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C

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
 
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.
calculateGreatCirclesDirection(Correction) - Method in class net.talvi.puffinplot.data.Site
Calculate a mean direction for the site using best-fit great circles.
calculateGreatCirclesDirections(boolean) - 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
 
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() - Method in class net.talvi.puffinplot.data.Suite
Calculates Fisher statistics on all the calculated PCA directions for samples within the suite.
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
 
CiteWindow() - Constructor for class net.talvi.puffinplot.window.CiteWindow
 
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.
clearFisher() - 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
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.
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.
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() - Constructor for class net.talvi.puffinplot.window.ControlPanel
Creates a new control panel
convertStringToColumnWidths(String) - Static method in class net.talvi.puffinplot.data.file.FileFormat
Turns a string containing comma-separated decimal integers into a List of {@link Integer.
copy() - Method in class Jama.Matrix
Make a deep copy of a matrix
copyPointSelection - Variable in class net.talvi.puffinplot.PuffinActions
Copies the range of selected points from the current sample onto a clipboard.
copyPointSelection() - Method in class net.talvi.puffinplot.PuffinApp
Copies the current pattern of selected points to 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.
CorrectionWindow - Class in net.talvi.puffinplot.window
A window allowing the user to edit orientation corrections.
CorrectionWindow() - Constructor for class net.talvi.puffinplot.window.CorrectionWindow
Creates a new correction window.
correctSample(double, double) - Method in class net.talvi.puffinplot.data.Vec3
Applies a sample correction to this vector.
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.
CustomFieldEditor - Class in net.talvi.puffinplot.window
An editing window for custom field headings.
CustomFieldEditor(CustomFields<String>, String) - 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.

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