- 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
-
Check 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.
- 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
{@link #alignSections(int, double, net.talvi.puffinplot.data.CoreSections.ReferenceAlignmentType) ).
- 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.