merges duplicate treatment steps within the selected samples.
mergeSamples(List<Sample>) - Static method in class net.talvi.puffinplot.data.Sample
Merges the demagnetization data of the supplied samples into the first sample in the list.
minus(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Subtracts another vector from this vector.
MissingSampleNameException(String) - Constructor for exception net.talvi.puffinplot.data.Suite.MissingSampleNameException
Creates a new MissingSampleNameException with the supplied message.
modifierKey - Static variable in class net.talvi.puffinplot.PuffinAction
The standard modifier key for the platform; generally, this will correspond to Ctrl on most systems, and ⌘ (‘Apple key’) on Mac OS X systems.
modifySelectedSamples(Consumer<Sample>) - Method in class net.talvi.puffinplot.PuffinApp
Applies the supplied function to each of the currently selected samples, then redoes any existing calculations for the selected samples and any sites that contain them.
MomentUnit - Enum in net.talvi.puffinplot.data
This enum represents a unit in which magnetic dipole moment per unit volume can be measured.
mouseClicked(Point2D, MouseEvent) - Method in class net.talvi.puffinplot.plots.Plot
Handles a mouse click event on the plot.
MultiRange - Class in net.talvi.puffinplot.data
Represents multiple ranges of floating-point values.
multiSuiteMeans - Variable in class net.talvi.puffinplot.PuffinActions
Calculate mean directions for data in all the currently open data suites.

N

nearestOnCircle(Vec3) - Method in class net.talvi.puffinplot.data.GreatCircle
For a supplied direction, returns the nearest direction which lies on this great circle.
nearestOnCircle(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Using the enclosing vector to define the pole of a great circle G, this method accepts another unit vector v and returns the nearest unit vector to v which lies on G.
net.talvi.puffinplot - package net.talvi.puffinplot
net.talvi.puffinplot is a library and GUI application for plotting and analysing palaeomagnetic data.
net.talvi.puffinplot.data - package net.talvi.puffinplot.data
This package contains code to read, store, analyse, and write palaeomagnetic data.
net.talvi.puffinplot.data.file - package net.talvi.puffinplot.data.file
This package contains classes for reading palaeomagnetic data from a file.
net.talvi.puffinplot.icons - package net.talvi.puffinplot.icons
This package contains the PuffinPlot icon in various sizes.
net.talvi.puffinplot.plots - package net.talvi.puffinplot.plots
This package contains classes for plotting palaeomagnetic data.
net.talvi.puffinplot.window - package net.talvi.puffinplot.window
This package contains windows and related GUI classes for PuffinPlot.
NONE - Static variable in class net.talvi.puffinplot.data.Correction
The null correction.
normalize() - Method in class net.talvi.puffinplot.data.Vec3
Normalizes this vector.
NORTH - Static variable in class net.talvi.puffinplot.data.Vec3
a unit vector pointing north
NrmHistogram - Class in net.talvi.puffinplot.plots
A histogram of the intensities of natural remanent magnetizations of a collection of samples.
NrmHistogram(PlotParams) - Constructor for class net.talvi.puffinplot.plots.NrmHistogram
Creates an NRM histogram with the supplied parameters
numberRangeStringToBitSet(String, int) - Static method in class net.talvi.puffinplot.Util
Converts a string specification of number ranges to a corresponding BitSet.

O

open - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to choose one or more files to open as a new data suite.
openFileDialog(String) - Method in class net.talvi.puffinplot.PuffinApp
Show an "open file" dialog.
openFiles(AppEvent.OpenFilesEvent) - Method in class net.talvi.puffinplot.AppleEventHandler
Handles an Apple Open File action by calling PuffinApp.openFiles
openFiles(List<File>, boolean) - Method in class net.talvi.puffinplot.PuffinApp
Reads data into the current suite, or a new suite, from the specified files.
openFolder - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to choose a folder to open as a new data suite.
openPuffinWebsite - Variable in class net.talvi.puffinplot.PuffinActions
Opens the PuffinPlot website.
openWebPage(String) - Method in class net.talvi.puffinplot.PuffinApp
Opens the specified URI in the default system browser.
operateOnTreatmentStepRange - Variable in class net.talvi.puffinplot.PuffinActions
Operates on specifies ranges of treatment steps.
opposite() - Method in enum net.talvi.puffinplot.data.MeasurementAxis
Returns an axis pointing in the opposite direction to this axis.
opposite() - Method in enum net.talvi.puffinplot.plots.Direction
 
OptionDefinition - Interface in net.talvi.puffinplot.data.file
A definition of an option which is accepted by a file loader class.
OrientationParameters - Class in net.talvi.puffinplot.data.file
A set of parameters defining conventions for orienting a sample.
OrientationParameters(OrientationParameters.AzimuthParameter, OrientationParameters.DipParameter, OrientationParameters.AzimuthParameter, OrientationParameters.DipParameter) - Constructor for class net.talvi.puffinplot.data.file.OrientationParameters
Creates an orientation parameter set from the specified parameters values.
OrientationParameters.AzimuthParameter - Enum in net.talvi.puffinplot.data.file
A parameter representing an orientation convention for an azimuthal angular value (e.g.
OrientationParameters.DipParameter - Enum in net.talvi.puffinplot.data.file
A parameter representing an orientation convention for a vertical angular measurement (e.g.
ORIGIN - Static variable in class net.talvi.puffinplot.data.Vec3
the origin vector (zero along each axis)
oTensor() - Method in class net.talvi.puffinplot.data.Vec3
Returns the orientation tensor of this vector.

P

p1 - Variable in class net.talvi.puffinplot.data.file.OrientationParameters
P1 is a clock value orientation of the Arrow which represents the x-axis of Specimen coordinate system (right hand rule, see Legend).
p2 - Variable in class net.talvi.puffinplot.data.file.OrientationParameters
P2 indicates which angle is measured as the specimen inclination.
p3 - Variable in class net.talvi.puffinplot.data.file.OrientationParameters
P3 is a clock value that indicates which Direction on the specimen frontal plane (x-y plane) is measured using geological compass and expressed as Azimuth.
p4 - Variable in class net.talvi.puffinplot.data.file.OrientationParameters
P4 indicates how mesoscopic foliation adjacent to the specimen is measured.
pageSetup - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to change the page setup for printing.
paint(Graphics) - Method in class net.talvi.puffinplot.window.GraphDisplay
Paints this graph display to a graphics context.
params - Variable in class net.talvi.puffinplot.plots.Plot
the plot parameters
parseDoubleSafely(String) - Static method in class net.talvi.puffinplot.Util
A wrapper around Double.parseDouble which returns a default value of 0 if the supplied string cannot be parsed.
pasteStepSelection - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, sets the selected points using the range currently copied to the clipboard.
pasteStepSelection() - Method in class net.talvi.puffinplot.PuffinApp
For each selected sample, selects the treatment steps corresponding to those last copied to the clipboard.
PcaAnnotated - Class in net.talvi.puffinplot.data
This class encapsulates a set of principal component analysis (PCA) parameters along with some data on the treatment steps from which the PCA was calculated.
pcaOnSelection - Variable in class net.talvi.puffinplot.PuffinActions
Performs principal component analysis on the selected points of the selected samples.
PcaValues - Class in net.talvi.puffinplot.data
This class performs three-dimension principal component analysis on a supplied collection of vectors and stores the results.
Plot - Class in net.talvi.puffinplot.plots
An abstract superclass for all plots and other data displays.
Plot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.Plot
Creates a plot with the supplied parameters.
PLOT_POINT_SIZE - Static variable in class net.talvi.puffinplot.plots.Plot
the default size of a plotted data point
PlotParams - Interface in net.talvi.puffinplot.plots
The current parameters for a plot.
PlotPoint - Interface in net.talvi.puffinplot.plots
PlotPoint represents a point on a PuffinPlot Plot.
plots - Variable in class net.talvi.puffinplot.window.GraphDisplay
A map from internal plot names to the plots themselves.
PlotTitle - Class in net.talvi.puffinplot.plots
A title for the graph display, showing the sample identifier and some other information.
PlotTitle(PlotParams) - Constructor for class net.talvi.puffinplot.plots.PlotTitle
Creates a plot title with the supplied parameters.
plus(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Adds this vector and another vector.
PmdLoader - Class in net.talvi.puffinplot.data.file
A loader for the PMD (Enkin) file format (filename suffix pmd), a text-based format used by the PMGSC program of R.
PmdLoader() - Constructor for class net.talvi.puffinplot.data.file.PmdLoader
 
PplLoader - Class in net.talvi.puffinplot.data.file
A loader for PuffinPlot's own file format.
PplLoader() - Constructor for class net.talvi.puffinplot.data.file.PplLoader
 
prefs - Variable in class net.talvi.puffinplot.PuffinActions
Opens the preferences window.
PrefsWindow - Class in net.talvi.puffinplot.window
A window which allows the user to change PuffinPlot's preferences.
PrefsWindow(PuffinApp) - Constructor for class net.talvi.puffinplot.window.PrefsWindow
Creates a new preferences window for a supplied PuffinPlot application.
print - Variable in class net.talvi.puffinplot.PuffinActions
Opens a printing dialog box allowing printing of the main window data display.
print(Graphics, PageFormat, int) - Method in class net.talvi.puffinplot.window.MainGraphDisplay
Prints this graph display.
print(Graphics, PageFormat, int) - Method in class net.talvi.puffinplot.window.SiteMeanDisplay
Prints this graph display.
print(Graphics, PageFormat, int) - Method in class net.talvi.puffinplot.window.SuiteEqAreaDisplay
Prints this graph display.
printPdfPage(Graphics2D, int) - Method in class net.talvi.puffinplot.window.MainGraphDisplay
Writes a requested page of the current suite to a given graphics context.
printPlots(PageFormat, Graphics) - Method in class net.talvi.puffinplot.window.GraphDisplay
Prints all this display's plots to a graphics context.
printSiteEqualArea - Variable in class net.talvi.puffinplot.PuffinActions
Opens a print dialog for the site equal-area plot window.
printSuiteEqualArea - Variable in class net.talvi.puffinplot.PuffinActions
Opens a printing dialog box allowing printing of the suite equal-area data display.
ProgressDialog - Class in net.talvi.puffinplot.window
A dialog which shows progress for a supplied SwingWorker task.
project(Vec3) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Projects the direction of a three-dimensional vector into plot co-ordinates.
projectGreatCircleSegment(Vec3, Vec3) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Create a projection of a great-circle segment.
projectLineSegments(List<Vec3>, LineCache) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Project and cache line segments.
propertyChange(PropertyChangeEvent) - Method in class net.talvi.puffinplot.window.ProgressDialog
 
PuffinAction - Class in net.talvi.puffinplot
PuffinAction is the superclass for most Actions used in PuffinPlot.
PuffinAction(String, String, Character, boolean, Integer, boolean, int) - Constructor for class net.talvi.puffinplot.PuffinAction
Creates a new PuffinAction with the specified parameters.
PuffinAction(String, String, Character, boolean, Integer) - Constructor for class net.talvi.puffinplot.PuffinAction
Creates a new PuffinAction with the specified parameters.
PuffinAction(String, String) - Constructor for class net.talvi.puffinplot.PuffinAction
Creates a new PuffinAction with the specified parameters.
PuffinActions - Class in net.talvi.puffinplot
A container class for individual instances of PuffinAction which represent particular user actions in PuffinPlot.
PuffinApp - Class in net.talvi.puffinplot
Instantiating PuffinApp starts the PuffinPlot desktop application.
PuffinPrefs - Class in net.talvi.puffinplot
PuffinPrefs stores, loads, and saves PuffinPlot's user preferences.
PuffinPrefs(PuffinApp) - Constructor for class net.talvi.puffinplot.PuffinPrefs
Instantiates a set of PuffinPlot preferences for the specified PuffinApp instance.
PuffinRenderingHints - Class in net.talvi.puffinplot.window
Rendering hints for the PuffinPlot graph display.
PuffinRenderingHints.Key - Class in net.talvi.puffinplot.window
A key for a PuffinPlot rendering hint.
PuffinUserException - Exception in net.talvi.puffinplot
An exception representing a condition which is not fatal, but which needs to be caught and reported to the user.
PuffinUserException(String) - Constructor for exception net.talvi.puffinplot.PuffinUserException
Creates a PuffinPlot user exception with the specified message.
PuffinUserException(IOException) - Constructor for exception net.talvi.puffinplot.PuffinUserException
Creates a PuffinPlot user exception wrapping the supplied exception.
put(String, File) - Method in class net.talvi.puffinplot.IdToFileMap
Set the directory associated with an identifier.
put(Object, Object) - Method in class net.talvi.puffinplot.window.PuffinRenderingHints
putAll(Map<?, ?>) - Method in class net.talvi.puffinplot.window.PuffinRenderingHints
putText(Graphics2D, AttributedString, double, double, Direction, double, double) - Method in class net.talvi.puffinplot.plots.Plot
Write some text on this plot.
putText(Graphics2D, String, double, double, Direction, double, double) - Method in class net.talvi.puffinplot.plots.Plot
Write some text on this plot.

Q

quit - Variable in class net.talvi.puffinplot.PuffinActions
Terminates the application immediately.
quit() - Method in class net.talvi.puffinplot.PuffinApp
Terminates this instance of PuffinApp immediately.

R

radius - Variable in class net.talvi.puffinplot.plots.EqualAreaPlot
The radius of the projection.
read(String) - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Parses a string as an integer and return an azimuth parameter with the corresponding index.
read(int) - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Returns an azimuth parameter for a specified index.
read(String) - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
Parses a string as an integer and return a dip parameter with the corresponding index.
read(int) - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
Returns a dip parameter for a specified index.
read(int, int, int, int) - Static method in class net.talvi.puffinplot.data.file.OrientationParameters
Creates a orientation parameter set from the specified index values for the required parameters.
read(String, String, String, String) - Static method in class net.talvi.puffinplot.data.file.OrientationParameters
Creates a orientation parameter set from the strings containing index values for the required parameters.
readDirectionalData(Collection<File>) - Method in class net.talvi.puffinplot.data.Suite
Reads sample direction data from text files.Text files should have no header lines.
Reader(List<String>) - Constructor for class net.talvi.puffinplot.data.TreatmentStep.Reader
Create a new reader using the supplied header strings.
readFile() - Method in class net.talvi.puffinplot.data.file.AmsLoader
Reads the file for which this loader was created.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.CaltechLoader
Read a file into a data object containing treatment steps.
readFile(File, Map<String, Object>) - Method in interface net.talvi.puffinplot.data.file.FileLoader
Read a file using a specified set of options.
readFile(File) - Method in interface net.talvi.puffinplot.data.file.FileLoader
Reads a file without any specified options.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.IapdLoader
Reads an IAPD file.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.Jr6Loader
Returns a JR6 loader for the specified file.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.PmdLoader
Return a PmdLoader containing the treatmentSteps from the supplied input stream.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.PplLoader
Reads data from a specified PuffinPlot file.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.TabularFileLoader
Reads a file.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.TwoGeeLoader
Reads a file in 2G format.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.UcDavisLoader
Read a file in the old UC Davis file format.
readFile(File, Map<String, Object>) - Method in class net.talvi.puffinplot.data.file.ZplotLoader
Reads a Zplot file.
readFiles(List<File>) - Method in class net.talvi.puffinplot.data.Suite
Convenience method for reading PuffinPlot files.This method is a wrapper for the fully specified method Suite.readFiles(List, FileType, Map) which provides defaults for all the arguments except for the list of file names.
readFiles(List<File>, FileType, Map<String, Object>) - Method in class net.talvi.puffinplot.data.Suite
Reads data into this suite from the specified files.
readFromPrefs(Preferences) - Static method in class net.talvi.puffinplot.data.file.FileFormat
Creates a format from a preferences object.
readLine(String) - Method in class net.talvi.puffinplot.data.file.FileFormat
Creates a TreatmentStep from a line formatted according to this format.
readLines(List<String>) - Method in class net.talvi.puffinplot.data.file.FileFormat
Reds a list of lines in this format and produces the corresponding TreatmentSteps.
readStream(InputStream, String, TreatmentType) - Method in class net.talvi.puffinplot.data.file.Jr6Loader
Reads JR6 data from a specified input stream.
readStream(InputStream, Map<String, Object>, String) - Method in class net.talvi.puffinplot.data.file.PmdLoader
Return a data object containing the treatment steps from a supplied input stream.
recalculateSamplesAndSites(Collection<Sample>) - Method in class net.talvi.puffinplot.PuffinApp
Redo existing sample and site calculations affected by specified samples.
RecentFileList - Class in net.talvi.puffinplot
RecentFileList manages a list of file-sets.
RecentFileList(UnaryOperator<String>) - Constructor for class net.talvi.puffinplot.RecentFileList
Creates a new file list, reading data (if any) using the supplied getter.
recreatePlots() - Method in class net.talvi.puffinplot.window.MainGraphDisplay
Deletes all plots and recreates them.
redoCalculationsForAllSuites() - Method in class net.talvi.puffinplot.PuffinApp
Recalculates all sample and site calculations in all currently open suites.
remove(int) - Method in class net.talvi.puffinplot.data.CustomFields
Removes a value from this custom field list.
remove(Object) - Method in class net.talvi.puffinplot.window.PuffinRenderingHints
RemoveByDepthRangeDialog - Class in net.talvi.puffinplot.window
A dialog for removing samples within a specified depth range.
RemoveByDepthRangeDialog(PuffinApp) - Constructor for class net.talvi.puffinplot.window.RemoveByDepthRangeDialog
Creates a new remove depth range dialog
removeCurrentTreatmentStepListener(CurrentTreatmentStepListener) - Method in class net.talvi.puffinplot.window.GraphDisplay
Remove a datum change listener.
removeData(Collection<TreatmentStep>) - Method in class net.talvi.puffinplot.data.Sample
Remove specified treatmentSteps from this sample.
removeSampleClickListener(SampleClickListener) - Method in class net.talvi.puffinplot.plots.Plot
Removes a sample click listener which was previously added to this plot.
removeSamples(Collection<Sample>) - Method in class net.talvi.puffinplot.data.Suite
Removes the specified samples from this suite.
removeSamplesByTreatmentType(Collection<Sample>, TreatmentType) - Method in class net.talvi.puffinplot.data.Suite
For every sample in the supplied collection: remove the sample from this suite if any of its treatment steps has the specified treatment type.
removeSamplesByTreatmentType - Variable in class net.talvi.puffinplot.PuffinActions
Removes samples with a particular treatment type.
removeSamplesOutsideDepthRange(double, double) - Method in class net.talvi.puffinplot.data.Suite
Retains the samples between the specified depths in the suite, and removes all samples outside this range.
removeSamplesOutsideDepthRange - Variable in class net.talvi.puffinplot.PuffinActions
Removes samples whose depth falls outside a specified range.
removeSavedListener(Suite.SavedListener) - Method in class net.talvi.puffinplot.data.Suite
Remove a listener for the Suite's save state
removeVisibilityChangedListener(Consumer<Boolean>) - Method in class net.talvi.puffinplot.plots.Plot
Removes a listener for visibility changes to this plot.
rescaleMagSus(double) - Method in class net.talvi.puffinplot.data.Suite
Multiplies all magnetic susceptibility measurements in this suite by the specified factor.
rescaleMagSus - Variable in class net.talvi.puffinplot.PuffinActions
Scales all magnetic susceptibility values in the current suite by a user-specified factor.
resetLayout - Variable in class net.talvi.puffinplot.PuffinActions
Resets the layout of the plots to the default.
resetLayout() - Method in class net.talvi.puffinplot.window.GraphDisplay
Resets each plot's size and position to their defaults.
rot180(MeasurementAxis) - Method in class net.talvi.puffinplot.data.TreatmentStep
Rotates magnetic moment data 180 degrees about the specified axis.
rot180(MeasurementAxis) - Method in class net.talvi.puffinplot.data.Vec3
Rotates the vector by 180 degrees about the specified axis.
rotateAroundZAxis(double) - Method in class net.talvi.puffinplot.data.Sample
Rotate all the magnetic moment vectors of this sample about the z axis.
rotateDeclinations(double) - Method in class net.talvi.puffinplot.data.CoreSection
Rotates the declinations of all the data points in all the samples by the specified angle.
rotateForP1(Vec3) - Method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Rotates a vector from a P1=this system to a P1=12 system.
rotateForP1(double[]) - Method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Rotates a tensor from a P1=this system to a P1=12 system.
rotateSampleAzimuthForP3(double) - Method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Rotates a sample azimuth from a P3=this system to a P3=12 system.
rotateSamplesByDiscreteId(Map<String, Double>) - Method in class net.talvi.puffinplot.data.Suite
Rotate the declination of magnetic moment data in this suite according to the discrete ID of the sample.
rotY(double) - Method in class net.talvi.puffinplot.data.Vec3
Rotates this vector about the y axis.
rotZ(double) - Method in class net.talvi.puffinplot.data.Vec3
Rotates this vector about the z axis.
RpiDialog - Class in net.talvi.puffinplot.window
A class to show a dialog to input settings for an RPI calculation.
RpiDialog(List<Suite>, JFrame) - Constructor for class net.talvi.puffinplot.window.RpiDialog
Create a new RPI dialog.
RpiEstimateType - Enum in net.talvi.puffinplot.data
The parameter used in normalizing an NRM to produce an RPI estimate.
RpiPlot - Class in net.talvi.puffinplot.plots
A plot which shows the current suite RPI estimate.
RpiPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.RpiPlot
Instantiates a new RPI plot.
runJavascriptScript - Variable in class net.talvi.puffinplot.PuffinActions
Runs a Python script using the Jython interpreter.
runJavascriptScript(String) - Method in class net.talvi.puffinplot.PuffinApp
Runs a specified script written in JavaScript
runningOnOsX() - Static method in class net.talvi.puffinplot.Util
Reports whether the JVM is running on Mac OS X.
runPythonScript - Variable in class net.talvi.puffinplot.PuffinActions
Runs a Python script using the Jython interpreter.
runPythonScriptInGui(String) - Method in class net.talvi.puffinplot.PuffinApp
Runs a specified Python script, first downloading Jython if required.

S

safeDirection(Point2D, Collection<Point2D>) - Static method in enum net.talvi.puffinplot.plots.Direction
Given a "central" point and a collection of "peripheral" points, safeDirection attempts to find a quadrant containing no peripheral points.
sameHemisphere(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Returns true if and only if the supplied vector is in the same (upper/lower) hemisphere as this one.
Sample - Class in net.talvi.puffinplot.data
This class represents a sample on which measurements have been made.
Sample(String, Suite) - Constructor for class net.talvi.puffinplot.data.Sample
Creates a new sample.
sampleAzimuth - Variable in class net.talvi.puffinplot.data.file.VectorAndOrientations
A sample azimuth value in degrees.
sampleChanged() - Method in class net.talvi.puffinplot.window.MainMenuBar
Alerts the menu bar that the current sample has changed.
sampleChanged() - Method in class net.talvi.puffinplot.window.MainWindow
Informs this window that the current sample has changed.
SampleChooser - Class in net.talvi.puffinplot.window
A component allowing a user to choose the current sample and the selected samples.
sampleClicked(Sample) - Method in interface net.talvi.puffinplot.plots.SampleClickListener
Invoked when a sample is clicked in a plot.
SampleClickListener - Interface in net.talvi.puffinplot.plots
An interface for classes which want to be notified of clicks on samples.
sampleDip - Variable in class net.talvi.puffinplot.data.file.VectorAndOrientations
A sample dip value in degrees.
SampleEqualAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot showing sample data.
SampleEqualAreaPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SampleEqualAreaPlot
Creates a sample equal-area plot with the supplied parameters.
SampleGroup - Interface in net.talvi.puffinplot.data
An interface for any grouping of samples (at time of writing: a Site, Suite, or CoreSection).
SampleParamsLegend - Class in net.talvi.puffinplot.plots
A textual display of a set of parameters for a single sample.
SampleParamsLegend(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SampleParamsLegend
Creates a new sample parameter legend with the supplied parameters.
SampleParamsTable - Class in net.talvi.puffinplot.plots
A table showing sample directions for the current site.
SampleParamsTable(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SampleParamsTable
Creates a sample parameter table with the supplied parameters.
SampleRpiEstimate - Interface in net.talvi.puffinplot.data
An estimate of relative palaeointensity for a single sample.
save(Preferences) - Method in class net.talvi.puffinplot.data.SensorLengths
Writes a string representation of the sensor lengths to a specified Preferences object.
save() - Method in class net.talvi.puffinplot.data.Suite
If a default PuffinPlot file is set for this suite, saves the suite data to that file.
save - Variable in class net.talvi.puffinplot.PuffinActions
If a PuffinPlot file is associated with the current suite, the suite is saved to that file.
save() - Method in class net.talvi.puffinplot.PuffinApp
Saves the current suite under its current filename.
save(Suite) - Method in class net.talvi.puffinplot.PuffinApp
Saves the specified suite under its current filename.
save() - Method in class net.talvi.puffinplot.PuffinPrefs
Saves the preferences to the preferences backing store.
save(Consumer<String>, BiConsumer<String, String>) - Method in class net.talvi.puffinplot.RecentFileList
Stores the recent file list using the supplied remover and putter functions.
saveAs(File) - Method in class net.talvi.puffinplot.data.Suite
Saves the data in this suite to a specified file.
saveAs - Variable in class net.talvi.puffinplot.PuffinActions
Opens a ‘save’ dialog box; the current suite is saved to the selected file in PuffinPlot format.
saveCalcsSample(File) - Method in class net.talvi.puffinplot.data.Suite
Exports sample calculations to a specified file in CSV format.
saveCalcsSite(File) - Method in class net.talvi.puffinplot.data.Suite
Exports site calculations to a specified file in CSV format.
saveCalcsSuite(File) - Method in class net.talvi.puffinplot.data.Suite
Saves the Fisher mean direction for the whole suite to a file in CSV format
savedStateChanged(boolean) - Method in interface net.talvi.puffinplot.data.Suite.SavedListener
This method is called when the Suite's save state changes.
saveToSvgBatik(String) - Method in class net.talvi.puffinplot.window.GraphDisplay
Writes the contents of this display to an SVG file using the Batik library.
saveToSvgFreehep(String) - Method in class net.talvi.puffinplot.window.GraphDisplay
Writes the contents of this display to an SVG file using the FreeHEP library.
scaleLine(Line2D, double) - Static method in class net.talvi.puffinplot.Util
Scales a line around its midpoint.
selectAll() - Method in class net.talvi.puffinplot.data.Sample
Selects all the treatment steps within this sample.
selectAll - Variable in class net.talvi.puffinplot.PuffinActions
Within each selected sample, selects all the points.
selectByRectangle(Rectangle2D, boolean) - Method in class net.talvi.puffinplot.plots.Plot
Sets selection state for data points in a rectangle.
selectByTreatmentLevelRange(double, double) - Method in class net.talvi.puffinplot.data.Sample
Selects all treatment steps within a certain treatment level range.
selectNone() - Method in class net.talvi.puffinplot.data.Sample
De-selects all the treatment steps within this sample.
selectVisible() - Method in class net.talvi.puffinplot.data.Sample
Selects all the visible (non-hidden) treatment steps within this sample.
SensorLengths - Class in net.talvi.puffinplot.data
Represents the effective SQUID sensor lengths of a magnetometer, as determined by the response curves of the SQUID sensors.
SeparateSuiteEqualAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot showing suite-level Fisher statistics.
SeparateSuiteEqualAreaPlot(PlotParams, Rectangle2D) - Constructor for class net.talvi.puffinplot.plots.SeparateSuiteEqualAreaPlot
Creates a suite equal-area plot with the supplied parameters.
set(int, T) - Method in class net.talvi.puffinplot.data.CustomFields
Sets a specified custom field to a specified value.
set2gProtocol(TwoGeeLoader.Protocol) - Method in class net.talvi.puffinplot.PuffinPrefs
Sets the measurement protocol to use when opening 2G data files.
setAfX(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For AF or ARM treatment, sets the x-axis AF field strength in tesla.
setAfY(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For AF or ARM treatment, sets the y-axis AF field strength in tesla.
setAfZ(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For AF or ARM treatment, sets the z-axis AF field strength in tesla.
setAmsDirections(double, double, double, double, double, double) - Method in class net.talvi.puffinplot.data.Sample
Sets the AMS data for the sample using the supplied principal directions.
setAmsFromTensor(double, double, double, double, double, double) - Method in class net.talvi.puffinplot.data.Sample
Sets the AMS data for this sample using the supplied tensor.
setArea(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For continuous measurements, sets the cross-sectional area of the core.
setArmAxis(ArmAxis) - Method in class net.talvi.puffinplot.data.TreatmentStep
For ARM treatment, sets the axis of the ARM field.
setArmField(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For ARM treatment, sets the ARM bias field strength.
setAxisScaleLocked(boolean) - Method in class net.talvi.puffinplot.PuffinPrefs
Sets whether the axis scale is locked across all samples in the current suite.
setCorrection(Correction) - Method in class net.talvi.puffinplot.PuffinApp
Sets the correction to apply to the displayed data.
setCorrection(Correction) - Method in class net.talvi.puffinplot.window.ControlPanel
Sets the correction to apply to magnetic moment data.
setCorrections(double, double, double, double, double) - Method in class net.talvi.puffinplot.data.Sample
Sets the orientation corrections for this sample's magnetic moment data.
setCurrentSampleIndex(int) - Method in class net.talvi.puffinplot.data.Suite
Sets the index defining the current sample.
setCurrentSuite(int) - Method in class net.talvi.puffinplot.PuffinApp
Sets the currently displayed Suite.
setDepth(String) - Method in class net.talvi.puffinplot.data.Sample
Set the depth of this sample.
setDepth(String) - Method in class net.talvi.puffinplot.data.TreatmentStep
For continuous measurements, sets the depth of this measurement within the core.
setDimensions(Rectangle2D) - Method in class net.talvi.puffinplot.plots.Plot
Sets the dimensions of this plot.
setDimensions(Rectangle2D) - Method in class net.talvi.puffinplot.plots.SiteEqualAreaPlot
 
setDimensionsToDefault() - Method in class net.talvi.puffinplot.plots.Plot
Resets the plot's dimensions to the default, as defined in Plot.DEFAULT_PLOT_POSITIONS.
setDiscreteId(String) - Method in class net.talvi.puffinplot.data.Sample
Sets the discrete ID of this sample by setting the discrete IDs of its TreatmentStep objects, if the sample has any TreatmentStep objects.
setDiscreteId(String) - Method in class net.talvi.puffinplot.data.TreatmentStep
For discrete samples, sets the sample identifier (name).
setDragPlotMode(boolean) - Method in class net.talvi.puffinplot.window.GraphDisplay
Sets whether the plots are draggable by the user.
setEmptySlot(boolean) - Method in class net.talvi.puffinplot.data.Sample
Sets whether this sample is an empty slot on the measurement tray.
setFormAz(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the formation dip azimuth.
setFormDip(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the formation dip angle.
setFormStrike(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the formation strike for this treatment step.
setGroupedBySite(boolean) - Method in class net.talvi.puffinplot.plots.SeparateSuiteEqualAreaPlot
Sets whether the Fisher means are to be grouped by site.
setHidden(boolean) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets whether this treatment step should be hidden on plots.
setImportedDirection(Vec3) - Method in class net.talvi.puffinplot.data.Sample
Sets an imported direction for this sample.
setInPca(boolean) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets whether this measurement is to be used for a PCA fit.
setIrmField(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For IRM treatment, sets the IRM field strength in tesla.
setLine(Line) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the measurement's data-file line.
setLocation(Location) - Method in class net.talvi.puffinplot.data.Site
Sets the location of this site.
setMagDev(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the local geomagnetic field declination for the sampling site.
setMagDevAppliedToFormation(boolean) - Method in class net.talvi.puffinplot.data.Correction
 
setMagSus(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the magnetic susceptibility of the sample at this stage of treatment.
setMeasurementType(MeasurementType) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the type of this measurement (discrete or continuous).
setMoment(Vec3) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the sample's magnetic dipole moment per unit volume in A/m.
setMomentToMean(List<TreatmentStep>) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the magnetization vector of this datum to the mean of the magnetization vectors of data.
setNamedSiteForSamples(Collection<Sample>, String) - Method in class net.talvi.puffinplot.data.Suite
Explicitly sets a site for the specified samples.
setNameOrDepth(String) - Method in class net.talvi.puffinplot.data.Sample
Set the identifier of a sample.
setOnCircle(boolean) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets whether this measurement is to be used for a great-circle fit.
setPcaAnchored(boolean) - Method in class net.talvi.puffinplot.data.Sample
Sets whether principal component analysis should be anchored for this sample
setPcaAnchored(boolean) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets whether PCA fits for this point should be anchored.
setPcaAnchored(boolean) - Method in class net.talvi.puffinplot.PuffinPrefs
Sets whether PCA fits should be anchored to the origin.
setRecentFiles(RecentFileList) - Method in class net.talvi.puffinplot.PuffinApp
Sets the list of recently used files (allowing it to be restored after restarting the application).
setRotation(Correction.Rotation) - Method in class net.talvi.puffinplot.data.Correction
Sets the rotation correction.
setRunNumber(int) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the number of the machine run during which this measurement was made.
setSampAz(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the sample's dip azimuth.
setSampDip(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the sample's dip angle.
setSampHade(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the sample hade for this treatment step.
setSample(Sample) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the sample on which this measurement was made.
setSaved(boolean) - Method in class net.talvi.puffinplot.data.Suite
Sets this suite's "saved" flag, which records whether the suite has been saved since its last modification.
setSelected(boolean) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the selection state of this treatment step.
setSelectionBitSet(BitSet) - Method in class net.talvi.puffinplot.data.Sample
Sets the selection state of the sample's treatment steps from a supplied bit set.
setSensorLengths(SensorLengths) - Method in class net.talvi.puffinplot.PuffinPrefs
Sets the effective sensor lengths for opening 2G data files.
setSite(Site) - Method in class net.talvi.puffinplot.data.Sample
Sets the site for this sample.
setSiteName - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to specify a site name for the selected samples.
setSiteNamesByDepth(Collection<Sample>, double) - Method in class net.talvi.puffinplot.data.Suite
Sets site names for a continuous suite according to the depth of the samples.
setSiteNamesBySubstring(Collection<Sample>, BitSet) - Method in class net.talvi.puffinplot.data.Suite
Sets site names for samples according to chosen characters from the sample names.
setSitesByDepth - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to specify a site thickness, which is then used to divide a long core suite into sites based on sample depths.
setSitesForSamples(Collection<Sample>, Suite.SiteNamer) - Method in class net.talvi.puffinplot.data.Suite
Sets sites for supplied samples according to a supplied site namer.
setSitesFromSampleNames - Variable in class net.talvi.puffinplot.PuffinActions
Opens a dialog box allowing the user to specify which characters of the currently selected samples should be used to determine the site name.
setSize(int, T) - Method in class net.talvi.puffinplot.data.CustomFields
Sets the size of the list of custom fields.
setSlotNumber(int) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the number of the measurement tray slot in which the sample was measured.
setSuite(Suite) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the data suite containing this measurement.
setTemperature(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For thermal treatment, sets the temperature in degrees Celsius.
setTimestamp(String) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the timestamp of this measurement.
setTreatmentSteps(List<TreatmentStep>) - Method in class net.talvi.puffinplot.data.file.SimpleLoadedData
Replace the current treatment step cache with a supplied list.
setTreatmentType(TreatmentType) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the treatment applied before this measurement (AF, thermal, etc.).
setTreatType - Variable in class net.talvi.puffinplot.PuffinActions
Shows a window allowing the user to set the treatment type for the selected samples.
setValue(TreatmentParameter, String) - Method in class net.talvi.puffinplot.data.Sample
Sets the value of a specified field for each treatment step in the sample.
setValue(TreatmentParameter, String, double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the value of a specified treatment parameter using a string.
setVisible(boolean) - Method in class net.talvi.puffinplot.plots.Plot
Sets whether this plot should be drawn.
setVolume(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
For discrete measurements, sets the volume of the sample.
setX(double) - Method in class net.talvi.puffinplot.data.Vec3
Sets the x component of this vector.
setXDrift(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the x drift correction value.
setY(double) - Method in class net.talvi.puffinplot.data.Vec3
Sets the y component of this vector.
setYDrift(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the y drift correction value.
setZ(double) - Method in class net.talvi.puffinplot.data.Vec3
Sets the z component of this vector.
setZDrift(double) - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets the z drift correction value.
show() - Method in class net.talvi.puffinplot.PuffinApp
Shows the main window of this PuffinApp.
show() - Method in class net.talvi.puffinplot.window.AlignDeclinationsDialog
Show the dialog, and perform the alignment if appropriate.
show() - Method in class net.talvi.puffinplot.window.RpiDialog
Show this RPI dialog.
showCalculateRpiDialog() - Method in class net.talvi.puffinplot.PuffinApp
Calculates RPI using two loaded suites.
showCiteDialog - Variable in class net.talvi.puffinplot.PuffinActions
Opens the Citation window.
showCreateBundleDialog() - Method in class net.talvi.puffinplot.PuffinApp
Shows the dialog for creating and exporting a data and code bundle.
showCustomFlagsWindow - Variable in class net.talvi.puffinplot.PuffinActions
Opens a window which allows the user to edit the list of user-defined flags for the current suite.
showCustomFlagsWindow() - Method in class net.talvi.puffinplot.PuffinApp
Shows the window for editing the titles of the custom flags.
showCustomNotesWindow - Variable in class net.talvi.puffinplot.PuffinActions
Opens a window which allows the user to edit the list of user-defined note headings for the current suite.
showCustomNotesWindow() - Method in class net.talvi.puffinplot.PuffinApp
Shows the window for editing the titles of the custom notes.
showDialog(String, Frame, SwingWorker<Void, Void>) - Static method in class net.talvi.puffinplot.window.ProgressDialog
Create and show a progress dialog for a supplied SwingWorker.
showDiscreteToContinuousDialog() - Method in class net.talvi.puffinplot.PuffinApp
Shows the dialog for a discrete to continuous sample conversion.
showEditSampleParametersDialog - Variable in class net.talvi.puffinplot.PuffinActions
Opens a window allowing the user to edit the sample and formation orientations and the local magnetic declination.
showImportAmsDialog() - Method in class net.talvi.puffinplot.PuffinApp
Shows an ‘open files’ dialog box; if the user selects any files, AMS data will be imported from them.
showImportPreferencesDialog() - Method in class net.talvi.puffinplot.PuffinApp
Shows an ‘open file’ dialog box; if the user selects a file, the current preferences will be overwritten with preferences data from that file.
showMacOpenFolderDialog() - Method in class net.talvi.puffinplot.PuffinApp
Show the "Open folder" dialog on Mac OS X.
showOpenFilesDialog(boolean) - Method in class net.talvi.puffinplot.PuffinApp
Shows an ‘open files’ dialog box.
showOverMainWindow() - Method in class net.talvi.puffinplot.window.RemoveByDepthRangeDialog
Show this dialog, centred over the PuffinPlot app's main window.
showOverMainWindow() - Method in class net.talvi.puffinplot.window.TreatmentRangesDialog
Show this dialog, centred over the PuffinPlot app's main window.
showPageSetupDialog() - Method in class net.talvi.puffinplot.PuffinApp
Opens the page setup dialog box.
showPreferences() - Method in class net.talvi.puffinplot.PuffinApp
Opens the preferences window.
showPrintDialog(String) - Method in class net.talvi.puffinplot.PuffinApp
Shows a print dialog.
showRescaleMagSusDialog() - Method in class net.talvi.puffinplot.PuffinApp
Scales all magnetic susceptibility values in the current suite by a user-specified factor.
showRunJavascriptScriptDialog() - Method in class net.talvi.puffinplot.PuffinApp
Opens a file selection dialog and runs the Javascript script (if any) which the user selects from that dialog.
showRunPythonScriptDialog() - Method in class net.talvi.puffinplot.PuffinApp
Opens a file selection dialog and runs the Python script (if any) which the user selects from that dialog.
SimpleLoadedData - Class in net.talvi.puffinplot.data.file
A simple implementation of the LoadedData interface.
SimpleLoadedData() - Constructor for class net.talvi.puffinplot.data.file.SimpleLoadedData
 
SimpleOptionDefinition - Class in net.talvi.puffinplot.data.file
A simple implementation of the OptionDefinition interface.
SimpleOptionDefinition(String, String, Class, Object, boolean) - Constructor for class net.talvi.puffinplot.data.file.SimpleOptionDefinition
 
Site - Class in net.talvi.puffinplot.data
A site is a grouping of samples within a suite.
Site(String, List<Sample>) - Constructor for class net.talvi.puffinplot.data.Site
Creates a site containing the specified samples.
Site(String) - Constructor for class net.talvi.puffinplot.data.Site
Creates a site containing no samples.
SiteEqualAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot showing data for a site.
SiteEqualAreaPlot(PlotParams, Rectangle2D) - Constructor for class net.talvi.puffinplot.plots.SiteEqualAreaPlot
Creates a site equal area plot with the supplied parameters.
SiteEqualAreaPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SiteEqualAreaPlot
Creates a site equal area plot with the supplied parameters.
SiteMeanDisplay - Class in net.talvi.puffinplot.window
A graph display containing a single equal-area plot which shows data for a site.
SiteMeanDisplay(PlotParams) - Constructor for class net.talvi.puffinplot.window.SiteMeanDisplay
Creates a new site mean graph display.
SiteMeanWindow - Class in net.talvi.puffinplot.window
A window containing a site mean graph display.
SiteMeanWindow(PlotParams) - Constructor for class net.talvi.puffinplot.window.SiteMeanWindow
Creates a new site mean window.
siteName(Sample) - Method in interface net.talvi.puffinplot.data.Suite.SiteNamer
Determines a site name from a sample name.
SiteParamsLegend - Class in net.talvi.puffinplot.plots
This plot shows site directions in textual form.
SiteParamsLegend(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SiteParamsLegend
Creates a site data table with the supplied parameters.
SiteParamsTable - Class in net.talvi.puffinplot.plots
A table showing site mean directions for the whole suite.
SiteParamsTable(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SiteParamsTable
Creates a site parameter table with the supplied parameters.
size() - Method in class net.talvi.puffinplot.data.CustomFields
Returns the number of values in this list.
sortSamplesByDepth() - Method in class net.talvi.puffinplot.data.Suite
Sorts this suite's samples in ascending order of depth
SOURCE_URL_STRING - Static variable in class net.talvi.puffinplot.JythonJarManager
A string representation of the URL from which the jython jar is downloaded.
specifiesDirection() - Method in class net.talvi.puffinplot.data.file.FileFormat
Determines whether this format specifies a three-dimensional direction.
specifiesFullVector() - Method in class net.talvi.puffinplot.data.file.FileFormat
Determines whether this format specifies a full magnetization vector.
spherInterpDir(Vec3, Vec3, Vec3, double) - Static method in class net.talvi.puffinplot.data.Vec3
Interpolates a great-circle path in a chosen direction between two specified vectors.
spherInterpolate(Vec3, Vec3, double) - Static method in class net.talvi.puffinplot.data.Vec3
Given two vectors, interpolates unit vectors along a great-circle path between them.
StepwiseSampleRpiEstimate - Class in net.talvi.puffinplot.data
An estimate of relative palaeointensity for a single sample, normalized by a stepwise series of AF fields.
Suite - Class in net.talvi.puffinplot.data
A suite of data, containing a number of samples.
Suite(String) - Constructor for class net.talvi.puffinplot.data.Suite
Creates a new, empty suite.
Suite.MissingSampleNameException - Exception in net.talvi.puffinplot.data
This exception indicates that a supplied argument did not contain an expected sample name.
Suite.SavedListener - Interface in net.talvi.puffinplot.data
A listener interface for modifications to the Suite's save state.
Suite.SiteNamer - Interface in net.talvi.puffinplot.data
A SiteNamer turns a sample name into a site name.
SuiteCalcs - Class in net.talvi.puffinplot.data
Represents a set of calculations for a suite of data.
SuiteCalcs(SuiteCalcs.Means, SuiteCalcs.Means, SuiteCalcs.Means, SuiteCalcs.Means) - Constructor for class net.talvi.puffinplot.data.SuiteCalcs
Creates a new SuiteCalcs object.
SuiteCalcs.Means - Class in net.talvi.puffinplot.data
Fisher statistics for the suite.
SuiteEqAreaDisplay - Class in net.talvi.puffinplot.window
A graph display which contains a single equal-area plot of Fisher means at suite level.
SuiteEqAreaDisplay(PlotParams) - Constructor for class net.talvi.puffinplot.window.SuiteEqAreaDisplay
Creates a new suite equal-area graph display
SuiteEqAreaWindow - Class in net.talvi.puffinplot.window
A window to hold a SuiteEqAreaDisplay.
SuiteEqAreaWindow(PuffinApp) - Constructor for class net.talvi.puffinplot.window.SuiteEqAreaWindow
Creates a new suite equal-area window.
SuiteEqualAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot data for an entire suite.
SuiteEqualAreaPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SuiteEqualAreaPlot
Creates a suite equal area plot with the supplied parameters.
suiteMeans - Variable in class net.talvi.puffinplot.PuffinActions
Calculates Fisher statistics on sample PCA directions for all selected samples, and on site means for all selected sites.
SuiteParamsTable - Class in net.talvi.puffinplot.plots
A table which displays site location and VGP data.
SuiteParamsTable(PlotParams) - Constructor for class net.talvi.puffinplot.plots.SuiteParamsTable
Creates a suite parameter table with the supplied parameters.
SuiteRpiEstimate<EstimateType extends SampleRpiEstimate> - Class in net.talvi.puffinplot.data
A collection of RPI estimates.
suitesChanged() - Method in class net.talvi.puffinplot.window.MainWindow
Informs this window that the list of currently loaded data suites has changed.
sum(Collection<Vec3>) - Static method in class net.talvi.puffinplot.data.Vec3
Returns the sum of a specified collection of vectors.
swapAdjacent(int) - Method in class net.talvi.puffinplot.data.CustomFields
Swaps the values in two adjacent positions within this custom field list.

T

t63 - Variable in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
θ63, the angular standard deviation, in degrees
TableWindow - Class in net.talvi.puffinplot.window
A window which shows all the data for a sample in tabular form.
TableWindow(PuffinApp) - Constructor for class net.talvi.puffinplot.window.TableWindow
Creates a new table window.
TabularFileLoader - Class in net.talvi.puffinplot.data.file
A loader for a tabular text file with a custom format.
TabularFileLoader() - Constructor for class net.talvi.puffinplot.data.file.TabularFileLoader
 
TabularImportWindow - Class in net.talvi.puffinplot.window
A window allowing the user to define a custom file format.
TabularImportWindow(Frame, Preferences) - Constructor for class net.talvi.puffinplot.window.TabularImportWindow
Creates a new tabular import window.
Tensor - Class in net.talvi.puffinplot.data
A second-order symmetric tensor used to represent the anisotropy of magnetic susceptibility.
Tensor(double, double, double, double, double, double, Matrix, Matrix) - Constructor for class net.talvi.puffinplot.data.Tensor
Creates a tensor with the specified components and transformed using the specified matrices.
TernaryPlot - Class in net.talvi.puffinplot.plots
An experimental ternary plot for a sample's magnetic moment data.
TernaryPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.TernaryPlot
Creates a ternary plot with the supplied parameters.
times(double) - Method in class net.talvi.puffinplot.data.Vec3
Multiplies this vector by a scalar value.
times(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Multiplies the components of this vector individually by the corresponding components of another vector.
timesTenToThe(String, String, Graphics2D) - Method in class net.talvi.puffinplot.plots.Plot
Returns an attributed string representing a number in scientific notation.
timesTenToThe(String, int, Graphics2D) - Method in class net.talvi.puffinplot.plots.Plot
Returns an attributed string representing a number in scientific notation.
toCommaSeparatedString() - Method in class net.talvi.puffinplot.data.MagSusSampleRpiEstimate
 
toCommaSeparatedString() - Method in interface net.talvi.puffinplot.data.SampleRpiEstimate
 
toCommaSeparatedString() - Method in class net.talvi.puffinplot.data.StepwiseSampleRpiEstimate
 
toggleSelected() - Method in class net.talvi.puffinplot.data.TreatmentStep
Toggles the treatment step's selection state.
toString() - Method in class net.talvi.puffinplot.data.Correction
Returns a parseable string representation of this correction.
toString() - Method in class net.talvi.puffinplot.data.FisherValues
Returns a string representation of the parameters.
toString() - Method in class net.talvi.puffinplot.data.SensorLengths
Returns a string representation of this object.
toString() - Method in class net.talvi.puffinplot.data.Site
Returns the name of this site.
toString() - Method in class net.talvi.puffinplot.data.Suite
Returns the name of this suite.
toString() - Method in class net.talvi.puffinplot.data.Vec3
Returns a string representation of this vector.
toStrings() - Method in class net.talvi.puffinplot.data.CustomFields
 
toStrings() - Method in class net.talvi.puffinplot.data.FisherValues
Returns the statistical parameters as a list of strings.
toStrings(FisherValues) - Static method in class net.talvi.puffinplot.data.FisherValues
Returns the statistical parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.GreatCircle
Returns the statistical parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.GreatCircles
Returns the statistical parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.Location
Returns the VGP parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.MedianDestructiveField
Returns the parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.PcaAnnotated
Returns the parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.PcaValues
Returns the parameters as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.Sample
Returns a list of Strings representing data pertaining to this sample.
toStrings() - Method in class net.talvi.puffinplot.data.Site
Returns a list of strings giving information about this site.
toStrings() - Method in class net.talvi.puffinplot.data.Suite
Returns strings representing data about this suite.
toStrings() - Method in class net.talvi.puffinplot.data.SuiteCalcs.Means
 
toStrings() - Method in class net.talvi.puffinplot.data.SuiteCalcs
 
toStrings() - Method in class net.talvi.puffinplot.data.Tensor
Returns the principal directions as a list of strings.
toStrings() - Method in class net.talvi.puffinplot.data.TreatmentStep
Produces a list of strings representing the data values within this treatment step object.
toStrings() - Method in class net.talvi.puffinplot.data.VGP
Returns the VGP parameters as a list of strings.
toSummaryString() - Method in class net.talvi.puffinplot.data.TreatmentStep
Produce a string summarizing the most important characteristics of this treatment step: step number, treatment type and level, moment vector (as declination, inclination, and intensity), and magnetic susceptibility.
toTensorComponentString() - Method in class net.talvi.puffinplot.data.Tensor
Returns a string giving the components of the tensor, separated by spaces.
touch() - Method in class net.talvi.puffinplot.data.Sample
Sets this sample's suite as "modified".
touch() - Method in class net.talvi.puffinplot.data.TreatmentStep
Sets this tratment steps's suite as "modified".
toVec3() - Method in class net.talvi.puffinplot.data.Location
 
toVector() - Method in class net.talvi.puffinplot.data.SensorLengths
Returns the sensor lengths as a three-dimensional vector.
transform(double[][]) - Method in class net.talvi.puffinplot.data.Vec3
Multiplies this vector by a supplied matrix.
TreatmentLevelComparator - Class in net.talvi.puffinplot.data
A comparator that compares treatment steps according to their treatment level.
TreatmentLevelComparator() - Constructor for class net.talvi.puffinplot.data.TreatmentLevelComparator
 
TreatmentParameter - Enum in net.talvi.puffinplot.data
This enum represents a data field in the TreatmentStep class which is associated with a measurement or other value.
TreatmentRangesDialog - Class in net.talvi.puffinplot.window
A dialog for editing treatment steps within specified ranges
TreatmentRangesDialog(PuffinApp) - Constructor for class net.talvi.puffinplot.window.TreatmentRangesDialog
Creates a new edit treatment step range dialog
TreatmentStep - Class in net.talvi.puffinplot.data
TreatmentStep is the fundamental data class of PuffinPlot.
TreatmentStep(double, double, double) - Constructor for class net.talvi.puffinplot.data.TreatmentStep
Creates a treatment step with a specified magnetization vector.
TreatmentStep(Vec3) - Constructor for class net.talvi.puffinplot.data.TreatmentStep
Creates a treatment step with a supplied magnetization vector.
TreatmentStep() - Constructor for class net.talvi.puffinplot.data.TreatmentStep
Creates a treatment step with no data.
TreatmentStep.Reader - Class in net.talvi.puffinplot.data
This class allows TreatmentStep objects to be created from string representations of a specified format.
treatmentStepChanged(TreatmentStep) - Method in interface net.talvi.puffinplot.window.CurrentTreatmentStepListener
Called when the current treatment step changes, generally as a result of the mouse pointer moving.
TreatmentStepMomentComparator - Class in net.talvi.puffinplot.data
This class implements a specific type of comparison for datum objects.
TreatmentStepMomentComparator(MeasurementAxis, Correction) - Constructor for class net.talvi.puffinplot.data.TreatmentStepMomentComparator
Creates a comparator which will compare magnetic moments along the specified axis after applying the specified correction.
TreatmentStepOperation - Enum in net.talvi.puffinplot.data
Represents an operation which can be performed on a treatment step.
TreatmentType - Enum in net.talvi.puffinplot.data
A type of treatment applied to a sample.
TreatmentWindow - Class in net.talvi.puffinplot.window
A window allowing the user to edit treatment type.
TreatmentWindow(PuffinApp) - Constructor for class net.talvi.puffinplot.window.TreatmentWindow
Creates a new correction window.
truncateTreatmentSteps(int) - Method in class net.talvi.puffinplot.data.Sample
Truncates the list of treatment steps to a specified number of entries.
tryToParseDouble(Component, String) - Static method in class net.talvi.puffinplot.Util
Try to parse a string to a Double object; if a NumberFormatException is thrown, show an error dialog and return null.
tryToParseInteger(Component, String) - Static method in class net.talvi.puffinplot.Util
Try to parse a string to an Integer object; if a NumberFormatException is thrown, show an error dialog and return null.
TwoGeeLoader - Class in net.talvi.puffinplot.data.file
A loader for the DAT files produced by the Long Core software supplied with 2G Enterprises magnetometers.
TwoGeeLoader() - Constructor for class net.talvi.puffinplot.data.file.TwoGeeLoader
Creates a new 2G loader.
TwoGeeLoader.MomentFields - Enum in net.talvi.puffinplot.data.file
The fields from which to read the magnetic moment (Cartesian or Polar).
TwoGeeLoader.Protocol - Enum in net.talvi.puffinplot.data.file
A measurement protocol.

U

UcDavisLoader - Class in net.talvi.puffinplot.data.file
Loader for the old UC Davis format.
UcDavisLoader() - Constructor for class net.talvi.puffinplot.data.file.UcDavisLoader
 
unhideAllPoints() - Method in class net.talvi.puffinplot.data.Sample
Unhides all treatment steps within this sample.
unhideAllSteps - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, makes all the points visible.
updateDisplay() - Method in class net.talvi.puffinplot.PuffinApp
Updates the main window and table window to reflect any changes in the currently displayed data.
updatePlotDimensions(Graphics2D) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Sets the fields EqualAreaPlot.cachedGraphics, EqualAreaPlot.radius, EqualAreaPlot.xo, and EqualAreaPlot.yo according to the supplied argument and the current plot dimensions.
updateRecentFiles() - Method in class net.talvi.puffinplot.window.MainMenuBar
Updates the submenu containing the list of recently used files.
updateReverseIndex() - Method in class net.talvi.puffinplot.data.Suite
Update this suit's internal index mapping samples to their indices within the suite.
updateSample() - Method in class net.talvi.puffinplot.window.ControlPanel
Updates this control panel's sample information display.
updateSampleDataPanel() - Method in class net.talvi.puffinplot.window.MainWindow
Updates this window's sample data panel.
updateSuite() - Method in class net.talvi.puffinplot.window.SampleChooser
Redraws the sample chooser to reflect a change in the Puffin application's current suite.
updateValueFromSuite() - Method in class net.talvi.puffinplot.window.SampleChooser
Updates the displayed value from the current PuffinPlot application.
useFixedWidthColumns() - Method in class net.talvi.puffinplot.data.file.FileFormat
 
useSelectionForCircleFit() - Method in class net.talvi.puffinplot.data.Sample
Flags the selected treatment steps for use in the next great-circle fit.
useSelectionForPca() - Method in class net.talvi.puffinplot.data.Sample
Flags all selected treatment steps for inclusion in principal component analysis.
Util - Class in net.talvi.puffinplot
This class collects miscellaneous, general-purpose utility functions which are useful to PuffinPlot.
Util() - Constructor for class net.talvi.puffinplot.Util
 

V

valueOf(String) - Static method in enum net.talvi.puffinplot.data.AmsCalculationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.ArmAxis
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.CoreSection.End
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.CoreSections.TargetDeclinationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.Correction.Rotation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.FieldUnit
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.file.TwoGeeLoader.MomentFields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.file.TwoGeeLoader.Protocol
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.FileType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.MeasurementAxis
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.MeasurementType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.MomentUnit
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.RpiEstimateType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.TreatmentStepOperation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.data.TreatmentType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.talvi.puffinplot.plots.Direction
Returns the enum constant of this type with the specified name.
values() - Static method in enum net.talvi.puffinplot.data.AmsCalculationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.ArmAxis
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.CoreSection.End
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.CoreSections.TargetDeclinationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.Correction.Rotation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.FieldUnit
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.AzimuthParameter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.file.OrientationParameters.DipParameter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.file.TwoGeeLoader.MomentFields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.file.TwoGeeLoader.Protocol
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.FileType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.MeasurementAxis
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.MeasurementType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.MomentUnit
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.RpiEstimateType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.TreatmentParameter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.TreatmentStepOperation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.data.TreatmentType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.talvi.puffinplot.plots.Direction
Returns an array containing the constants of this enum type, in the order they are declared.
Vec3 - Class in net.talvi.puffinplot.data
An immutable three-dimensional Cartesian vector.
Vec3(double, double, double) - Constructor for class net.talvi.puffinplot.data.Vec3
Creates a vector with the specified components.
vector - Variable in class net.talvi.puffinplot.data.file.VectorAndOrientations
A vector measured relative to a sample's own co-ordinate system; in practice, most likely to be a magnetization vector.
VectorAndOrientations - Class in net.talvi.puffinplot.data.file
VectorAndOrientations encapsulates a vector (in practice, most probably a magnetization vector) and orientation parameters for the sample and the rock formation.
VectorAndOrientations(Vec3, double, double, double, double) - Constructor for class net.talvi.puffinplot.data.file.VectorAndOrientations
Instantiate a VectorAndOrientations object.
vectorsToPath(List<Vec3>) - Method in class net.talvi.puffinplot.plots.EqualAreaPlot
Projects a list of three-dimensional vectors into a two-dimensional path in the current plot co-ordinates.
Version - Class in net.talvi.puffinplot
A class containing information about PuffinPlot's version.
VGP - Class in net.talvi.puffinplot.data
A class representing a virtual geomagnetic pole.
VgpMap - Class in net.talvi.puffinplot.plots
A plot which shows VGP positions on a world map.
VgpMap(PlotParams) - Constructor for class net.talvi.puffinplot.plots.VgpMap
Instantiates a new VGP map.
VgpTable - Class in net.talvi.puffinplot.plots
A table which displays site location and VGP data.
VgpTable(PlotParams) - Constructor for class net.talvi.puffinplot.plots.VgpTable
Creates a sample parameter table with the supplied parameters.

W

wasOkPressed() - Method in class net.talvi.puffinplot.window.IapdImportDialog
 
writeCsv(Object...) - Method in class net.talvi.puffinplot.data.CsvWriter
Writes a line to the writer provided to the constructor.
writeString(Graphics2D, String, float, float) - Method in class net.talvi.puffinplot.plots.Plot
Writes a text string onto this plot.
writeString(Graphics2D, AttributedString, float, float) - Method in class net.talvi.puffinplot.plots.Plot
Writes an attributed text string onto this plot.
writeToFile(String) - Method in class net.talvi.puffinplot.data.SuiteRpiEstimate
Write this RPI estimate to a CSV file.
writeToPrefs(Preferences) - Method in class net.talvi.puffinplot.data.file.FileFormat
Saves this format to a preferences object.

X

x - Variable in class net.talvi.puffinplot.data.Vec3
the x component of the vector
xo - Variable in class net.talvi.puffinplot.plots.EqualAreaPlot
The x co-ordinate of the projection's origin.

Y

y - Variable in class net.talvi.puffinplot.data.Vec3
the y component of the vector
yo - Variable in class net.talvi.puffinplot.plots.EqualAreaPlot
The y co-ordinate of the projection's origin.

Z

z - Variable in class net.talvi.puffinplot.data.Vec3
the z component of the vector
zipDirectory(Path, Path) - Static method in class net.talvi.puffinplot.Util
Create a zip file from the contents of a directory.
zoomTransform - Variable in class net.talvi.puffinplot.window.GraphDisplay
A transformation applied to the graphics before painting them, intended to be used for zooming in and out of the display.
ZPlot - Class in net.talvi.puffinplot.plots
A Zijderveld plot for a sample's demagnetization data.
ZPlot(PlotParams) - Constructor for class net.talvi.puffinplot.plots.ZPlot
Creates a Zijderveld plot with the supplied parameters.
ZPlot.ZplotLegend - Class in net.talvi.puffinplot.plots
A legend for a Zijderveld plot.
ZplotLoader - Class in net.talvi.puffinplot.data.file
A file loader for the file format used by Steve Hurst's Zplot program.
ZplotLoader() - Constructor for class net.talvi.puffinplot.data.file.ZplotLoader
 
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