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P

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
pastePointSelection - Variable in class net.talvi.puffinplot.PuffinActions
For each selected sample, sets the selected points using the range currently copied to the clipboard.
pastePointSelection() - Method in class net.talvi.puffinplot.PuffinApp
For each selected sample, selects the points 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(GraphDisplay, PlotParams, Preferences) - 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.window
The current parameters for a 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(GraphDisplay, PlotParams, Preferences) - Constructor for class net.talvi.puffinplot.plots.PlotTitle
Creates a plot title with the supplied parameters.
plus(Matrix) - Method in class Jama.Matrix
C = A + B
plus(Vec3) - Method in class net.talvi.puffinplot.data.Vec3
Adds this vector and another vector.
plusEquals(Matrix) - Method in class Jama.Matrix
A = A + B
PplLoader - Class in net.talvi.puffinplot.data.file
A loader for PuffinPlot's own file format.
PplLoader(File) - Constructor for class net.talvi.puffinplot.data.file.PplLoader
Creates a PuffinPlot file loader for the specified file.
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() - Constructor for class net.talvi.puffinplot.window.PrefsWindow
Creates a new preferences window.
print(int, int) - Method in class Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class Jama.Matrix
Print the matrix to the output stream.
print(NumberFormat, int) - Method in class Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class Jama.Matrix
Print the matrix to the output stream.
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.
printGc - Variable in class net.talvi.puffinplot.PuffinActions
Opens a print dialog for the site equal-area plot window.
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.
printSuiteEqArea - Variable in class net.talvi.puffinplot.PuffinActions
Opens a printing dialog box allowing printing of the suite equal-area data display.
project(Vec3) - Method in class net.talvi.puffinplot.plots.EqAreaPlot
Projects the direction of a three-dimensional vector into plot co-ordinates.
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
This class constitutes the main PuffinPlot application.
PuffinApp() - Constructor for class net.talvi.puffinplot.PuffinApp
Instantiates a new PuffinPlot application object.
PuffinApp.Version - Class in net.talvi.puffinplot
 
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.
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.

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