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

C

calculate(Collection<Double>) - Static method in class net.talvi.puffinplot.data.ArasonLevi.ArithMean
 
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<Datum>) - 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>, Suite.AmsCalcType, 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) - 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
Calculates the position of 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 data 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 suite.
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.
calculateRpi() - Method in class net.talvi.puffinplot.PuffinApp
Calculate RPI using two loaded suites.
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.
calculateWithArm(Suite, Suite, double, double) - Static method in class net.talvi.puffinplot.data.SuiteRpiEstimate
Estimate RPI by normalizing a stepwise demagnetized NRM to a stepwise demagnetized ARM.
calculateWithMagSus(Suite, Suite) - Static method in class net.talvi.puffinplot.data.SuiteRpiEstimate
Estimate RPI by normalizing NRM to MS.
CaltechLoader - Class in net.talvi.puffinplot.data.file
A file loader for CIT (Caltech) data files.
CaltechLoader(File) - Constructor for class net.talvi.puffinplot.data.file.CaltechLoader
Creates a new CIT loader to read a specified file.
checkInstalled(boolean) - Static method in class net.talvi.puffinplot.JythonJarManager
Checks whether the Jython jar file is installed locally and has the correct size.
checkSha1Digest(boolean) - Static method in class net.talvi.puffinplot.JythonJarManager
Calculates the SHA-1 digest of the Jython jar file and verified it against a hard-coded reference value.
chol() - Method in class Jama.Matrix
Cholesky Decomposition
CholeskyDecomposition - Class in Jama
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class Jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
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 data points.
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.
clearSelectedSampleCalculations() - Method in class net.talvi.puffinplot.PuffinApp
Clear selected points and stored calculations for selected samples.
clearSelectedSampleGcs() - Method in class net.talvi.puffinplot.PuffinApp
Clear great circle fits for selected samples.
clearSelectedSamplePcas() - Method in class net.talvi.puffinplot.PuffinApp
Clear PCA calculations for selected samples.
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() - Method in class net.talvi.puffinplot.data.Suite
Clears all sites for this suite.
clearSites - Variable in class net.talvi.puffinplot.PuffinActions
Clears all site definitions.
clipLineToRectangle(Line2D, Rectangle2D) - Static method in class net.talvi.puffinplot.Util
Clips a line to a supplied rectangle.
clone() - Method in class Jama.Matrix
Clone the Matrix object.
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.
compare(Datum, Datum) - Method in class net.talvi.puffinplot.data.DatumComparator
Compares the magnetic moments of the supplied datum objects using the criteria specified in the constructor.
cond() - Method in class Jama.Matrix
Matrix condition (2 norm)
cond() - Method in class Jama.SingularValueDecomposition
Two norm condition number
constructWithCopy(double[][]) - Static method in class Jama.Matrix
Construct a matrix from a copy of a 2-D array.
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
 
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 Integer.
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.
copy() - Method in class Jama.Matrix
Make a deep copy of a matrix
copyPointSelection() - Method in class net.talvi.puffinplot.PuffinApp
Copies the current pattern of selected points to a clipboard.
copyStepSelection - Variable in class net.talvi.puffinplot.PuffinActions
Copies the range of selected points from the current sample onto a clipboard.
correctForm(double, double) - Method in class net.talvi.puffinplot.data.Vec3
Applies a sample correction to this vector.
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.
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 delimited 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 delimit 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 delimiter.
CurrentDatumListener - Interface in net.talvi.puffinplot.window
 
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.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Skip navigation links