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

## A

AbortDotFileGenerationException - Exception in pipe.io
AbortDotFileGenerationException() - Constructor for exception pipe.io.AbortDotFileGenerationException
AbortDotFileGenerationException(String) - Constructor for exception pipe.io.AbortDotFileGenerationException
accept(File) - Method in class pipe.gui.ExtensionFilter
actionPerformed(ActionEvent) - Method in class pipe.gui.DeletePetriNetObjectAction
actionPerformed(ActionEvent) - Method in class pipe.gui.EditAnnotationAction
  Action for editing the text in an AnnotationNote
actionPerformed(ActionEvent) - Method in class pipe.gui.EditAnnotationBackgroundAction
actionPerformed(ActionEvent) - Method in class pipe.gui.EditAnnotationBorderAction
  Action for editing the border of an AnnotationNote
actionPerformed(ActionEvent) - Method in class pipe.gui.EditRateAction
  Action changing an attribute of the transition
actionPerformed(ActionEvent) - Method in class pipe.gui.EditTimedAction
  Action for toggling timing on/off
actionPerformed(ActionEvent) - Method in class pipe.gui.EditTokenAction
  Prompts the user for the number of tokens they want the place to have
actionPerformed(ActionEvent) - Method in class pipe.gui.EditWeightAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GetIndexAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GuiFrame
actionPerformed(ActionEvent) - Method in class pipe.gui.HelpBox
actionPerformed(ActionEvent) - Method in class pipe.gui.LabelAction
  Prompts the user for a label
actionPerformed(ActionEvent) - Method in class pipe.gui.RotateTransitionAction
actionPerformed(ActionEvent) - Method in class pipe.gui.SplitArcAction
actionPerformed(ActionEvent) - Method in class pipe.gui.SplitArcPointAction
actionPerformed(ActionEvent) - Method in class pipe.gui.ToggleArcPointAction
add(int[]) - Method in class pipe.dataLayer.calculations.StateList
add(int[], int) - Method in class pipe.dataLayer.calculations.StateList
add(PetriNetObject) - Method in class pipe.gui.GuiView
addAnimationHistory() - Static method in class pipe.gui.CreateGui
  Creates a new animationHistory text area, and returns a reference to it
addArc(Arc) - Method in class pipe.dataLayer.DataLayer
  Add arcInput to back of the Arc ArrayList All observers are notified of this change (Model-View Architecture)
addClassRootToPath(Class) - Method in class pipe.gui.ExtFileManager
addConnectFrom(Arc) - Method in class pipe.dataLayer.PlaceTransitionObject
  Adds inwards arc to place/transition
addConnectTo(Arc) - Method in class pipe.dataLayer.PlaceTransitionObject
  Adds outwards arc to place/transition
addedToGui() - Method in class pipe.dataLayer.Arc
addedToGui() - Method in class pipe.dataLayer.PetriNetObject
addedToGui() - Method in class pipe.dataLayer.PlaceTransitionObject
addHistoryItem(String) - Method in class pipe.gui.AnimationHistory
addLabelToContainer() - Method in class pipe.dataLayer.PetriNetObject
addModuleToTree(DefaultMutableTreeNode) - Method in class pipe.gui.ModuleManager
addNewPetriNetObject(PetriNetObject) - Method in class pipe.gui.GuiView
addPetriNetObject(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Add any PetriNetObject - the object will be added to the appropriate list.
addPoint(float, float, boolean) - Method in class pipe.dataLayer.ArcPath
addPoint(double, double, boolean) - Method in class pipe.dataLayer.ArcPath
addPoint() - Method in class pipe.dataLayer.ArcPath
addPointsToGui(GuiView) - Method in class pipe.dataLayer.ArcPath
addSearchPath(File) - Static method in class pipe.gui.ExtFileManager
addSearchPath(URL[]) - Static method in class pipe.gui.ExtFileManager
ADDTOKEN - Static variable in interface pipe.gui.Constants
addWeightLabelToContainer() - Method in class pipe.dataLayer.Arc
addZoomController(ZoomController) - Method in class pipe.dataLayer.PetriNetObject
adjustBottom(int) - Method in class pipe.dataLayer.AnnotationNote
adjustLeft(int) - Method in class pipe.dataLayer.AnnotationNote
adjustRight(int) - Method in class pipe.dataLayer.AnnotationNote
adjustTop(int) - Method in class pipe.dataLayer.AnnotationNote
alphaCoef(int, int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  adjust linear combination coefficients according to sign if sign(j) <> sign(k) then alpha = abs(j) beta = abs(k) if sign(j) == sign(k) then alpha = -abs(j) beta = abs(k)
ANIMATE - Static variable in interface pipe.gui.Constants
AnimationHandler - Class in pipe.gui
  This class handles mouse clicks by the user.
AnimationHandler() - Constructor for class pipe.gui.AnimationHandler
AnimationHistory - Class in pipe.gui
  Class to represent the history of the net animation
AnimationHistory(String) - Constructor for class pipe.gui.AnimationHistory
animationmode - Variable in class pipe.gui.GuiView
Animator - Class in pipe.gui
  This class is used to process clicks by the user to manually step through enabled transitions in the net.
Animator() - Constructor for class pipe.gui.Animator
animBox - Static variable in class pipe.gui.CreateGui
ANNOTATION - Static variable in interface pipe.gui.Constants
ANNOTATION_DEFAULT_FONT - Static variable in interface pipe.gui.Constants
ANNOTATION_DEFAULT_FONT_SIZE - Static variable in interface pipe.gui.Constants
ANNOTATION_LAYER_OFFSET - Static variable in interface pipe.gui.Constants
ANNOTATION_MIN_WIDTH - Static variable in interface pipe.gui.Constants
ANNOTATION_SIZE_OFFSET - Static variable in interface pipe.gui.Constants
AnnotationNote - Class in pipe.dataLayer
AnnotationNote(int, int) - Constructor for class pipe.dataLayer.AnnotationNote
AnnotationNote(String, String, int, int) - Constructor for class pipe.dataLayer.AnnotationNote
AnnotationNote(String, int, int, int, int, boolean) - Constructor for class pipe.dataLayer.AnnotationNote
AnnotationNote.AnnotationKeyUpdateHandler - Class in pipe.dataLayer
AnnotationNote.AnnotationKeyUpdateHandler(AnnotationNote) - Constructor for class pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler
AnnotationNote.ResizePoint - Class in pipe.dataLayer
AnnotationNote.ResizePoint(AnnotationNote, int) - Constructor for class pipe.dataLayer.AnnotationNote.ResizePoint
AnnotationNote.ResizePointHandler - Class in pipe.dataLayer
AnnotationNote.ResizePointHandler(AnnotationNote.ResizePoint) - Constructor for class pipe.dataLayer.AnnotationNote.ResizePointHandler
AnnotationNoteHandler - Class in pipe.gui
AnnotationNoteHandler(Container, AnnotationNote) - Constructor for class pipe.gui.AnnotationNoteHandler
appendVector(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Append a column matrix (vector) to the right of another matrix.
appGui - Static variable in class pipe.gui.CreateGui
Arc - Class in pipe.dataLayer
  Arc - Petri-Net Arc Class
Arc(double, double, double, double, PlaceTransitionObject, PlaceTransitionObject, int, String, Color) - Constructor for class pipe.dataLayer.Arc
  Create Petri-Net Arc object
Arc(double, double, double, double, PlaceTransitionObject, PlaceTransitionObject, String, Color) - Constructor for class pipe.dataLayer.Arc
  Create Petri-Net Arc object
Arc(double, double, double, double, String) - Constructor for class pipe.dataLayer.Arc
  Create Petri-Net Arc object
Arc(double, double, double, double) - Constructor for class pipe.dataLayer.Arc
  Create Petri-Net Arc object
Arc(PlaceTransitionObject) - Constructor for class pipe.dataLayer.Arc
  Create Petri-Net Arc object
ARC - Static variable in interface pipe.gui.Constants
ARC_CONTROL_POINT_CONSTANT - Static variable in interface pipe.gui.Constants
ARC_LAYER_OFFSET - Static variable in interface pipe.gui.Constants
ARC_PATH_PROXIMITY_WIDTH - Static variable in interface pipe.gui.Constants
ARC_PATH_SELECTION_WIDTH - Static variable in interface pipe.gui.Constants
ARC_POINT_LAYER_OFFSET - Static variable in interface pipe.gui.Constants
arcboundsLeft - Variable in class pipe.dataLayer.NameLabel
arcboundsTop - Variable in class pipe.dataLayer.NameLabel
ArcHandler - Class in pipe.gui
  Class used to implement methods corresponding to mouse events on arcs.
ArcHandler(Container, Arc) - Constructor for class pipe.gui.ArcHandler
ArcKeyboardEventHandler - Class in pipe.gui
ArcKeyboardEventHandler(Arc) - Constructor for class pipe.gui.ArcKeyboardEventHandler
ArcPath - Class in pipe.dataLayer
ArcPath(Arc) - Constructor for class pipe.dataLayer.ArcPath
ArcPathPoint - Class in pipe.dataLayer
ArcPathPointHandler - Class in pipe.gui
ArcPathPointHandler(Container, ArcPathPoint) - Constructor for class pipe.gui.ArcPathPointHandler
areNotSameType(PlaceTransitionObject) - Method in class pipe.dataLayer.PlaceTransitionObject
ArrowHead - Class in pipe.gui
ArrowHead() - Constructor for class pipe.gui.ArrowHead
averageTokens(double[], StateList) - Method in class pipe.modules.gspn.GSPNNew
  averageTokens() Determines the average number of tokens on each place at steady state.

## B

betaCoef(int, int) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  adjust linear combination coefficients according to sign if sign(j) <> sign(k) then alpha = abs(j) beta = abs(k) if sign(j) == sign(k) then alpha = -abs(j) beta = abs(k)
BOTTOM - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
bounds - Variable in class pipe.dataLayer.PetriNetObject
boundsHeight() - Method in class pipe.dataLayer.Place
  Returns the height bounds we want to use when initially creating the place on the gui
boundsHeight() - Method in class pipe.dataLayer.PlaceTransitionObject
  Returns the height bounds we want to use when initially creating the place on the gui
boundsHeight() - Method in class pipe.dataLayer.Transition
  Returns the height bounds we want to use when initially creating the place on the gui
boundsWidth() - Method in class pipe.dataLayer.Place
  Returns the width bounds we want to use when initially creating the place on the gui
boundsWidth() - Method in class pipe.dataLayer.PlaceTransitionObject
  Returns the width bounds we want to use when initially creating the place on the gui
boundsWidth() - Method in class pipe.dataLayer.Transition
  Returns the width bounds we want to use when initially creating the place on the gui
ButtonBar - Class in pipe.gui.widgets
  ButtonBar object Create one with
ButtonBar(String[], ActionListener[]) - Constructor for class pipe.gui.widgets.ButtonBar
  Multiple button constructor
ButtonBar(String, ActionListener) - Constructor for class pipe.gui.widgets.ButtonBar
  Single button constructor

## C

calcNaturalCubic(int, int[]) - Method in class pipe.dataLayer.ArcPath
cardinalityCondition() - Method in class pipe.dataLayer.PNMatrix
  Check if a matrix has a row that satisfies the cardinality condition 1.1.b of the algorithm.
cardinalityOne() - Method in class pipe.dataLayer.PNMatrix
  Find the column index of the element in the pPlus or pMinus set, where pPlus or pMinus has cardinality == 1.
centreOffsetLeft() - Method in class pipe.dataLayer.PlaceTransitionObject
  Returns the distance between the outside of the component to the centre, in order to position the centre of the place where the mouse clicks on the screen
centreOffsetTop() - Method in class pipe.dataLayer.PlaceTransitionObject
  Returns the distance between the outside of the component to the centre, in order to position the centre of the place where the mouse clicks on the screen
changeAnimationMode(boolean) - Method in class pipe.gui.GuiView
changeBackground() - Method in class pipe.dataLayer.AnnotationNote
changeText(String) - Method in class pipe.gui.StatusBar
changeText(int) - Method in class pipe.gui.StatusBar
checkCase11() - Method in class pipe.dataLayer.PNMatrix
  Check if a matrix satisfies condition 1.1 of the algorithm.
checkForSave() - Method in class pipe.gui.GuiFrame
  If current net has modifications, asks if you want to save and does it if you want.
checkForSaveAll() - Method in class pipe.gui.GuiFrame
CLASS_FILE_DESC - Static variable in interface pipe.gui.Constants
CLASS_FILE_EXTENSION - Static variable in interface pipe.gui.Constants
Classification - Class in pipe.modules.classification
  Classification class implements petri net classification
Classification() - Constructor for class pipe.modules.classification.Classification
clearSelection() - Method in class pipe.gui.SelectionObject
clearStepsForward() - Method in class pipe.gui.AnimationHistory
clone() - Method in class pipe.dataLayer.PNMatrix
  Clone the IntMatrix object.
CMinus - Variable in class pipe.dataLayer.calculations.myTree
colsToUpdate() - Method in class pipe.dataLayer.PNMatrix
  Find the comlumn indices to be changed by linear combination.
compareMarking(int[], int[]) - Method in class pipe.dataLayer.calculations.StateList
Comparison - Class in pipe.modules.comparison
Comparison() - Constructor for class pipe.modules.comparison.Comparison
COMPONENT_DRAW_OFFSET - Static variable in class pipe.dataLayer.PetriNetObject
componentHeight - Variable in class pipe.dataLayer.PlaceTransitionObject
componentWidth - Variable in class pipe.dataLayer.PlaceTransitionObject
CompressedState - Class in pipe.dataLayer.calculations
CompressedState(int, int) - Constructor for class pipe.dataLayer.calculations.CompressedState
Constants - Interface in pipe.gui
construct() - Method in class pipe.modules.dnamaca.SwingWorker
  Compute the value to be returned by the `get` method.
constructGraphFrame(Graph) - Method in class pipe.gui.widgets.GraphFrame
constructWithCopy(int[][]) - Static method in class pipe.dataLayer.PNMatrix
  Construct a matrix from a copy of a 2-D array.
contains(int, int) - Method in class pipe.dataLayer.AnnotationNote
contains(int, int) - Method in class pipe.dataLayer.Arc
contains(double, double) - Method in class pipe.dataLayer.ArcPath
contains(double, double, double, double) - Method in class pipe.dataLayer.ArcPath
contains(Point2D) - Method in class pipe.dataLayer.ArcPath
contains(Rectangle2D) - Method in class pipe.dataLayer.ArcPath
contains(int, int) - Method in class pipe.dataLayer.Place
  Determines whether the point (x,y) is "in" this component.
contains(int, int) - Method in class pipe.dataLayer.Transition
contains(double, double) - Method in class pipe.gui.ArrowHead
contains(Point2D) - Method in class pipe.gui.ArrowHead
contains(double, double, double, double) - Method in class pipe.gui.ArrowHead
contains(Rectangle2D) - Method in class pipe.gui.ArrowHead
contains(int, int) - Method in class pipe.gui.SelectionObject
contentPane - Variable in class pipe.gui.PetriNetObjectHandler
copy() - Method in class pipe.dataLayer.PNMatrix
  Make a deep copy of a matrix
count - Static variable in class pipe.gui.Animator
CPlus - Variable in class pipe.dataLayer.calculations.myTree
createArc - Variable in class pipe.gui.GuiView
createFromPNML(Document) - Method in class pipe.dataLayer.DataLayer
  Create model from transformed PNML file
CreateGui - Class in pipe.gui
CreateGui() - Constructor for class pipe.gui.CreateGui
createNewTab(String) - Method in class pipe.gui.GuiFrame
  Creates a new tab with the selected file, or a new file if filename==null
createPath() - Method in class pipe.dataLayer.ArcPath
CREATING - Static variable in interface pipe.gui.Constants
currentPNMLData() - Static method in class pipe.gui.CreateGui
  returns the current dataLayer object - used to get a reference to pass to the modules
CURVED - Static variable in class pipe.dataLayer.ArcPathPoint

## D

DataLayer - Class in pipe.dataLayer
  DataLayer - Encapsulates entire Petri-Net, also contains functions to perform calculations
DataLayer(String) - Constructor for class pipe.dataLayer.DataLayer
  Create Petri-Net object from PNML file with URI pnmlFileName
DataLayer(File) - Constructor for class pipe.dataLayer.DataLayer
  Create Petri-Net object from pnmlFile
DataLayer() - Constructor for class pipe.dataLayer.DataLayer
  Create empty Petri-Net object
DataLayerWriter - Class in pipe.dataLayer
  Create DataLayerWriter object
DataLayerWriter(DataLayer) - Constructor for class pipe.dataLayer.DataLayerWriter
  Create a writer with the DataLayer object to save
decCount() - Method in class pipe.dataLayer.Token
DEFAULT_ELEMENT_TYPE - Static variable in interface pipe.gui.Constants
delete() - Method in class pipe.dataLayer.Arc
delete() - Method in class pipe.dataLayer.ArcPath
delete() - Method in class pipe.dataLayer.ArcPathPoint
delete() - Method in class pipe.dataLayer.PetriNetObject
delete() - Method in class pipe.dataLayer.PlaceTransitionObject
DELETE - Static variable in interface pipe.gui.Constants
deletePetriNetObject(PetriNetObject) - Method in class pipe.gui.SelectionObject
DeletePetriNetObjectAction - Class in pipe.gui
DeletePetriNetObjectAction(PetriNetObject) - Constructor for class pipe.gui.DeletePetriNetObjectAction
deletePoint(ArcPathPoint) - Method in class pipe.dataLayer.ArcPath
deleteSelection() - Method in class pipe.gui.SelectionObject
DELTA - Variable in class pipe.dataLayer.ArcPathPoint
DELTOKEN - Static variable in interface pipe.gui.Constants
dequeue() - Method in class pipe.dataLayer.calculations.Queue
  dequeue() Removes an object from the FRONT of the queue.
deselect() - Method in class pipe.dataLayer.AnnotationNote
deselect() - Method in class pipe.dataLayer.PetriNetObject
deselectPoint(int) - Method in class pipe.dataLayer.ArcPath
DIAMETER - Static variable in class pipe.dataLayer.Place
DIAMETER - Static variable in class pipe.dataLayer.Token
disableEditMode() - Method in class pipe.dataLayer.AnnotationNote
disableGrid() - Static method in class pipe.gui.Grid
disableGuiMenu() - Method in class pipe.gui.GuiFrame
disableSelection() - Method in class pipe.gui.SelectionObject
disableTransitions() - Method in class pipe.gui.Animator
displayResults() - Method in class pipe.modules.dnamaca.Dnamaca
divideEquals(int) - Method in class pipe.dataLayer.PNMatrix
  Divide a matrix by an int in place, A = s*A
Dnamaca - Class in pipe.modules.dnamaca
Dnamaca() - Constructor for class pipe.modules.dnamaca.Dnamaca
doRandomFiring() - Method in class pipe.gui.Animator
  This method randomly fires one of the enabled transitions.
drag(int, int) - Method in class pipe.dataLayer.AnnotationNote.ResizePoint
DRAG - Static variable in interface pipe.gui.Constants
draggable - Variable in class pipe.dataLayer.PetriNetObject
dragInit - Variable in class pipe.gui.PetriNetObjectHandler
DRAW - Static variable in interface pipe.gui.Constants
drawGrid(Graphics) - Static method in class pipe.gui.Grid

## E

EditAnnotationAction - Class in pipe.gui
EditAnnotationAction(AnnotationNote) - Constructor for class pipe.gui.EditAnnotationAction
EditAnnotationBackgroundAction - Class in pipe.gui
  Action to toggle the background of a note between white and transparent
EditAnnotationBackgroundAction(AnnotationNote) - Constructor for class pipe.gui.EditAnnotationBackgroundAction
EditAnnotationBorderAction - Class in pipe.gui
EditAnnotationBorderAction(AnnotationNote) - Constructor for class pipe.gui.EditAnnotationBorderAction
EditRateAction - Class in pipe.gui
  Action object that can be used to add a rate to a transition.
EditRateAction(Container, Component) - Constructor for class pipe.gui.EditRateAction
EditTimedAction - Class in pipe.gui
  Action object that can be used to alternate a transition between timed and immediate.
EditTimedAction(Transition) - Constructor for class pipe.gui.EditTimedAction
EditTokenAction - Class in pipe.gui
  Action object that can be used to add or remove tokens from a place
EditTokenAction(Container, Place) - Constructor for class pipe.gui.EditTokenAction
EditWeightAction - Class in pipe.gui
  This class allows the user to change the weight on an arc.
EditWeightAction(Container, Arc) - Constructor for class pipe.gui.EditWeightAction
effectiveSetLength(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  find the number of non-zero elements in a set
ELEMENT_FILL_COLOUR - Static variable in interface pipe.gui.Constants
ELEMENT_LINE_COLOUR - Static variable in interface pipe.gui.Constants
eliminateCol(int) - Method in class pipe.dataLayer.PNMatrix
  Eliminate a column from the matrix, column index is toDelete
enabled() - Static method in class pipe.gui.Grid
ENABLED_TRANSITION_COLOUR - Static variable in interface pipe.gui.Constants
enableDrawingActions(boolean) - Method in class pipe.gui.GuiFrame
  Enables either the drawing buttons ("drawing" = true) or the animation buttons ("drawing" = false)
enableEditMode() - Method in class pipe.dataLayer.AnnotationNote
enableGrid() - Static method in class pipe.gui.Grid
enableGuiMenu() - Method in class pipe.gui.GuiFrame
enablePopup - Variable in class pipe.gui.PetriNetObjectHandler
enablePopupMenu(boolean) - Method in class pipe.gui.PetriNetObjectHandler
enableSelection() - Method in class pipe.gui.SelectionObject
EndNodes - Variable in class pipe.dataLayer.calculations.myTree
enqueue(Object) - Method in class pipe.dataLayer.calculations.Queue
  enqueue() Adds an object to the END of the queue.
equals(Marking) - Method in class pipe.dataLayer.calculations.Marking
equals(State) - Method in class pipe.dataLayer.calculations.State
  equals() Overloads the Object.equals() method.
equals(TransitionRecord) - Method in class pipe.io.TransitionRecord
  equals() Overrides the Object.equals method.
execute(DataLayer) - Method in class pipe.gui.ModuleMethod
  Executes the Method that this class represents.
ExponentialDistribution - Class in pipe.modules.iai
  This class is used to calculate exponentially distributed random variables.
ExponentialDistribution(double) - Constructor for class pipe.modules.iai.ExponentialDistribution
Export - Class in pipe.gui
  Class for exporting things to other formats, as well as printing.
Export() - Constructor for class pipe.gui.Export
exportGuiView(GuiView, int) - Static method in class pipe.gui.Export
extendedFreeChoiceNet(DataLayer) - Method in class pipe.modules.classification.Classification
  Extended free choice net detection
extendedSimpleNet(DataLayer) - Method in class pipe.modules.classification.Classification
  Extended simple net (ESPL-net) detection
ExtensionFilter - Class in pipe.gui
ExtensionFilter(String, String) - Constructor for class pipe.gui.ExtensionFilter
ExtFileManager - Class in pipe.gui
ExtFileManager() - Constructor for class pipe.gui.ExtFileManager

## F

FileBrowser - Class in pipe.gui.widgets
FileBrowser(String, String, String) - Constructor for class pipe.gui.widgets.FileBrowser
FileBrowser(String) - Constructor for class pipe.gui.widgets.FileBrowser
FileBrowser() - Constructor for class pipe.gui.widgets.FileBrowser
FindMarkup(myNode) - Method in class pipe.dataLayer.calculations.myNode
findNetInvariants(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Find the net invariants.
findNonMinimal() - Method in class pipe.dataLayer.PNMatrix
  Find a column with non-minimal support.
findPEquations(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Find the P equations of the net.
findRemainingNZCoef(int) - Method in class pipe.dataLayer.PNMatrix
  Find the coefficients corresponding to column indices of all but the first non zero elements of row h.
findRemainingNZIndices(int) - Method in class pipe.dataLayer.PNMatrix
  Find the column indices of all but the first non zero elements of row h.
findVectors(PNMatrix) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Transform a matrix to obtain the minimal generating set of vectors.
finished() - Method in class pipe.modules.dnamaca.SwingWorker
  Called on the event dispatching thread (not on the worker thread) after the `construct` method has returned.
fire(int) - Method in class pipe.dataLayer.calculations.myNode
FIRE - Static variable in interface pipe.gui.Constants
firedTransitions - Static variable in class pipe.gui.Animator
fireRandomTransition() - Method in class pipe.dataLayer.DataLayer
  This method will fire a random transition, and gives precedence to immediate transitions before considering "timed" transitions.
fireRandomTransitionBackwards() - Method in class pipe.dataLayer.DataLayer
fireTransition(Transition) - Method in class pipe.dataLayer.DataLayer
  Fire a specified transition, no affect if transtions not enabled
fireTransition(Transition) - Method in class pipe.gui.Animator
fireTransitionBackwards(Transition) - Method in class pipe.dataLayer.DataLayer
firstNonZeroElementIndex(int) - Method in class pipe.dataLayer.PNMatrix
  Find the column index of the first non zero element of row h.
firstNonZeroRowIndex() - Method in class pipe.dataLayer.PNMatrix
  Find the first non-zero row of a matrix.
Found_An_Omega - Variable in class pipe.dataLayer.calculations.myTree
freeChoiceNet(DataLayer) - Method in class pipe.modules.classification.Classification
  Free choice net detection
fSeq - Variable in class pipe.gui.AnimationHistory
  Holds all the transitions in the sequence

## G

gcd() - Method in class pipe.dataLayer.PNMatrix
  Find the greatest common divisor of a column matrix (vector) of integers.
generate(DataLayer, File) - Static method in class pipe.dataLayer.calculations.StateSpaceGenerator
generate(DataLayer, File, ResultsHTMLPane) - Static method in class pipe.dataLayer.calculations.StateSpaceGenerator
  generate() This static method generates the statespace from a GSPN It uses a hashtable so that it can quickly check whether a state has already been explored.
generateDotFile(File) - Static method in class pipe.modules.reachability.ReachabilityGraphGenerator
  displayResults() Takes the reachability graph file and the steady state distribution and produces nicely formatted output showing these results plus more results based on them.
generateReachabilityGraph(File) - Method in class pipe.modules.reachability.ReachabilityGraphGenerator
get(int) - Method in class pipe.dataLayer.calculations.StateList
get(int, int) - Method in class pipe.dataLayer.PNMatrix
  Get a single element.
get() - Method in class pipe.modules.dnamaca.SwingWorker
  Return the value created by the `construct` method.
getAngle(ArcPathPoint) - Method in class pipe.dataLayer.ArcPathPoint
getAngle(Point2D.Float) - Method in class pipe.dataLayer.ArcPathPoint
getAngle() - Method in class pipe.dataLayer.Transition
getAngle() - Method in class pipe.gui.ArrowHead
getAnimationHistory() - Static method in class pipe.gui.CreateGui
getAnimator() - Static method in class pipe.gui.CreateGui
getApp() - Static method in class pipe.gui.CreateGui
getArc() - Method in class pipe.dataLayer.ArcPath
getArc(String) - Method in class pipe.dataLayer.DataLayer
  Return the Arc called arcName from the Petri-Net
getArcPath() - Method in class pipe.dataLayer.Arc
getArcPath() - Method in class pipe.dataLayer.ArcPathPoint
getArcPathDetails() - Method in class pipe.dataLayer.ArcPath
getArcs() - Method in class pipe.dataLayer.DataLayer
  Get an List of all the Arcs objects in the Petri-Net
getArcSelection() - Method in class pipe.dataLayer.ArcPath
getArray() - Method in class pipe.dataLayer.PNMatrix
  Access the internal two-dimensional array.
getArrayCopy() - Method in class pipe.dataLayer.PNMatrix
  Copy the internal two-dimensional array.
getBackwardsIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Return the Backward Incidence Matrix for the Petri-Net
getBounds() - Method in class pipe.dataLayer.ArcPath
getBounds() - Method in class pipe.dataLayer.Token
  Get boundaries of java.awt.Rectangle
getBounds() - Method in class pipe.gui.ArrowHead
getBounds2D() - Method in class pipe.dataLayer.ArcPath
getBounds2D() - Method in class pipe.gui.ArrowHead
getCentre() - Method in class pipe.dataLayer.PlaceTransitionObject
getClassRoot(Class) - Static method in class pipe.gui.ExtFileManager
getColumnDimension() - Method in class pipe.dataLayer.PNMatrix
  Get column dimension.
getColumnPackedCopy() - Method in class pipe.dataLayer.PNMatrix
  Make a one-dimensional column packed copy of the internal array.
getConnectFromIterator() - Method in class pipe.dataLayer.PlaceTransitionObject
getConnectToIterator() - Method in class pipe.dataLayer.PlaceTransitionObject
getControl1() - Method in class pipe.dataLayer.ArcPathPoint
getControl2() - Method in class pipe.dataLayer.ArcPathPoint
getCount() - Method in class pipe.dataLayer.Token
getCurrentMarking() - Method in class pipe.dataLayer.Place
  Get current marking
getCurrentMarkingObject() - Method in class pipe.dataLayer.Place
  Get current marking
getCurrentMarkupMatrix() - Method in class pipe.dataLayer.DataLayer
  Return the Initial Markup Matrix for the Petri-Net
getDataLayer() - Method in class pipe.gui.widgets.PetriNetChooserPanel
getDelay() - Method in class pipe.dataLayer.Transition
  This is a getter for the delay for this transition.
getDescription() - Method in class pipe.gui.ExtensionFilter
getDiameter() - Method in class pipe.dataLayer.Place
  Returns the diameter of this Place at the current zoom
getDOM(String) - Method in class pipe.dataLayer.PNMLTransformer
  Return a DOM for the PNML file at URI pnmlFileName
getDOM(File) - Method in class pipe.dataLayer.PNMLTransformer
  Return a DOM for the PNML File pnmlFile
getEndAngle() - Method in class pipe.dataLayer.ArcPath
getEndIndex() - Method in class pipe.dataLayer.ArcPath
getEndPositionX() - Method in class pipe.dataLayer.Arc
  Get X-axis value of end position
getEndPositionY() - Method in class pipe.dataLayer.Arc
  Get Y-axis value of end position
getFastTransitionThroughput(DataLayer, StateList, double[]) - Method in class pipe.modules.gspn.GSPNNew
getFile() - Static method in class pipe.gui.CreateGui
getForwardsIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Return the Foward Incidence Matrix for the Petri-Net
getFreeSpace() - Static method in class pipe.gui.CreateGui
getFromState() - Method in class pipe.io.TransitionRecord
getGraph() - Method in class pipe.gui.widgets.GraphPanelPane
getGridSpacing() - Static method in class pipe.gui.Grid
getHashCode2() - Method in class pipe.dataLayer.calculations.CompressedState
getID() - Method in class pipe.dataLayer.AnnotationNote
getId() - Method in class pipe.dataLayer.Arc
  Get id
getID() - Method in class pipe.dataLayer.calculations.CompressedState
getID() - Method in class pipe.dataLayer.calculations.Marking
getID(int) - Method in class pipe.dataLayer.calculations.StateList
getID() - Method in class pipe.dataLayer.NameLabel
getId() - Method in class pipe.dataLayer.PetriNetObject
  Get id returns null if value not yet entered
getId() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get id
getID() - Method in class pipe.io.StateRecord
getIDNum() - Method in class pipe.dataLayer.calculations.Marking
getIDNum(int) - Method in class pipe.dataLayer.calculations.StateList
getIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Return the Incidence Matrix for the Petri-Net
getIndex() - Method in class pipe.dataLayer.ArcPathPoint
GetIndexAction - Class in pipe.gui
GetIndexAction(ArcPathPoint, Point2D.Float) - Constructor for class pipe.gui.GetIndexAction
getInitialMarking() - Method in class pipe.dataLayer.Place
  Get initial marking
getInitialMarkingObject() - Method in class pipe.dataLayer.Place
  Get initial marking
getInitialMarkupMatrix() - Method in class pipe.dataLayer.DataLayer
  Return the Initial Markup Matrix for the Petri-Net
getisTangible() - Method in class pipe.dataLayer.calculations.Marking
getLabels() - Method in class pipe.dataLayer.DataLayer
  Get a List of all the net-level NameLabel objects in the Petri-Net
getMarking() - Method in class pipe.dataLayer.calculations.Marking
getMarkingOffsetX() - Method in class pipe.dataLayer.Place
  Get X-axis offset for initial marking
getMarkingOffsetXObject() - Method in class pipe.dataLayer.Place
  Get X-axis offset for initial marking
getMarkingOffsetY() - Method in class pipe.dataLayer.Place
  Get Y-axis offset for initial marking
getMarkingOffsetYObject() - Method in class pipe.dataLayer.Place
  Get Y-axis offset for initial marking
getMatrix(int, int, int, int) - Method in class pipe.dataLayer.PNMatrix
  Get a submatrix.
getMatrix(int[], int[]) - Method in class pipe.dataLayer.PNMatrix
  Get a submatrix.
getMatrix(int, int, int[]) - Method in class pipe.dataLayer.PNMatrix
  Get a submatrix.
getMatrix(int[], int, int) - Method in class pipe.dataLayer.PNMatrix
  Get a submatrix.
getMidPoint(ArcPathPoint) - Method in class pipe.dataLayer.ArcPathPoint
getModClass() - Method in class pipe.gui.ModuleMethod
getMode() - Method in class pipe.gui.GuiFrame
getModel() - Static method in class pipe.gui.CreateGui
getModel(int) - Static method in class pipe.gui.CreateGui
getModifiedX(double) - Static method in class pipe.gui.Grid
getModifiedY(double) - Static method in class pipe.gui.Grid
getModuleClasses(File) - Method in class pipe.gui.ModuleManager
  Finds all the fully qualified (ie: full package names) module classnames by recursively searching the rootDirectories
getModuleDir() - Method in class pipe.gui.ModuleManager
  Returns the directory under which the module properties files will be found.
getModuleTree() - Method in class pipe.gui.ModuleManager
getName() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get name
getName() - Method in class pipe.modules.classification.Classification
getName() - Method in class pipe.modules.comparison.Comparison
getName() - Method in class pipe.modules.dnamaca.Dnamaca
getName() - Method in class pipe.modules.gspn.GSPNNew
getName() - Method in class pipe.modules.iai.SimulationClockWatcher
getName() - Method in class pipe.modules.iai.SimulationFiringCounter
getName() - Method in class pipe.modules.iai.SimulationPlaceWatcher
getName() - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
getName() - Method in class pipe.modules.matrixes.Matrixes
getName() - Method in interface pipe.modules.Module
getName() - Method in class pipe.modules.reachability.ReachabilityGraphGenerator
getName() - Method in class pipe.modules.simulation.Simulation
getName() - Method in class pipe.modules.stateSpace.StateSpace
getNameLabel() - Method in class pipe.dataLayer.PetriNetObject
  Returns Name Label - is used by GuiView
getNegativeIndices(int) - Method in class pipe.dataLayer.PNMatrix
  For row rowNo of the matrix received return the column indices of all the negative elements
getNote() - Method in class pipe.dataLayer.AnnotationNote
getNoteHeight() - Method in class pipe.dataLayer.AnnotationNote
getNoteText() - Method in class pipe.dataLayer.AnnotationNote
getNoteWidth() - Method in class pipe.dataLayer.AnnotationNote
getNumberSequences() - Method in class pipe.gui.Animator
getNumPoints() - Method in class pipe.dataLayer.ArcPath
getNumStates() - Method in class pipe.io.RGFileHeader
getNumTransitions() - Method in class pipe.io.RGFileHeader
getOffsetToTransitions() - Method in class pipe.io.RGFileHeader
getOriginalX() - Method in class pipe.dataLayer.AnnotationNote
getOriginalY() - Method in class pipe.dataLayer.AnnotationNote
getPath() - Method in class pipe.dataLayer.ArcPath
getPathIterator(AffineTransform) - Method in class pipe.dataLayer.ArcPath
getPathIterator(AffineTransform, double) - Method in class pipe.dataLayer.ArcPath
getPathIterator(AffineTransform) - Method in class pipe.gui.ArrowHead
getPathIterator(AffineTransform, double) - Method in class pipe.gui.ArrowHead
getPathPoint(int) - Method in class pipe.dataLayer.ArcPath
getPercent() - Method in class pipe.gui.ZoomController
getPetriNetObjects() - Method in class pipe.dataLayer.DataLayer
  Returns an iterator of all PetriNetObjects - the order of these cannot be guaranteed.
getPlace(String) - Method in class pipe.dataLayer.DataLayer
  Return the Place called placeName from the Petri-Net
getPlace(int) - Method in class pipe.dataLayer.DataLayer
  Return the Place called placeName from the Petri-Net
getPlaces() - Method in class pipe.dataLayer.DataLayer
  Get an List of all the Place objects in the Petri-Net
getPlacesCount() - Method in class pipe.dataLayer.DataLayer
getPlaceTransitionObject(String) - Method in class pipe.dataLayer.DataLayer
  Return the PlaceTransitionObject called ptoName from the Petri-Net
getPoint(int) - Method in class pipe.dataLayer.ArcPath
getPoint() - Method in class pipe.dataLayer.ArcPathPoint
getPointSelection() - Method in class pipe.dataLayer.ArcPath
getPointType() - Method in class pipe.dataLayer.ArcPathPoint
getPopup(MouseEvent) - Method in class pipe.gui.AnnotationNoteHandler
  Creates the popup menu that the user will see when they right click on a component
getPopup(MouseEvent) - Method in class pipe.gui.ArcHandler
  Creates the popup menu that the user will see when they right click on a component
getPopup(MouseEvent) - Method in class pipe.gui.ArcPathPointHandler
  Creates the popup menu that the user will see when they right click on a component
getPopup(MouseEvent) - Method in class pipe.gui.PetriNetObjectHandler
  Creates the popup menu that the user will see when they right click on a component
getPopup(MouseEvent) - Method in class pipe.gui.PlaceHandler
  Creates the popup menu that the user will see when they right click on a component
getPopup(MouseEvent) - Method in class pipe.gui.PlaceTransitionObjectHandler
getPopup(MouseEvent) - Method in class pipe.gui.TransitionHandler
  Creates the popup menu that the user will see when they right click on a component
getPositionX() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get X-axis position
getPositionXObject() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get X-axis position returns null if value not yet entered
getPositionY() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get Y-axis position
getPositionYObject() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get Y-axis position returns null if value not yet entered
getPositiveIndices(int) - Method in class pipe.dataLayer.PNMatrix
  For row rowNo of the matrix received return the column indices of all the positive elements
getRate() - Method in class pipe.dataLayer.calculations.VanishingState
getRate() - Method in class pipe.dataLayer.Transition
getRate() - Method in class pipe.io.TransitionRecord
getReachabilitySet(DataLayer) - Method in class pipe.modules.gspn.GSPN
  Generate the reachability set using myTree function Add each marking to an arraylist, testing to see if the marking is already present before adding.
getRecordSize() - Method in class pipe.io.TransitionRecord
getRowDimension() - Method in class pipe.dataLayer.PNMatrix
  Get row dimension.
getRowPackedCopy() - Method in class pipe.dataLayer.PNMatrix
  Make a one-dimensional row packed copy of the internal array.
getSelectionCount() - Method in class pipe.gui.SelectionObject
getSelectionObject() - Method in class pipe.gui.GuiView
getShape() - Method in class pipe.dataLayer.Token
  Get shape of object for drawing on screen
getSource() - Method in class pipe.dataLayer.Arc
  Get source returns null if value not yet entered
getStartAngle() - Method in class pipe.dataLayer.ArcPath
getStartPositionX() - Method in class pipe.dataLayer.Arc
  Get X-axis value of start position
getStartPositionY() - Method in class pipe.dataLayer.Arc
  Get Y-axis value of start position
getState() - Method in class pipe.dataLayer.calculations.State
getState() - Method in class pipe.io.StateRecord
getStateArraySize() - Method in class pipe.io.RGFileHeader
getStatusBar() - Method in class pipe.gui.GuiFrame
getTab() - Static method in class pipe.gui.CreateGui
getTangible() - Method in class pipe.io.StateRecord
getTangibleTransitionEnabledStatusArray(DataLayer, int[]) - Method in class pipe.modules.gspn.GSPN
getTarget() - Method in class pipe.dataLayer.Arc
  Get target returns null if value not yet entered
getText() - Method in class pipe.gui.widgets.ResultsHTMLPane
getTimed() - Method in class pipe.dataLayer.Transition
  Get the timed transition attribute (for GSPNs)
getToState() - Method in class pipe.io.TransitionRecord
getTransform() - Method in class pipe.gui.ZoomController
getTransition(String) - Method in class pipe.dataLayer.DataLayer
  Return the Transition called transitionName from the Petri-Net
getTransition(int) - Method in class pipe.dataLayer.DataLayer
  Return the Transition called transitionName from the Petri-Net
getTransitionEnabledStatus(DataLayer, int[], int) - Method in class pipe.modules.gspn.GSPN
  Caluculate whether a transition is enabled given a specific marking
getTransitionEnabledStatusArray(DataLayer, int[]) - Method in class pipe.modules.gspn.GSPN
  Caluculate which transitions are enabled given a specific marking
getTransitionNo() - Method in class pipe.io.TransitionRecord
getTransitionRecordSize() - Method in class pipe.io.RGFileHeader
getTransitions() - Method in class pipe.dataLayer.DataLayer
  Get an List of all the Transition objects in the Petri-Net
getTransitionsCount() - Method in class pipe.dataLayer.DataLayer
getUniqueId() - Method in class pipe.dataLayer.Token
  returns a unique id for an arc of the form to_n
getUnzoomedValue(double) - Method in class pipe.gui.ZoomController
  Calculates the value of the screen distance val at 100% zoom
getURI() - Method in class pipe.dataLayer.DataLayer
  Return a URI for the PNML file for the Petri-Net
getValue() - Method in class pipe.modules.dnamaca.SwingWorker
  Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getView(int) - Static method in class pipe.gui.CreateGui
getView() - Static method in class pipe.gui.CreateGui
getWeight() - Method in class pipe.dataLayer.Arc
  Get weight
getWeightObject() - Method in class pipe.dataLayer.Arc
  Get weight returns null if value not yet entered
getWeightOffsetX() - Method in class pipe.dataLayer.Arc
  Get X-axis offset for weight position
getWeightOffsetXObject() - Method in class pipe.dataLayer.Arc
  Get X-axis offset for weight position returns null if value not yet entered
getWeightOffsetY() - Method in class pipe.dataLayer.Arc
  Get Y-axis offset for weight position
getWeightOffsetYObject() - Method in class pipe.dataLayer.Arc
  Get Y-axis offset for weight position returns null if value not yet entered
getXPosition() - Method in class pipe.dataLayer.NameLabel
getYPosition() - Method in class pipe.dataLayer.NameLabel
getZoomController() - Method in class pipe.dataLayer.PetriNetObject
getZoomController() - Method in class pipe.gui.GuiView
getZoomPositionForXLocation(double) - Method in class pipe.gui.ZoomController
  Calculates where the correct screen x position at the current zoom is for an object with "real" x value locationX.
getZoomPositionForYLocation(double) - Method in class pipe.gui.ZoomController
  Calculates where the correct screen y position at the current zoom is for an object with "real" y value locationY.
GraphFrame - Class in pipe.gui.widgets
GraphFrame() - Constructor for class pipe.gui.widgets.GraphFrame
GraphPanel - Class in pipe.gui.widgets
GraphPanel(ArrayList, ArrayList) - Constructor for class pipe.gui.widgets.GraphPanel
GraphPanel() - Constructor for class pipe.gui.widgets.GraphPanel
GraphPanelPane - Class in pipe.gui.widgets
GraphPanelPane() - Constructor for class pipe.gui.widgets.GraphPanelPane
GRID - Static variable in interface pipe.gui.Constants
Grid - Class in pipe.gui
Grid() - Constructor for class pipe.gui.Grid
GSPN - Class in pipe.modules.gspn
GSPN() - Constructor for class pipe.modules.gspn.GSPN
GSPNNew - Class in pipe.modules.gspn
GSPNNew() - Constructor for class pipe.modules.gspn.GSPNNew
GuiAction - Class in pipe.gui
  GuiAction class
GuiFrame - Class in pipe.gui
GuiFrame(String) - Constructor for class pipe.gui.GuiFrame
GuiView - Class in pipe.gui
  The petrinet is drawn onto this frame.
GuiView() - Constructor for class pipe.gui.GuiView

## H

hashCode() - Method in class pipe.dataLayer.calculations.State
  hashCode() This overrides the Object.hashCode() method.
hashCode2() - Method in class pipe.dataLayer.calculations.State
  hashCode2() This is an extra hashing function used for collision resolution.
hasImmediateTransitions(DataLayer) - Method in class pipe.modules.gspn.GSPN
  See if the supplied net has any timed transitions.
hasNegativeElements() - Method in class pipe.dataLayer.PNMatrix
  Find if a column vector has negative elements.
hasTimedTransitions(DataLayer) - Method in class pipe.modules.gspn.GSPN
  See if the supplied net has any timed transitions.
HelpBox - Class in pipe.gui
HelpBox(String, String, String, String) - Constructor for class pipe.gui.HelpBox
hidePoints() - Method in class pipe.dataLayer.ArcPath
highlighted - Variable in class pipe.dataLayer.Transition
highlightEnabledTransitions() - Method in class pipe.gui.Animator
hyperlinkUpdate(HyperlinkEvent) - Method in class pipe.gui.HelpBox
hyperlinkUpdate(HyperlinkEvent) - Method in class pipe.gui.widgets.ResultsHTMLPane

## I

id - Variable in class pipe.dataLayer.PetriNetObject
  Id
identity(int, int) - Static method in class pipe.dataLayer.PNMatrix
  Generate identity matrix]
ignoreSelection - Static variable in class pipe.dataLayer.PetriNetObject
ignoreSelection(boolean) - Static method in class pipe.dataLayer.PetriNetObject
imgPath - Static variable in class pipe.gui.CreateGui
ImmediateAbortException - Exception in pipe.io
ImmediateAbortException() - Constructor for exception pipe.io.ImmediateAbortException
ImmediateAbortException(String) - Constructor for exception pipe.io.ImmediateAbortException
IMMTRANS - Static variable in interface pipe.gui.Constants
importExternalModule(File) - Static method in class pipe.gui.ModuleLoader
importModule(File) - Static method in class pipe.gui.ModuleLoader
incCount() - Method in class pipe.dataLayer.Token
  Methods used to manipulate the transition count
IncorrectFileFormatException - Exception in pipe.io
IncorrectFileFormatException(String) - Constructor for exception pipe.io.IncorrectFileFormatException
increment() - Static method in class pipe.gui.Grid
init() - Static method in class pipe.gui.CreateGui
InsertOmegas() - Method in class pipe.dataLayer.calculations.myNode
insertPoint(int, ArcPathPoint) - Method in class pipe.dataLayer.ArcPath
  insertPoint() Inserts a new point into the Array List of path points at the specified index and shifts all the following points along
interrupt() - Method in class pipe.modules.dnamaca.SwingWorker
  A new method that interrupts the worker thread.
intersectionBetweenSets(int[], int[]) - Method in class pipe.modules.classification.Classification
intersects(double, double, double, double) - Method in class pipe.dataLayer.ArcPath
intersects(Rectangle2D) - Method in class pipe.dataLayer.ArcPath
intersects(double, double, double, double) - Method in class pipe.gui.ArrowHead
intersects(Rectangle2D) - Method in class pipe.gui.ArrowHead
InvariantAnalysis - Class in pipe.modules.invariantAnalysis
InvariantAnalysis() - Constructor for class pipe.modules.invariantAnalysis.InvariantAnalysis
inverse(double) - Method in class pipe.modules.iai.ExponentialDistribution
isCovered() - Method in class pipe.dataLayer.PNMatrix
  Find if a matrix of invariants is covered.
isDelayValid() - Method in class pipe.dataLayer.Transition
  This method is a getter for the boolean indicating if the delay is valid or not.
isDeleteable() - Method in class pipe.dataLayer.ArcPathPoint
isDraggable() - Method in class pipe.dataLayer.PetriNetObject
isDragging - Variable in class pipe.gui.PetriNetObjectHandler
isEmpty() - Method in class pipe.dataLayer.calculations.Queue
isEmpty() - Method in class pipe.dataLayer.calculations.StateList
isEmptySet(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  check if an array is empty (only zeros)
isEnabled(boolean) - Method in class pipe.dataLayer.Transition
  Determines whether Transition is enabled
isEnabled() - Method in class pipe.dataLayer.Transition
  Determines whether Transition is enabled
isEnabledBackwards() - Method in class pipe.dataLayer.Transition
  Determines whether Transition is enabled backwards
isFilled() - Method in class pipe.dataLayer.AnnotationNote
isModule(Class) - Static method in class pipe.gui.ModuleLoader
isPointSelected(int) - Method in class pipe.dataLayer.ArcPath
isSelectable() - Method in class pipe.dataLayer.PetriNetObject
isSelected() - Method in class pipe.dataLayer.PetriNetObject
isSelected() - Method in class pipe.gui.GuiAction
isShowingBorder() - Method in class pipe.dataLayer.AnnotationNote
isStepBackOK() - Method in class pipe.gui.AnimationHistory
isStepForwardOK() - Method in class pipe.gui.AnimationHistory
isTangible - Static variable in class pipe.dataLayer.calculations.Marking
isTangibleState(DataLayer, int[]) - Method in class pipe.modules.gspn.GSPN
  Work out if a specified marking describes a tangible state.
isZeroMatrix() - Method in class pipe.dataLayer.PNMatrix
  Check if a matrix is all zeros.
isZeroRow(int) - Method in class pipe.dataLayer.PNMatrix
  isZeroRow returns true if the ith row is all zeros

## J

justSelected - Static variable in class pipe.gui.PetriNetObjectHandler

## K

keyPressed(KeyEvent) - Method in class pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler
keyPressed(KeyEvent) - Method in class pipe.gui.ArcKeyboardEventHandler
keyReleased(KeyEvent) - Method in class pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler
keyReleased(KeyEvent) - Method in class pipe.gui.ArcKeyboardEventHandler
keyTyped(KeyEvent) - Method in class pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler
keyTyped(KeyEvent) - Method in class pipe.gui.ArcKeyboardEventHandler
kill() - Method in class pipe.dataLayer.ArcPathPoint

## L

LabelAction - Class in pipe.gui
  Action object that can be used to effect labelling a component.
LabelAction(Container, Component) - Constructor for class pipe.gui.LabelAction
LEFT - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
leftOffset() - Method in class pipe.dataLayer.Transition
  Returns the distance between the outside of the component to the centre, in order to position the centre of the place where the mouse clicks on the screen
leftPane - Static variable in class pipe.gui.CreateGui
  The Module will go in the top pane, the animation window in the bottom pane
linearlyCombine(int, int, int[], int[]) - Method in class pipe.dataLayer.PNMatrix
  Add a linear combination of column k to columns in array j[].
linearlyCombine(int, int[], int[], int[]) - Method in class pipe.dataLayer.PNMatrix
  Add a linear combination of column k to columns in array j[].
loadExtClass(String) - Static method in class pipe.gui.ExtFileManager
loadExtClass(File) - Static method in class pipe.gui.ExtFileManager
loadExtClass(URL) - Static method in class pipe.gui.ExtFileManager
LOWEST_LAYER_OFFSET - Static variable in interface pipe.gui.Constants

## M

makeTable(Object[], int, boolean, boolean, boolean, boolean) - Static method in class pipe.gui.widgets.ResultsHTMLPane
markedGraph(DataLayer) - Method in class pipe.modules.classification.Classification
  Marked graph detection
Marking - Class in pipe.dataLayer.calculations
Marking(State, int) - Constructor for class pipe.dataLayer.calculations.Marking
Marking(State, int, boolean) - Constructor for class pipe.dataLayer.calculations.Marking
Marking(int[], int) - Constructor for class pipe.dataLayer.calculations.Marking
Marking(int[], String) - Constructor for class pipe.dataLayer.calculations.Marking
MarkupCompare(int[]) - Method in class pipe.dataLayer.calculations.myNode
matrixChanged - Variable in class pipe.dataLayer.PNMatrix
  Used to determine whether the matrixes have been modified
Matrixes - Class in pipe.modules.matrixes
Matrixes() - Constructor for class pipe.modules.matrixes.Matrixes
minus(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  C = A - B
minusEquals(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  A = A - B
modify(double, double, double, double) - Method in class pipe.dataLayer.Token
  Modifies start and end X and Y coords - does nothing.
Module - Interface in pipe.modules
ModuleClassContainer - Class in pipe.gui
  ModuleClass encapsulates information about the Module class and is designed to be used as a userobject in nodes in a JTree, in this case for nodes representing module classes.
ModuleClassContainer(Class) - Constructor for class pipe.gui.ModuleClassContainer
  Sets up the private fields, includes instantiating an object and calling the getName method used to set the displayName.
ModuleLoader - Class in pipe.gui
ModuleLoader() - Constructor for class pipe.gui.ModuleLoader
ModuleManager - Class in pipe.gui
  The ModuleManager class contains methods to create swing components to allow the user to load modules and execute methods within them.
ModuleManager() - Constructor for class pipe.gui.ModuleManager
ModuleManager.TreeHandler - Class in pipe.gui
ModuleManager.TreeHandler() - Constructor for class pipe.gui.ModuleManager.TreeHandler
ModuleMethod - Class in pipe.gui
  ModuleMethod encapsulates information about a module method and is designed to be used as a userobject in nodes in a JTree.
ModuleMethod(Class, Method) - Constructor for class pipe.gui.ModuleMethod
more_Than_One_Token - Variable in class pipe.dataLayer.calculations.myTree
mouseClicked(MouseEvent) - Method in class pipe.gui.AnimationHandler
mouseClicked(MouseEvent) - Method in class pipe.gui.AnnotationNoteHandler
mouseClicked(MouseEvent) - Method in class pipe.gui.ModuleManager.TreeHandler
mouseClicked(MouseEvent) - Method in class pipe.gui.PlaceHandler
mouseClicked(MouseEvent) - Method in class pipe.gui.SelectionObject
mouseDragged(MouseEvent) - Method in class pipe.dataLayer.AnnotationNote.ResizePointHandler
mouseDragged(MouseEvent) - Method in class pipe.gui.AnnotationNoteHandler
mouseDragged(MouseEvent) - Method in class pipe.gui.ArcHandler
mouseDragged(MouseEvent) - Method in class pipe.gui.ArcPathPointHandler
mouseDragged(MouseEvent) - Method in class pipe.gui.PetriNetObjectHandler
  Handler for dragging PlaceTransitionObjects around
mouseDragged(MouseEvent) - Method in class pipe.gui.SelectionObject
mouseEntered(MouseEvent) - Method in class pipe.gui.SelectionObject
mouseExited(MouseEvent) - Method in class pipe.gui.SelectionObject
mouseMoved(MouseEvent) - Method in class pipe.gui.SelectionObject
mousePressed(MouseEvent) - Method in class pipe.dataLayer.AnnotationNote.ResizePointHandler
mousePressed(MouseEvent) - Method in class pipe.gui.AnnotationNoteHandler
mousePressed(MouseEvent) - Method in class pipe.gui.ArcHandler
mousePressed(MouseEvent) - Method in class pipe.gui.ArcPathPointHandler
mousePressed(MouseEvent) - Method in class pipe.gui.ModuleManager.TreeHandler
mousePressed(MouseEvent) - Method in class pipe.gui.PetriNetObjectHandler
mousePressed(MouseEvent) - Method in class pipe.gui.PlaceTransitionObjectHandler
mousePressed(MouseEvent) - Method in class pipe.gui.SelectionObject
mouseReleased(MouseEvent) - Method in class pipe.dataLayer.AnnotationNote.ResizePointHandler
mouseReleased(MouseEvent) - Method in class pipe.gui.AnnotationNoteHandler
mouseReleased(MouseEvent) - Method in class pipe.gui.ArcPathPointHandler
mouseReleased(MouseEvent) - Method in class pipe.gui.ModuleManager.TreeHandler
mouseReleased(MouseEvent) - Method in class pipe.gui.PetriNetObjectHandler
  Event handler for when the user releases the mouse, used in conjunction with mouseDragged and mouseReleased to implement the moving action
mouseReleased(MouseEvent) - Method in class pipe.gui.SelectionObject
myExtensionDesc - Variable in class pipe.gui.ExtensionFilter
myExtensionString - Variable in class pipe.gui.ExtensionFilter
myNode - Class in pipe.dataLayer.calculations
myNode(int[], myTree, int) - Constructor for class pipe.dataLayer.calculations.myNode
myNode(int[], myNode, myTree, int) - Constructor for class pipe.dataLayer.calculations.myNode
myObject - Variable in class pipe.gui.PetriNetObjectHandler
myTree - Class in pipe.dataLayer.calculations
myTree(int[], PNMatrix, PNMatrix) - Constructor for class pipe.dataLayer.calculations.myTree
myTree(int[], PNMatrix, PNMatrix, StateList, DataLayer) - Constructor for class pipe.dataLayer.calculations.myTree

## N

NameLabel - Class in pipe.dataLayer
  NameLabel - This class is for the labels of PN Objects
NameLabel() - Constructor for class pipe.dataLayer.NameLabel
NameLabel(String) - Constructor for class pipe.dataLayer.NameLabel
NameLabel(double, double, String, String) - Constructor for class pipe.dataLayer.NameLabel
netChanged - Variable in class pipe.gui.GuiView
no_Enabled_Transitions - Variable in class pipe.dataLayer.calculations.myTree
nodeCount - Variable in class pipe.dataLayer.calculations.myTree
nodes - Variable in class pipe.dataLayer.calculations.myTree
nonZeroIndices() - Method in class pipe.dataLayer.PNMatrix
  Form a matrix with columns the row indices of non-zero elements.
NOTE_DISABLED_COLOUR - Static variable in interface pipe.gui.Constants
NOTE_EDITING_COLOUR - Static variable in interface pipe.gui.Constants
nullModel(int) - Static method in class pipe.gui.CreateGui
nullView(int) - Static method in class pipe.gui.CreateGui
number_places - Variable in class pipe.dataLayer.calculations.myTree
number_transitions - Variable in class pipe.dataLayer.calculations.myTree

## O

objectColour - Variable in class pipe.dataLayer.PetriNetObject
onSimulate() - Method in class pipe.modules.iai.SimulationClockWatcher
onSimulate() - Method in class pipe.modules.iai.SimulationPlaceWatcher
openFile() - Method in class pipe.gui.widgets.FileBrowser
output(int) - Method in class pipe.dataLayer.calculations.StateList

## P

paintComponent(Graphics) - Method in class pipe.dataLayer.AnnotationNote
paintComponent(Graphics) - Method in class pipe.dataLayer.AnnotationNote.ResizePoint
paintComponent(Graphics) - Method in class pipe.dataLayer.Arc
  Get Y-axis offset for inscription position returns null if value not yet entered
paintComponent(Graphics) - Method in class pipe.dataLayer.ArcPathPoint
paintComponent(Graphics) - Method in class pipe.dataLayer.PetriNetObject
paintComponent(Graphics) - Method in class pipe.dataLayer.Place
  Paints the Place component taking into account the number of tokens from the currentMarking
paintComponent(Graphics) - Method in class pipe.dataLayer.PlaceTransitionObject
paintComponent(Graphics) - Method in class pipe.dataLayer.Transition
paintComponent(Graphics) - Method in class pipe.gui.GuiView
  This method is called whenever the frame is moved, resized etc.
paintComponent(Graphics) - Method in class pipe.gui.SelectionObject
paintComponent(Graphics) - Method in class pipe.gui.widgets.GraphPanel
pathToDeadlock - Variable in class pipe.dataLayer.calculations.myTree
PetriNetChooserPanel - Class in pipe.gui.widgets
  Makes a filebrowser panel which is a JPanel containing the required stuff
PetriNetChooserPanel(String, DataLayer) - Constructor for class pipe.gui.widgets.PetriNetChooserPanel
PetriNetObject - Class in pipe.dataLayer
  PetriNetObject - Petri-Net Object Class - Abstract
PetriNetObject(String) - Constructor for class pipe.dataLayer.PetriNetObject
  Create PetriNetObject
PetriNetObject() - Constructor for class pipe.dataLayer.PetriNetObject
  Create default PetriNetObject
PetriNetObjectHandler - Class in pipe.gui
  Class used to implement methods corresponding to mouse events on all PetriNetObjects.
PetriNetObjectHandler(Container, PetriNetObject) - Constructor for class pipe.gui.PetriNetObjectHandler
pipe.dataLayer - package pipe.dataLayer
pipe.dataLayer.calculations - package pipe.dataLayer.calculations
pipe.gui - package pipe.gui
pipe.gui.widgets - package pipe.gui.widgets
pipe.io - package pipe.io
pipe.modules - package pipe.modules
pipe.modules.classification - package pipe.modules.classification
pipe.modules.comparison - package pipe.modules.comparison
pipe.modules.dnamaca - package pipe.modules.dnamaca
pipe.modules.gspn - package pipe.modules.gspn
pipe.modules.iai - package pipe.modules.iai
pipe.modules.invariantAnalysis - package pipe.modules.invariantAnalysis
pipe.modules.matrixes - package pipe.modules.matrixes
pipe.modules.reachability - package pipe.modules.reachability
pipe.modules.simulation - package pipe.modules.simulation
pipe.modules.stateSpace - package pipe.modules.stateSpace
Place - Class in pipe.dataLayer
  Place - Petri-Net Place Class
Place(double, double, String, String, double, double, int, double, double) - Constructor for class pipe.dataLayer.Place
  Create Petri-Net Place object
Place(double, double, String) - Constructor for class pipe.dataLayer.Place
  Create Petri-Net Place object
Place(double, double) - Constructor for class pipe.dataLayer.Place
  Create Petri-Net Place object
Place() - Constructor for class pipe.dataLayer.Place
  Create empty Petri-Net Place object
PLACE - Static variable in interface pipe.gui.Constants
PLACE_TRANSITION_HEIGHT - Static variable in interface pipe.gui.Constants
PLACE_TRANSITION_LAYER_OFFSET - Static variable in interface pipe.gui.Constants
PLACE_TRANSITION_PROXIMITY_RADIUS - Static variable in interface pipe.gui.Constants
PlaceHandler - Class in pipe.gui
  Class used to implement methods corresponding to mouse events on places.
PlaceHandler(Container, Place) - Constructor for class pipe.gui.PlaceHandler
PlaceTransitionObject - Class in pipe.dataLayer
  PlaceTransitionObject - Petri-Net PLace or Transition SuperClass - Abstract
PlaceTransitionObject(double, double, String, String, double, double) - Constructor for class pipe.dataLayer.PlaceTransitionObject
  Create Petri-Net Object
PlaceTransitionObject(double, double, String) - Constructor for class pipe.dataLayer.PlaceTransitionObject
  Create Petri-Net Object
PlaceTransitionObject(double, double) - Constructor for class pipe.dataLayer.PlaceTransitionObject
  Create Petri-Net Object This constructor does all the work, the others just call it.
PlaceTransitionObject() - Constructor for class pipe.dataLayer.PlaceTransitionObject
  Create empty Petri-Net Object
PlaceTransitionObjectHandler - Class in pipe.gui
  Class used to implement methods corresponding to mouse events on places.
PlaceTransitionObjectHandler(Container, PlaceTransitionObject) - Constructor for class pipe.gui.PlaceTransitionObjectHandler
plus(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  C = A + B
plusEquals(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  A = A + B
PNG - Static variable in class pipe.gui.Export
PNMatrix - Class in pipe.dataLayer
PNMatrix(int, int) - Constructor for class pipe.dataLayer.PNMatrix
  Construct an m-by-n matrix of zeros.
PNMatrix(int, int, int) - Constructor for class pipe.dataLayer.PNMatrix
  Construct an m-by-n constant matrix.
PNMatrix(int[][]) - Constructor for class pipe.dataLayer.PNMatrix
  Construct a matrix from a 2-D array.
PNMatrix(int[][], int, int) - Constructor for class pipe.dataLayer.PNMatrix
  Construct a matrix quickly without checking arguments.
PNMatrix(int[], int) - Constructor for class pipe.dataLayer.PNMatrix
  Construct a matrix from a one-dimensional packed array
pnmlName - Static variable in class pipe.dataLayer.DataLayer
  PNML File Name
PNMLTransformer - Class in pipe.dataLayer
  Create pnmlTransformer object, which deals with getting information from the XML file, then passes this back to DataLayer constructor for construction
PNMLTransformer() - Constructor for class pipe.dataLayer.PNMLTransformer
  Create a Transformer
pnName - Variable in class pipe.dataLayer.PetriNetObject
  Name Label for displaying name
positionX - Variable in class pipe.dataLayer.NameLabel
positionX - Variable in class pipe.dataLayer.PlaceTransitionObject
  X-axis Position on screen
positionY - Variable in class pipe.dataLayer.NameLabel
positionY - Variable in class pipe.dataLayer.PlaceTransitionObject
  Y-axis Position on screen
POSTSCRIPT - Static variable in class pipe.gui.Export
print(boolean[]) - Method in class pipe.dataLayer.calculations.myNode
print() - Method in class pipe.dataLayer.calculations.StateList
print(int[]) - Method in class pipe.dataLayer.calculations.StateList
print() - Method in class pipe.dataLayer.DataLayer
  prints out a brief representation of the dataLayer object
print(int, int) - Method in class pipe.dataLayer.PNMatrix
  Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class pipe.dataLayer.PNMatrix
  Print the matrix to the output stream.
print(NumberFormat, int) - Method in class pipe.dataLayer.PNMatrix
  Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class pipe.dataLayer.PNMatrix
  Print the matrix to the output stream.
print(Graphics, PageFormat, int) - Method in class pipe.gui.GuiView
printArray(int[]) - Method in class pipe.dataLayer.PNMatrix
  Used to display intermediate results for checking
PRINTER - Static variable in class pipe.gui.Export
printString(int, int) - Method in class pipe.dataLayer.PNMatrix
  Print the matrix to a string.
processSelection(MouseEvent) - Method in class pipe.gui.SelectionObject
PROPERTY_FILE_DESC - Static variable in interface pipe.gui.Constants
PROPERTY_FILE_EXTENSION - Static variable in interface pipe.gui.Constants
proximityContains(Point2D) - Method in class pipe.dataLayer.ArcPath
proximityIntersects(Rectangle2D) - Method in class pipe.dataLayer.ArcPath
purgePathPoints() - Method in class pipe.dataLayer.ArcPath

## Q

Queue - Class in pipe.dataLayer.calculations
Queue() - Constructor for class pipe.dataLayer.calculations.Queue
QueueRecord - Class in pipe.modules.iai
  This is a placeholder for a class to be added as part of the support of exponential distributions.
QueueRecord() - Constructor for class pipe.modules.iai.QueueRecord

## R

RANDOM - Static variable in interface pipe.gui.Constants
ReachabilityGraphGenerator - Class in pipe.modules.reachability
ReachabilityGraphGenerator() - Constructor for class pipe.modules.reachability.ReachabilityGraphGenerator
read(RandomAccessFile) - Method in class pipe.io.RGFileHeader
read(int, RandomAccessFile) - Method in class pipe.io.StateRecord
read(RandomAccessFile) - Method in class pipe.io.TransitionRecord
  read() Reads a TransitionRecord from the specified input file.
read1(int, RandomAccessFile) - Method in class pipe.io.StateRecord
read1(RandomAccessFile) - Method in class pipe.io.TransitionRecord
RecordDeadlockPath() - Method in class pipe.dataLayer.calculations.myNode
RecursiveExpansion() - Method in class pipe.dataLayer.calculations.myNode
RecursiveExpansion(StateList, boolean[]) - Method in class pipe.dataLayer.calculations.myNode
  This function recursively generates potential state spaces from existing state spaces (as per algorithm written by James Bloom & Clare Clark for PIPE 2003) and adds new state spaces to the StateList array supplied as a parameter.
reduction(Matrix) - Method in class pipe.modules.gspn.GSPN
  This function performs a Gaussian reduction on a given Matrix, returning an array of values representing the solution.
removeAnimationHistory() - Static method in class pipe.gui.CreateGui
removeArcCompareObject(Arc) - Method in class pipe.dataLayer.Transition
removeFromArc(Arc) - Method in class pipe.dataLayer.PlaceTransitionObject
removeFromContainer() - Method in class pipe.dataLayer.PetriNetObject
removeModuleFromTree(DefaultMutableTreeNode) - Method in class pipe.gui.ModuleManager
  Removes a node from the Module subtree
removePetriNetObject(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Removes the specified object from the appropriate ArrayList of objects.
removeTab(int) - Static method in class pipe.gui.CreateGui
removeToArc(Arc) - Method in class pipe.dataLayer.PlaceTransitionObject
renderAverages(DataLayer, double[]) - Method in class pipe.modules.gspn.GSPNNew
  renderAverages() Turns the array containing the average number of tokens on a place into a table in the form of a long string with embedded HTML ready for display.
renderLists(double[], StateList) - Method in class pipe.modules.gspn.GSPN
renderLists(double[], Place[], String[]) - Method in class pipe.modules.gspn.GSPN
renderProbabilities(double[][], StateList, StateList) - Method in class pipe.modules.gspn.GSPN
renderProbabilityDensity(Place[], double[][]) - Method in class pipe.modules.gspn.GSPNNew
renderStateSpace(DataLayer, StateList) - Method in class pipe.modules.gspn.GSPN
renderStateSpaceLinked(DataLayer, StateList) - Method in class pipe.modules.gspn.GSPN
renderThroughput(DataLayer, double[]) - Method in class pipe.modules.gspn.GSPN
reportPInvariants(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Reports on the P invariants.
reportTInvariants(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Reports on the T invariants.
RESERVED_BORDER - Static variable in interface pipe.gui.Constants
resetArray(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
resetEnabledTransitions() - Method in class pipe.dataLayer.DataLayer
RESIZE_POINT_DOWN_COLOUR - Static variable in interface pipe.gui.Constants
restoreMode() - Method in class pipe.gui.GuiFrame
restoreModel() - Method in class pipe.gui.Animator
restoreState() - Method in class pipe.dataLayer.DataLayer
  Restores To previous Stored Markup
results - Variable in class pipe.modules.gspn.GSPN
ResultsHTMLPane - Class in pipe.gui.widgets
  This class is used by the analysis modules to display the results of their analysis as HTML.
ResultsHTMLPane() - Constructor for class pipe.gui.widgets.ResultsHTMLPane
ResultsHTMLPane(String) - Constructor for class pipe.gui.widgets.ResultsHTMLPane
returnClass() - Method in class pipe.gui.ModuleClassContainer
  Returns the class object that the ModuleClass encapsulates
returnTransitions() - Method in class pipe.dataLayer.DataLayer
RGFileHeader - Class in pipe.io
RGFileHeader(int, int, int, int, long) - Constructor for class pipe.io.RGFileHeader
  Sets up a Reachability Graph File Header Object ready for writing.
RGFileHeader(RandomAccessFile) - Constructor for class pipe.io.RGFileHeader
RGFileHeader() - Constructor for class pipe.io.RGFileHeader
  Sets up a blank Reachability Graph File Header Object
RIGHT - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
root - Variable in class pipe.dataLayer.calculations.myTree
rotate(int) - Method in class pipe.dataLayer.Transition
  Rotates the Transition through the specified angle around the midpoint
RotateTransitionAction - Class in pipe.gui
RotateTransitionAction(Container, Transition, int, String) - Constructor for class pipe.gui.RotateTransitionAction
rowWithNegativeElement() - Method in class pipe.dataLayer.PNMatrix
  Find the first row with a negative element in a matrix.
run(DataLayer) - Method in class pipe.modules.classification.Classification
run(DataLayer) - Method in class pipe.modules.comparison.Comparison
run(DataLayer) - Method in class pipe.modules.dnamaca.Dnamaca
run(DataLayer) - Method in class pipe.modules.gspn.GSPNNew
run(DataLayer) - Method in class pipe.modules.iai.SimulationClockWatcher
run(DataLayer) - Method in class pipe.modules.iai.SimulationFiringCounter
run(DataLayer) - Method in class pipe.modules.iai.SimulationPlaceWatcher
run(DataLayer) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Call the methods that find the net invariants.
run(DataLayer) - Method in class pipe.modules.matrixes.Matrixes
run(DataLayer) - Method in interface pipe.modules.Module
run(DataLayer) - Method in class pipe.modules.reachability.ReachabilityGraphGenerator
run(DataLayer) - Method in class pipe.modules.simulation.Simulation
run(DataLayer) - Method in class pipe.modules.stateSpace.StateSpace

## S

saveFile() - Method in class pipe.gui.widgets.FileBrowser
savePNML(File) - Method in class pipe.dataLayer.DataLayerWriter
  Save the Petri-Net
scroller - Static variable in class pipe.gui.CreateGui
select() - Method in class pipe.dataLayer.PetriNetObject
select() - Method in class pipe.dataLayer.PlaceTransitionObject
  Handles selection for Place/Transitions
SELECT - Static variable in interface pipe.gui.Constants
selectable - Variable in class pipe.dataLayer.PetriNetObject
selected - Variable in class pipe.dataLayer.PetriNetObject
SELECTION_FILL_COLOUR - Static variable in interface pipe.gui.Constants
SELECTION_LAYER_OFFSET - Static variable in interface pipe.gui.Constants
SELECTION_LINE_COLOUR - Static variable in interface pipe.gui.Constants
selectionBorderColour - Variable in class pipe.dataLayer.PetriNetObject
SelectionObject - Class in pipe.gui
SelectionObject(GuiView) - Constructor for class pipe.gui.SelectionObject
SelectionObject() - Constructor for class pipe.gui.SelectionObject
selectPoint(int) - Method in class pipe.dataLayer.ArcPath
set(int, int, int) - Method in class pipe.dataLayer.PNMatrix
  Set a single element.
setCentre(double, double) - Method in class pipe.dataLayer.PlaceTransitionObject
  Sets the center of the component to position x, y
setControl1(float, float) - Method in class pipe.dataLayer.ArcPathPoint
setControl1(Point2D.Float) - Method in class pipe.dataLayer.ArcPathPoint
setControl2(float, float) - Method in class pipe.dataLayer.ArcPathPoint
setControl2(Point2D.Float) - Method in class pipe.dataLayer.ArcPathPoint
setCurrentMarking(int) - Method in class pipe.dataLayer.Place
  Set current marking
setDelay(double) - Method in class pipe.dataLayer.Transition
  This is a setter for the delay for this transition.
setDelayValid(boolean) - Method in class pipe.dataLayer.Transition
  This method is used to set a flag to indicate that the delay is valid or invalid.
setDraggable(boolean) - Method in class pipe.dataLayer.PetriNetObject
setEnabled(boolean) - Method in class pipe.dataLayer.Transition
  Sets whether Transition is enabled
setEnabledBackwards(boolean) - Method in class pipe.dataLayer.Transition
  Sets whether Transition is enabled
setEnabledFalse() - Method in class pipe.dataLayer.Transition
setEnabledTransitions() - Method in class pipe.dataLayer.DataLayer
  Determines whether all transitions are enabled and sets the correct value of the enabled boolean
setEndPoint(double, double, boolean) - Method in class pipe.dataLayer.Arc
setFile(File, int) - Static method in class pipe.gui.CreateGui
setFinalPointType(boolean) - Method in class pipe.dataLayer.ArcPath
setGridSpacing(double) - Static method in class pipe.gui.Grid
setID(String) - Method in class pipe.dataLayer.AnnotationNote
setId(String) - Method in class pipe.dataLayer.Arc
  Set id
setID(String) - Method in class pipe.dataLayer.NameLabel
setId(String) - Method in class pipe.dataLayer.PetriNetObject
  Set id
setId(String) - Method in class pipe.dataLayer.PlaceTransitionObject
  Set id
setInitialMarking(int) - Method in class pipe.dataLayer.Place
  Set initial marking
setLocation(double, double) - Method in class pipe.dataLayer.AnnotationNote.ResizePoint
setLocation(double, double, double) - Method in class pipe.gui.ArrowHead
setLocation(Point2D.Double, Point2D.Double) - Method in class pipe.gui.ArrowHead
setLocation(double, double, double, double) - Method in class pipe.gui.ArrowHead
setmarkingOffsetX(double) - Method in class pipe.dataLayer.Place
  Set X-axis offset for initial marking
setmarkingOffsetY(double) - Method in class pipe.dataLayer.Place
  Set Y-axis offset for initial marking
setMatrix(int, int, int, int, PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Set a submatrix.
setMatrix(int[], int[], PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Set a submatrix.
setMatrix(int[], int, int, PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Set a submatrix.
setMatrix(int, int, int[], PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Set a submatrix.
setMode(int) - Method in class pipe.gui.GuiFrame
setName(String) - Method in class pipe.dataLayer.PlaceTransitionObject
  Set name
setName(String) - Method in class pipe.gui.ModuleMethod
setNumberSequences(int) - Method in class pipe.gui.Animator
setObjectColour(Color) - Method in class pipe.dataLayer.PetriNetObject
setObjects() - Method in class pipe.gui.GuiFrame
setObjects(int) - Method in class pipe.gui.GuiFrame
setObjectsNull(int) - Method in class pipe.gui.GuiFrame
setOriginalX(int) - Method in class pipe.gui.ViewExpansionComponent
setOriginalY(int) - Method in class pipe.gui.ViewExpansionComponent
setPage(String) - Method in class pipe.gui.HelpBox
  Sets the page to the given non-absolute filename assumed to be in the Docs directory
setPathToTransitionAngle(int) - Method in class pipe.dataLayer.Arc
setPercent(int) - Method in class pipe.gui.ZoomController
setPointLocation(int, double, double) - Method in class pipe.dataLayer.ArcPath
setPointLocation(int, Point2D.Double) - Method in class pipe.dataLayer.ArcPath
setPointLocation(float, float) - Method in class pipe.dataLayer.ArcPathPoint
setPointType(int, boolean) - Method in class pipe.dataLayer.ArcPath
setPointType(boolean) - Method in class pipe.dataLayer.ArcPathPoint
setPointVisibilityLock(boolean) - Method in class pipe.dataLayer.ArcPath
setPosition(int, int) - Method in class pipe.dataLayer.NameLabel
setPositionX(double) - Method in class pipe.dataLayer.PlaceTransitionObject
  Set X-axis position
setPositionY(double) - Method in class pipe.dataLayer.PlaceTransitionObject
  Set Y-axis position
setRandomAnimationMode(boolean) - Method in class pipe.gui.GuiFrame
setRate(double) - Method in class pipe.dataLayer.calculations.VanishingState
setRate(double) - Method in class pipe.dataLayer.Transition
setSelectable(boolean) - Method in class pipe.dataLayer.PetriNetObject
setSelected(boolean) - Method in class pipe.gui.GuiAction
setSelectionBorderColour(Color) - Method in class pipe.dataLayer.PetriNetObject
setShiftDown(boolean) - Method in class pipe.gui.GuiView
setSource(PlaceTransitionObject) - Method in class pipe.dataLayer.Arc
  Set source
setSourceLocation(double, double) - Method in class pipe.dataLayer.Arc
setState(int[]) - Method in class pipe.dataLayer.calculations.State
setTab() - Method in class pipe.gui.GuiFrame
setTarget(PlaceTransitionObject) - Method in class pipe.dataLayer.Arc
  Set target
setTargetLocation(double, double) - Method in class pipe.dataLayer.Arc
setText(String) - Method in class pipe.gui.widgets.ResultsHTMLPane
setTimed(boolean) - Method in class pipe.dataLayer.Transition
  Set the timed transition attribute (for GSPNs)
setTitle(String) - Method in class pipe.gui.GuiFrame
setToZero() - Method in class pipe.dataLayer.PNMatrix
setTransitionAngle(int) - Method in class pipe.dataLayer.ArcPath
setValues(ArrayList, ArrayList) - Method in class pipe.gui.widgets.GraphPanel
setVisibilityLock(boolean) - Method in class pipe.dataLayer.ArcPathPoint
setWeight(int) - Method in class pipe.dataLayer.Arc
  Set weight
setWeightLabelPosition() - Method in class pipe.dataLayer.Arc
setWeightOffsetX(double) - Method in class pipe.dataLayer.Arc
  Set X-axis offset for weight position
setWeightOffsetY(double) - Method in class pipe.dataLayer.Arc
  Set Y-axis offset for weight position
setZoom(int) - Method in class pipe.gui.ZoomController
shiftDown - Static variable in class pipe.gui.ArcKeyboardEventHandler
showBorder(boolean) - Method in class pipe.dataLayer.AnnotationNote
showPoints() - Method in class pipe.dataLayer.ArcPath
simpleNet(DataLayer) - Method in class pipe.modules.classification.Classification
  Simple net (SPL-net) detection
Simulation - Class in pipe.modules.simulation
Simulation() - Constructor for class pipe.modules.simulation.Simulation
SimulationClockWatcher - Class in pipe.modules.iai
SimulationClockWatcher() - Constructor for class pipe.modules.iai.SimulationClockWatcher
SimulationClockWatcherDialog - Class in pipe.modules.iai
SimulationClockWatcherDialog(String, Module) - Constructor for class pipe.modules.iai.SimulationClockWatcherDialog
SimulationFiringCounter - Class in pipe.modules.iai
SimulationFiringCounter() - Constructor for class pipe.modules.iai.SimulationFiringCounter
SimulationFiringCounterDialog - Class in pipe.modules.iai
SimulationFiringCounterDialog(String, Module) - Constructor for class pipe.modules.iai.SimulationFiringCounterDialog
SimulationPlaceWatcher - Class in pipe.modules.iai
SimulationPlaceWatcher() - Constructor for class pipe.modules.iai.SimulationPlaceWatcher
SimulationPlaceWatcherDialog - Class in pipe.modules.iai
SimulationPlaceWatcherDialog(String, Module) - Constructor for class pipe.modules.iai.SimulationPlaceWatcherDialog
SIZE - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
SIZE - Static variable in class pipe.dataLayer.ArcPathPoint
size() - Method in class pipe.dataLayer.calculations.StateList
SIZE_OFFSET - Static variable in class pipe.dataLayer.ArcPathPoint
solve(File) - Static method in class pipe.dataLayer.calculations.SteadyStateSolver
someArc - Static variable in class pipe.dataLayer.PlaceTransitionObject
sourceFilePanel - Variable in class pipe.modules.gspn.GSPN
split(Point2D.Float) - Method in class pipe.dataLayer.Arc
SplitArcAction - Class in pipe.gui
SplitArcAction(Arc, Point) - Constructor for class pipe.gui.SplitArcAction
SplitArcPointAction - Class in pipe.gui
SplitArcPointAction(ArcPathPoint) - Constructor for class pipe.gui.SplitArcPointAction
splitPoint() - Method in class pipe.dataLayer.ArcPathPoint
  splitPoint() This method is called when the user selects the popup menu option Split Point on an Arc Point.
splitSegment(Point2D.Float) - Method in class pipe.dataLayer.ArcPath
  splitSegment() Goes through neighbouring pairs of ArcPathPoints determining the midpoint between them.
START - Static variable in interface pipe.gui.Constants
start() - Method in class pipe.modules.dnamaca.SwingWorker
  Start the worker thread.
startRandomFiring() - Method in class pipe.gui.Animator
State - Class in pipe.dataLayer.calculations
State(int[]) - Constructor for class pipe.dataLayer.calculations.State
State(State) - Constructor for class pipe.dataLayer.calculations.State
StateList - Class in pipe.dataLayer.calculations
StateList() - Constructor for class pipe.dataLayer.calculations.StateList
StateList(File, boolean) - Constructor for class pipe.dataLayer.calculations.StateList
  StateList()
stateMachine(DataLayer) - Method in class pipe.modules.classification.Classification
  State machine detection
StateRecord - Class in pipe.io
StateRecord() - Constructor for class pipe.io.StateRecord
StateRecord(Marking) - Constructor for class pipe.io.StateRecord
StateSpace - Class in pipe.modules.stateSpace
StateSpace() - Constructor for class pipe.modules.stateSpace.StateSpace
StateSpaceGenerator - Class in pipe.dataLayer.calculations
StateSpaceTooBigException - Exception in pipe.dataLayer.calculations
StateSpaceTooBigException() - Constructor for exception pipe.dataLayer.calculations.StateSpaceTooBigException
StateSpaceTooBigException(int) - Constructor for exception pipe.dataLayer.calculations.StateSpaceTooBigException
StatusBar - Class in pipe.gui
StatusBar() - Constructor for class pipe.gui.StatusBar
SteadyStateSolver - Class in pipe.dataLayer.calculations
SteadyStateSolver() - Constructor for class pipe.dataLayer.calculations.SteadyStateSolver
stepBack() - Method in class pipe.gui.Animator
STEPBACKWARD - Static variable in interface pipe.gui.Constants
stepBackwards() - Method in class pipe.gui.AnimationHistory
stepForward() - Method in class pipe.gui.AnimationHistory
stepForward() - Method in class pipe.gui.Animator
STEPFORWARD - Static variable in interface pipe.gui.Constants
STOP - Static variable in interface pipe.gui.Constants
stopRandomFiring() - Method in class pipe.gui.Animator
storeModel() - Method in class pipe.gui.Animator
storeState() - Method in class pipe.dataLayer.DataLayer
  Stores Current Markup
STRAIGHT - Static variable in class pipe.dataLayer.ArcPathPoint
SwingWorker - Class in pipe.modules.dnamaca
  This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class pipe.modules.dnamaca.SwingWorker
  Start a thread that will call the `construct` method and then exit.

## T

test() - Static method in class pipe.dataLayer.calculations.StateSpaceGenerator
testEqualConflict(DataLayer) - Method in class pipe.modules.gspn.GSPN
  Test for condition Equal Conflict.
textforAddtoken - Variable in class pipe.gui.StatusBar
textforAnimation - Variable in class pipe.gui.StatusBar
textforArc - Variable in class pipe.gui.StatusBar
textforDeltoken - Variable in class pipe.gui.StatusBar
textforDrawing - Variable in class pipe.gui.StatusBar
textforMove - Variable in class pipe.gui.StatusBar
textforPlace - Variable in class pipe.gui.StatusBar
textforTimedTrans - Variable in class pipe.gui.StatusBar
textforTrans - Variable in class pipe.gui.StatusBar
tHeight - Static variable in class pipe.dataLayer.Place
  Token Height
TIMEDTRANS - Static variable in interface pipe.gui.Constants
TimelessTrapException - Exception in pipe.dataLayer.calculations
TimelessTrapException() - Constructor for exception pipe.dataLayer.calculations.TimelessTrapException
timesEquals(int) - Method in class pipe.dataLayer.PNMatrix
  Multiply a matrix by an int in place, A = s*A
ToggleArcPointAction - Class in pipe.gui
ToggleArcPointAction(ArcPathPoint) - Constructor for class pipe.gui.ToggleArcPointAction
togglePointType(int) - Method in class pipe.dataLayer.ArcPath
togglePointType() - Method in class pipe.dataLayer.ArcPathPoint
Token - Class in pipe.dataLayer
  Token - Petri-Net Token Class
Token(int, int) - Constructor for class pipe.dataLayer.Token
  Create Petri-Net Token object
Token() - Constructor for class pipe.dataLayer.Token
  Create empty Petri-Net Token object
token - Variable in class pipe.dataLayer.Token
  Ellipse2D.Double token
tokenDistribution(double[], StateList) - Method in class pipe.modules.gspn.GSPNNew
  tokenDistribution() Calculates the steady state probability of there being n tokens at place p
tooBig - Variable in class pipe.dataLayer.calculations.myTree
TOP - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
toPNG(JComponent, String) - Static method in class pipe.gui.Export
topOffset() - Method in class pipe.dataLayer.Transition
  Returns the distance between the outside of the component to the centre, in order to position the centre of the place where the mouse clicks on the screen
toPostScript(Object, String) - Static method in class pipe.gui.Export
toPrinter(Object) - Static method in class pipe.gui.Export
toString() - Method in class pipe.dataLayer.calculations.State
toString() - Method in class pipe.gui.ModuleClassContainer
  Overides the object method in order to provide the correct display name
toString() - Method in class pipe.gui.ModuleMethod
  Returns the name of the modMeth
transformPNML(String) - Method in class pipe.dataLayer.PNMLTransformer
  Transform a PNML file into a Document which is returned and used to construct the DataLayer
Transition - Class in pipe.dataLayer
  Transition - Petri-Net Transition Class
Transition(double, double, String, String, double, double, double, boolean, int) - Constructor for class pipe.dataLayer.Transition
  Create Petri-Net Transition object
Transition(double, double) - Constructor for class pipe.dataLayer.Transition
  Create Petri-Net Transition object
Transition() - Constructor for class pipe.dataLayer.Transition
  Create Petri-Net Transition object
TRANSITION_HEIGHT - Static variable in class pipe.dataLayer.Transition
  Place Width
TRANSITION_WIDTH - Static variable in class pipe.dataLayer.Transition
  Place Width
TransitionEnabled(int) - Method in class pipe.dataLayer.calculations.myNode
TransitionHandler - Class in pipe.gui
  Class used to implement methods corresponding to mouse events on transitions.
TransitionHandler(Container, Transition) - Constructor for class pipe.gui.TransitionHandler
TransitionRecord - Class in pipe.io
TransitionRecord(Marking, Marking, double) - Constructor for class pipe.io.TransitionRecord
  Sets up the record ready for writing to a file.
TransitionRecord(int, int, double) - Constructor for class pipe.io.TransitionRecord
TransitionRecord(int, int, double, int) - Constructor for class pipe.io.TransitionRecord
TransitionRecord() - Constructor for class pipe.io.TransitionRecord
transitions - Variable in class pipe.dataLayer.calculations.myTree
translate(int, int) - Method in class pipe.dataLayer.AnnotationNote
  Translates the component by x,y
translate(int, int) - Method in class pipe.dataLayer.NameLabel
translate(int, int) - Method in class pipe.dataLayer.PlaceTransitionObject
  Translates the component by x,y
translatePoint(int, float, float) - Method in class pipe.dataLayer.ArcPath
translateSelection(int, int) - Method in class pipe.gui.SelectionObject
transpose() - Method in class pipe.dataLayer.PNMatrix
  Matrix transpose.
TreeTooBigException - Exception in pipe.dataLayer.calculations
tWidth - Static variable in class pipe.dataLayer.Place
  Token Width
type - Static variable in class pipe.dataLayer.Arc
type - Static variable in class pipe.dataLayer.Place
type - Static variable in class pipe.dataLayer.Transition

## U

uminus() - Method in class pipe.dataLayer.PNMatrix
  Unary minus
unhighlightDisabledTransitions() - Method in class pipe.gui.Animator
uniteSets(int[], int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Unite two sets (arrays of integers) so that if there is a common entry in the arrays it appears only once, and all the entries of each array appear in the union.
update(Observable, Object) - Method in class pipe.gui.GuiFrame
update(Observable, Object) - Method in class pipe.gui.GuiView
updateArc() - Method in class pipe.dataLayer.ArcPath
updateArcPosition() - Method in class pipe.dataLayer.Arc
  Updates the start position of the arc, resets the arrowhead and updates the bounds
updateArrow() - Method in class pipe.dataLayer.Arc
updateBounds() - Method in class pipe.dataLayer.AnnotationNote
updateBounds() - Method in class pipe.dataLayer.Arc
  Updates the bounding box of the arc component based on the arcs bounds
updateBounds() - Method in class pipe.dataLayer.PlaceTransitionObject
  Calculates the BoundsOffsets used for setBounds() method
updateBounds() - Method in class pipe.gui.SelectionObject
updateConnected() - Method in class pipe.dataLayer.PlaceTransitionObject
  Updates location of any attached arcs
updateEndPoint(Arc) - Method in class pipe.dataLayer.Place
updateEndPoint(Arc) - Method in class pipe.dataLayer.PlaceTransitionObject
updateEndPoint(Arc) - Method in class pipe.dataLayer.Token
updateEndPoint(Arc) - Method in class pipe.dataLayer.Transition
updateEndPoints() - Method in class pipe.dataLayer.Transition
updatePointLocation() - Method in class pipe.dataLayer.ArcPathPoint
updatePosition() - Method in class pipe.dataLayer.NameLabel
updatePreferredSize() - Method in class pipe.gui.GuiView
updateRate(double) - Method in class pipe.io.TransitionRecord
  updateRate() When recording a transition from one state to another, it is possible that there will be multiple paths between them through vanishing states.
updateSize() - Method in class pipe.dataLayer.NameLabel
updateSize(MouseEvent) - Method in class pipe.dataLayer.Token
updateSize(Container) - Static method in class pipe.gui.Grid
updateZoomCombo() - Method in class pipe.gui.GuiFrame
userPath - Static variable in class pipe.gui.CreateGui

## V

validate() - Method in class pipe.gui.GuiView
VanishingState - Class in pipe.dataLayer.calculations
vectorTimes(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Multiply a row matrix by a column matrix, A = s*A
ViewExpansionComponent - Class in pipe.gui
ViewExpansionComponent() - Constructor for class pipe.gui.ViewExpansionComponent
ViewExpansionComponent(int, int) - Constructor for class pipe.gui.ViewExpansionComponent

## W

write(RandomAccessFile) - Method in class pipe.io.RGFileHeader
write(RandomAccessFile) - Method in class pipe.io.StateRecord
write(RandomAccessFile, boolean) - Method in class pipe.io.StateRecord
write(RandomAccessFile) - Method in class pipe.io.TransitionRecord
write1(RandomAccessFile) - Method in class pipe.io.TransitionRecord
  write() Writes a TransitionRecord to the specified file.

## Z

zoom() - Method in class pipe.gui.GuiView
Zoomable - Interface in pipe.gui
ZoomController - Class in pipe.gui
ZoomController(GuiView) - Constructor for class pipe.gui.ZoomController
ZoomController(int, GuiView) - Constructor for class pipe.gui.ZoomController
zoomIn() - Method in class pipe.gui.ZoomController
zoomOut() - Method in class pipe.gui.ZoomController
zoomUpdate() - Method in class pipe.dataLayer.AnnotationNote
zoomUpdate() - Method in class pipe.dataLayer.ArcPathPoint
zoomUpdate() - Method in class pipe.dataLayer.PlaceTransitionObject
zoomUpdate() - Method in class pipe.gui.ViewExpansionComponent
zoomUpdate() - Method in interface pipe.gui.Zoomable

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