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S

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.
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.
SampleEqAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot showing sample data.
SampleEqAreaPlot(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.SampleEqAreaPlot
Creates a sample equal-area plot with the supplied parameters.
SampleParamsLegend - Class in net.talvi.puffinplot.plots
A textual display of a set of PCA and great circle parameters for a single sample.
SampleParamsLegend(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.SampleParamsLegend
Creates a new PCA table with the supplied parameters.
SampleParamsTable - Class in net.talvi.puffinplot.plots
A table showing sample directions for the current site.
SampleParamsTable(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.SampleParamsTable
Creates a sample parameter table with the supplied parameters.
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.PuffinPrefs
Saves the preferences to the preferences backing store.
save(Preferences) - Method in class net.talvi.puffinplot.RecentFileList
Saves the recent file list to the specified Preferences object.
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
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
 
selectAll() - Method in class net.talvi.puffinplot.data.Sample
Selects all the data points within this sample.
selectAll - Variable in class net.talvi.puffinplot.PuffinActions
Within each selected sample, selects all the points.
selectByRectangle(Rectangle2D) - Method in class net.talvi.puffinplot.plots.Plot
Selects all the plotted data points within a specified rectangle.
selectNone() - Method in class net.talvi.puffinplot.data.Sample
De-selects all the data points within this sample.
selectVisible() - Method in class net.talvi.puffinplot.data.Sample
Selects all the visible (non-hidden) data points 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.
SeparateSuiteEaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot showing suite-level Fisher statistics.
SeparateSuiteEaPlot(GraphDisplay, PlotParams, Rectangle2D, Preferences) - Constructor for class net.talvi.puffinplot.plots.SeparateSuiteEaPlot
Creates a suite equal-area plot with the supplied parameters.
set(int, int, double) - Method in class Jama.Matrix
Set a single element.
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.Datum
For AF or ARM treatment, sets the AF field strength in the x axis.
setAfY(double) - Method in class net.talvi.puffinplot.data.Datum
For AF or ARM treatment, sets the AF field strength in the y axis.
setAfZ(double) - Method in class net.talvi.puffinplot.data.Datum
For AF or ARM treatment, sets the AF field strength in the z axis.
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.Datum
For continuous measurements, sets the cross-sectional area of the core.
setArmAxis(ArmAxis) - Method in class net.talvi.puffinplot.data.Datum
For ARM treatment, sets the axis of the ARM field.
setArmField(double) - Method in class net.talvi.puffinplot.data.Datum
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.
setDepth(String) - Method in class net.talvi.puffinplot.data.Datum
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.
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.Datum
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.
setEmptyCorrectionActive(boolean) - Method in class net.talvi.puffinplot.PuffinApp
Activates or deactivates the empty-slot correction.
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.Datum
Sets the formation dip azimuth.
setFormDip(double) - Method in class net.talvi.puffinplot.data.Datum
Sets the formation dip angle.
setFormStrike(double) - Method in class net.talvi.puffinplot.data.Datum
Sets the formation strike for this datum.
setGroupedBySite(boolean) - Method in class net.talvi.puffinplot.plots.SeparateSuiteEaPlot
Sets whether the Fisher means are to be grouped by site.
setHidden(boolean) - Method in class net.talvi.puffinplot.data.Datum
Sets whether this datum should be hidden on plots.
setInPca(boolean) - Method in class net.talvi.puffinplot.data.Datum
Sets whether this measurement is to be used for a PCA fit.
setIrmField(double) - Method in class net.talvi.puffinplot.data.Datum
For IRM treatment, sets the IRM field strength.
setLine(Line) - Method in class net.talvi.puffinplot.data.Datum
Sets the measurement's data-file line.
setMagDev(double) - Method in class net.talvi.puffinplot.data.Datum
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.Datum
Sets the magnetic susceptibility of the sample at this stage of treatment.
setMatrix(int, int, int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMeasType(MeasType) - Method in class net.talvi.puffinplot.data.Datum
Sets the type of this measurement (discrete or continuous).
setMoment(Vec3) - Method in class net.talvi.puffinplot.data.Datum
Sets the sample's magnetic dipole moment per unit volume in A/m.
setNamedSiteForSamples(Collection<Sample>, String) - Method in class net.talvi.puffinplot.data.Suite
Explicitly sets a site for the specified samples.
setOnCircle(boolean) - Method in class net.talvi.puffinplot.data.Datum
Sets whether this measurement is to be used for a great-circle fit.
setPcaAnchored(boolean) - Method in class net.talvi.puffinplot.data.Datum
Sets whether PCA fits for this point should be anchored.
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.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.Datum
Sets the number of the machine run during which this measurement was made.
setSampAz(double) - Method in class net.talvi.puffinplot.data.Datum
Sets the sample's dip azimuth.
setSampDip(double) - Method in class net.talvi.puffinplot.data.Datum
Sets the sample's dip angle.
setSampHade(double) - Method in class net.talvi.puffinplot.data.Datum
Sets the sample hade for this datum.
setSample(Sample) - Method in class net.talvi.puffinplot.data.Datum
Sets the sampe on which this measurement was made.
setSelected(boolean) - Method in class net.talvi.puffinplot.data.Datum
Sets the selection state of this datum.
setSelectionBitSet(BitSet) - Method in class net.talvi.puffinplot.data.Sample
Sets the selection state of the sample's data points 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.Datum
Sets the number of the measurement tray slot in which the sample was measured.
setSuite(Suite) - Method in class net.talvi.puffinplot.data.Datum
Sets the data suite containing this measurement.
setSuite(int) - Method in class net.talvi.puffinplot.PuffinApp
Sets the currently displayed Suite.
setTemp(double) - Method in class net.talvi.puffinplot.data.Datum
For thermal treatment, sets the temperature in degrees Celsius.
setTimestamp(String) - Method in class net.talvi.puffinplot.data.Datum
Sets the timestamp of this measurement.
setTreatType(TreatType) - Method in class net.talvi.puffinplot.data.Datum
Sets the treatment applied before this measurement (AF, thermal, etc.).
setValue(DatumField, String) - Method in class net.talvi.puffinplot.data.Datum
Sets the value of a specified data field using a string.
setValue(DatumField, String) - Method in class net.talvi.puffinplot.data.Sample
Sets the value of a specified field for each data point in the sample.
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.Datum
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.Datum
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.Datum
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.Datum
Sets the z drift correction value.
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.
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.
showTabularImportDialog() - Method in class net.talvi.puffinplot.PuffinApp
 
SingularValueDecomposition - Class in Jama
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class Jama.SingularValueDecomposition
Construct the singular value decomposition
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.
SiteEqAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot showing data for a site.
SiteEqAreaPlot(GraphDisplay, PlotParams, Rectangle2D, Preferences) - Constructor for class net.talvi.puffinplot.plots.SiteEqAreaPlot
Creates a site equal area plot with the supplied parameters.
SiteEqAreaPlot(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.SiteEqAreaPlot
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() - 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() - 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(GraphDisplay, PlotParams, Preferences) - 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(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.SiteParamsTable
Creates a sample parameter table with the supplied parameters.
size() - Method in class net.talvi.puffinplot.data.CustomFields
Returns the number of values in this list.
solve(Matrix) - Method in class Jama.CholeskyDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class Jama.QRDecomposition
Least squares solution of A*X = B
solveTranspose(Matrix) - Method in class Jama.Matrix
Solve X*A = B, which is also A'*X' = B'
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.
Suite - Class in net.talvi.puffinplot.data
A suite of data, containing a number of samples.
Suite(List<File>) - Constructor for class net.talvi.puffinplot.data.Suite
Creates a new suite from the specified files.
Suite(List<File>, SensorLengths, TwoGeeLoader.Protocol, boolean, FileFormat) - Constructor for class net.talvi.puffinplot.data.Suite
Creates a new suite from the specified files.
Suite.AmsCalcType - Enum in net.talvi.puffinplot.data
The type of a statistical calculation on AMS tensors.
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) - Constructor for class net.talvi.puffinplot.data.SuiteCalcs
 
SuiteCalcs.Means - Class in net.talvi.puffinplot.data
 
SuiteCalcs.Means(FisherValues, FisherValues, FisherValues) - Constructor for class net.talvi.puffinplot.data.SuiteCalcs.Means
 
SuiteEqAreaDisplay - Class in net.talvi.puffinplot.window
A graph display which contains a single equal-area plot of Fisher means at suite level.
SuiteEqAreaDisplay() - Constructor for class net.talvi.puffinplot.window.SuiteEqAreaDisplay
Creates a new suite equal-area graph display
SuiteEqAreaPlot - Class in net.talvi.puffinplot.plots
An equal-area plot data for an entire suite.
SuiteEqAreaPlot(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.SuiteEqAreaPlot
Creates a suite equal area plot with the supplied parameters.
SuiteEqAreaWindow - Class in net.talvi.puffinplot.window
A window to hold a SuiteEqAreaDisplay.
SuiteEqAreaWindow() - Constructor for class net.talvi.puffinplot.window.SuiteEqAreaWindow
Creates a new suite equal-area window.
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.
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.
svd() - Method in class Jama.Matrix
Singular Value Decomposition
swapAdjacent(int) - Method in class net.talvi.puffinplot.data.CustomFields
Swaps the values in two adjacent positions within this custom field list.

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