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

## A

A - Variable in class pipe.dataLayer.PNMatrix
  Array for internal storage of elements.
ADDTOKEN - Static variable in interface pipe.gui.Constants
ANIMATE - Static variable in interface pipe.gui.Constants
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
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
Analysis - class pipe.modules.predatorInvariantAnalysis.Analysis.
Analysis() - Constructor for class pipe.modules.predatorInvariantAnalysis.Analysis
AnimationHandler - class pipe.gui.AnimationHandler.
AnimationHandler() - Constructor for class pipe.gui.AnimationHandler
AnimationHistory - class pipe.gui.AnimationHistory.
  Class to represent the history of the net animation
AnimationHistory(String) - Constructor for class pipe.gui.AnimationHistory
Animator - class pipe.gui.Animator.
Animator() - Constructor for class pipe.gui.Animator
AnnotationNote - class pipe.dataLayer.AnnotationNote.
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 pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler.
AnnotationNote.AnnotationKeyUpdateHandler(AnnotationNote) - Constructor for class pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler
AnnotationNote.ResizePoint - class pipe.dataLayer.AnnotationNote.ResizePoint.
AnnotationNote.ResizePoint(AnnotationNote, int) - Constructor for class pipe.dataLayer.AnnotationNote.ResizePoint
AnnotationNote.ResizePointHandler - class pipe.dataLayer.AnnotationNote.ResizePointHandler.
AnnotationNote.ResizePointHandler(AnnotationNote.ResizePoint) - Constructor for class pipe.dataLayer.AnnotationNote.ResizePointHandler
AnnotationNoteHandler - class pipe.gui.AnnotationNoteHandler.
AnnotationNoteHandler(Container, AnnotationNote) - Constructor for class pipe.gui.AnnotationNoteHandler
Arc - class pipe.dataLayer.Arc.
  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
ArcHandler - class pipe.gui.ArcHandler.
  Class used to implement methods corresponding to mouse events on arcs.
ArcHandler(Container, Arc) - Constructor for class pipe.gui.ArcHandler
ArcKeyboardEventHandler - class pipe.gui.ArcKeyboardEventHandler.
ArcKeyboardEventHandler(Arc) - Constructor for class pipe.gui.ArcKeyboardEventHandler
ArcPath - class pipe.dataLayer.ArcPath.
ArcPath(Arc) - Constructor for class pipe.dataLayer.ArcPath
ArcPathPoint - class pipe.dataLayer.ArcPathPoint.
ArcPathPoint(ArcPath) - Constructor for class pipe.dataLayer.ArcPathPoint
ArcPathPoint(float, float, boolean, ArcPath) - Constructor for class pipe.dataLayer.ArcPathPoint
ArcPathPointHandler - class pipe.gui.ArcPathPointHandler.
ArcPathPointHandler(Container, ArcPathPoint) - Constructor for class pipe.gui.ArcPathPointHandler
ArrowHead - class pipe.gui.ArrowHead.
ArrowHead() - Constructor for class pipe.gui.ArrowHead
a - Variable in class pipe.dataLayer.Cubic
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.EditAnnotationBorderAction
  Action for editing the text in an AnnotationNote
actionPerformed(ActionEvent) - Method in class pipe.gui.EditRateAction
  Actions deleting the component
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.GuiFrame.AnimateAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GuiFrame.DeleteAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GuiFrame.ExampleFileAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GuiFrame.FileAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GuiFrame.GridAction
actionPerformed(ActionEvent) - Method in class pipe.gui.GuiFrame.TypeAction
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.ModuleManager.RemoveModuleAction
actionPerformed(ActionEvent) - Method in class pipe.gui.RotateTransitionAction
actionPerformed(ActionEvent) - Method in class pipe.gui.ToggleArcPointAction
actionPerformed(ActionEvent) - Method in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.TimerListener
actionPerformed(ActionEvent) - Method in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
add(int[]) - Method in class pipe.dataLayer.calculations.StateList
add(int[], String) - 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
addAnnotation(AnnotationNote) - Method in class pipe.dataLayer.DataLayer
  Add placeInput to the back of the Place ArrayList All observers are notified of this change (Model-View Architecture)
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)
addArcSourceTarget(String, String) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
addArcToArcsMap(Arc) - Method in class pipe.dataLayer.DataLayer
  Update the arcsMap hashtable to reflect the new arc
addArcValue(int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
addButton(JToolBar, GuiAction) - Method in class pipe.gui.GuiFrame
addClassRootToPath(Class) - Method in class pipe.gui.ExtFileManager
addClassToTree(Class) - Method in class pipe.gui.ModuleManager
  Method creates and returns a Module management tree.
addColumnToB() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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
addDataToC(String, String, boolean, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
addHistoryItem(String) - Method in class pipe.gui.AnimationHistory
addLabelToContainer() - Method in class pipe.dataLayer.PetriNetObject
addMenuItem(JMenu, Action) - Method in class pipe.gui.GuiFrame
addModuleToTree(DefaultMutableTreeNode) - Method in class pipe.gui.ModuleManager
  Adds a new node to the Module subtree
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.
addPlace(Place) - Method in class pipe.dataLayer.DataLayer
  Add placeInput to the back of the Place ArrayList All observers are notified of this change (Model-View Architecture)
addPlaceName(String) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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
addPoint(Rectangle, float, float) - Method in class pipe.gui.ArrowHead
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
addSubnetArcsToC() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
addToPlaceMarkings(Integer) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
addToken(Token) - Method in class pipe.dataLayer.DataLayer
  Add tokenInput to the back of the Token ArrayList All observers are notified of this change.
addTotal(int[], int[]) - Method in class pipe.modules.simulation.Simulation
addTransition(Transition) - Method in class pipe.dataLayer.DataLayer
  Add transitionInput to back of the Transition ArrayList All observers are notified of this change (Model-View Architecture)
addTransitionName(String) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
addWeightLabelToContainer() - Method in class pipe.dataLayer.Arc
addedToGui() - Method in class pipe.dataLayer.Arc
addedToGui() - Method in class pipe.dataLayer.PetriNetObject
addedToGui() - Method in class pipe.dataLayer.PlaceTransitionObject
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
algorithm1_1() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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)
analyse(DataLayer) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
analyseButtonClick - Variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
  Classify button click handler
analyseButtonClick - Variable in class pipe.modules.stateSpace.StateSpace
  Analyse button click handler
angle - Variable in class pipe.dataLayer.Transition.ArcAngleCompare
angle - Variable in class pipe.dataLayer.Transition
angle - Variable in class pipe.gui.ArrowHead
angle - Variable in class pipe.gui.RotateTransitionAction
animBox - Static variable in class pipe.gui.CreateGui
animBox - Variable in class pipe.gui.GuiFrame.AnimateAction
animationHandler - Variable in class pipe.gui.GuiView
animationmode - Variable in class pipe.gui.GuiView
animator - Static variable in class pipe.gui.CreateGui
annotationAction - Variable in class pipe.gui.GuiFrame
appFile - Variable in class pipe.gui.CreateGui.TabData
appGui - Static variable in class pipe.gui.CreateGui
appGui - Variable in class pipe.gui.GuiFrame
appModel - Variable in class pipe.gui.CreateGui.TabData
appModel - Variable in class pipe.gui.GuiFrame
appPath - Static variable in class pipe.gui.CreateGui
appTab - Static variable in class pipe.gui.CreateGui
appTab - Variable in class pipe.gui.GuiFrame
appView - Variable in class pipe.gui.CreateGui.TabData
appView - Variable in class pipe.gui.GuiFrame
appendVector(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Append a column matrix (vector) to the right of another matrix.
arc - Variable in class pipe.dataLayer.Transition.ArcAngleCompare
arcAction - Variable in class pipe.gui.GuiFrame
arcAngleList - Variable in class pipe.dataLayer.Transition
  The transform
arcBeingDrawn - Variable in class pipe.gui.ArcKeyboardEventHandler
arcSelection - Variable in class pipe.dataLayer.ArcPath
arcSource - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
arcSources - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
arcTarget - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
arcTargets - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
arcValues - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
arcboundsLeft - Variable in class pipe.dataLayer.NameLabel
arcboundsTop - Variable in class pipe.dataLayer.NameLabel
arcsArray - Variable in class pipe.dataLayer.DataLayer
  ArrayList containing all the Arc objects in the Petri-Net
arcsMap - Variable in class pipe.dataLayer.DataLayer
  Hashtable which maps PlaceTransitionObjects to their list of connected arcs
areNotSameType(PlaceTransitionObject) - Method in class pipe.dataLayer.PlaceTransitionObject
arrayInitialisation() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
arrow - Variable in class pipe.dataLayer.Arc
  Arc is of type Line2D.Double
arrowsArray - Variable in class pipe.dataLayer.DataLayer
  ArrayList containing all the Arrow objects in the Petri-Net

## B

BOTTOM - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
ButtonBar - class pipe.gui.widgets.ButtonBar.
  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
b - Variable in class pipe.dataLayer.Cubic
b - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
bCols - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
bRows - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
backwardsIncidenceMatrix - Variable in class pipe.dataLayer.DataLayer
  Backward Incidence Matrix
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)
bold - Variable in class pipe.gui.AnimationHistory
boundTextArea - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
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
browse - Variable in class pipe.gui.widgets.PetriNetChooserPanel
browseButtonClick - Variable in class pipe.gui.widgets.PetriNetChooserPanel

## C

CMinus - Variable in class pipe.dataLayer.calculations.myTree
COMPONENT_DRAW_OFFSET - Static variable in class pipe.dataLayer.PetriNetObject
CPlus - Variable in class pipe.dataLayer.calculations.myTree
CREATING - Static variable in interface pipe.gui.Constants
CURVED - Static variable in class pipe.dataLayer.ArcPathPoint
Classification - class pipe.modules.classification.Classification.
  Classification class implements petri net classification
Classification() - Constructor for class pipe.modules.classification.Classification
Comparison - class pipe.modules.comparison.Comparison.
Comparison() - Constructor for class pipe.modules.comparison.Comparison
Constants - interface pipe.gui.Constants.
CopyHandler - Variable in class pipe.gui.widgets.ResultsHTMLPane
CreateGui - class pipe.gui.CreateGui.
CreateGui() - Constructor for class pipe.gui.CreateGui
CreateGui.TabData - class pipe.gui.CreateGui.TabData.
CreateGui.TabData() - Constructor for class pipe.gui.CreateGui.TabData
Cubic - class pipe.dataLayer.Cubic.
Cubic(float, float, float, float) - Constructor for class pipe.dataLayer.Cubic
c - Variable in class pipe.dataLayer.Cubic
c - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
cLoader - Static variable in class pipe.gui.ExtFileManager
calcAngle() - Method in class pipe.dataLayer.Transition.ArcAngleCompare
calcMeanCycleTimes(double[], double) - Method in class pipe.modules.gspn.GSPN
calcMeanNumVisits(double[]) - Method in class pipe.modules.gspn.GSPN
  This function calculates the mean number of visits at a particular transition, given a particular embedded Markov Process
calcNaturalCubic(int, int[]) - Method in class pipe.dataLayer.ArcPath
calcSojournTime(DataLayer, StateList) - Method in class pipe.modules.gspn.GSPN
  This function determines the sojourn time for each state in a specified set of states.
calculateButtonClick - Variable in class pipe.modules.matrixes.Matrixes
  Calculate button click handler
calculateRange() - Method in class pipe.gui.widgets.GraphPanel
cancel() - Method in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
cardinality(int[]) - Static method in class pipe.modules.classification.Classification
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
changeArrayList - Variable in class pipe.dataLayer.DataLayer
  An ArrayList used to point to either the Arc, Place or Transition ArrayLists when these ArrayLists are being update
changeText(String) - Method in class pipe.gui.StatusBar
changeText(int) - Method in class pipe.gui.StatusBar
characters(char[], int, int) - Method in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
checkCase11() - Method in class pipe.dataLayer.PNMatrix
  Check if a matrix satisfies condition 1.1 of the algorithm.
checkForPopup(MouseEvent) - Method in class pipe.gui.PetriNetObjectHandler
  Displays the popup menu
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
checkMatrixDimensions(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Throws IllegalArgumentException if dimensions of A and B differ.
children - Variable in class pipe.dataLayer.calculations.myNode
classifyButtonClick - Variable in class pipe.modules.classification.Classification
  Classify button click handler
clear() - Method in class pipe.modules.dnamaca.SwingWorker.ThreadVar
clearAllArrays() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
clearAllVectors() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
clearSelection() - Method in class pipe.gui.SelectionObject
clipboard - Variable in class pipe.gui.widgets.ResultsHTMLPane
clone() - Method in class pipe.dataLayer.PNMatrix
  Clone the IntMatrix object.
closeAction - Variable in class pipe.gui.GuiFrame
cminus - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
colsToUpdate() - Method in class pipe.dataLayer.PNMatrix
  Find the comlumn indices to be changed by linear combination.
compareArcID - Variable in class pipe.modules.comparison.Comparison
compareArcName - Variable in class pipe.modules.comparison.Comparison
compareArcWeighting - Variable in class pipe.modules.comparison.Comparison
compareArcs(Arc[], Arc[], boolean, boolean, boolean) - Method in class pipe.modules.comparison.Comparison
compareButtonClick - Variable in class pipe.modules.comparison.Comparison
  Compare button click handler
compareMarking(int[], int[]) - Method in class pipe.dataLayer.calculations.StateList
comparePlaceID - Variable in class pipe.modules.comparison.Comparison
comparePlaceMarking - Variable in class pipe.modules.comparison.Comparison
comparePlaceName - Variable in class pipe.modules.comparison.Comparison
comparePlaces(Place[], Place[], boolean, boolean, boolean) - Method in class pipe.modules.comparison.Comparison
compareTo(Object) - Method in class pipe.dataLayer.Transition.ArcAngleCompare
compareTransitionID - Variable in class pipe.modules.comparison.Comparison
compareTransitionName - Variable in class pipe.modules.comparison.Comparison
compareTransitionRate - Variable in class pipe.modules.comparison.Comparison
compareTransitions(Transition[], Transition[], boolean, boolean, boolean) - Method in class pipe.modules.comparison.Comparison
comparisonFilePanel - Variable in class pipe.modules.comparison.Comparison
componentHeight - Variable in class pipe.dataLayer.PlaceTransitionObject
componentWidth - Variable in class pipe.dataLayer.PlaceTransitionObject
connectFrom - Variable in class pipe.dataLayer.PlaceTransitionObject
connectTo - Variable in class pipe.dataLayer.PlaceTransitionObject
construct() - Method in class pipe.modules.dnamaca.SwingWorker
  Compute the value to be returned by the `get` method.
constructTransition() - Method in class pipe.dataLayer.Transition
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
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
content - Variable in class pipe.gui.HelpBox
contentPane - Variable in class pipe.gui.EditRateAction
contentPane - Variable in class pipe.gui.EditTokenAction
contentPane - Variable in class pipe.gui.EditWeightAction
contentPane - Variable in class pipe.gui.LabelAction
contentPane - Variable in class pipe.gui.PetriNetObjectHandler
contentPane - Variable in class pipe.gui.RotateTransitionAction
control1 - Variable in class pipe.dataLayer.ArcPathPoint
control2 - Variable in class pipe.dataLayer.ArcPathPoint
copy() - Method in class pipe.dataLayer.PNMatrix
  Make a deep copy of a matrix
copyB() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
count - Static variable in class pipe.gui.Animator
countPlaceInputs(DataLayer, int) - Method in class pipe.modules.classification.Classification
  Counts inputs to given place
countPlaceOutputs(DataLayer, int) - Method in class pipe.modules.classification.Classification
countTransitionInputs(DataLayer, int) - Method in class pipe.modules.classification.Classification
countTransitionOutputs(DataLayer, int) - Method in class pipe.modules.classification.Classification
  Counts outputs from given transition
cplus - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
createAction - Variable in class pipe.gui.GuiFrame
createAnnotation(Element) - Method in class pipe.dataLayer.DataLayer
  Creates a Label object from a Label DOM Element
createAnnotationNoteElement(AnnotationNote, Document) - Method in class pipe.dataLayer.DataLayer
  Creates a Place Element for a PNML Petri-Net DOM
createArc(Element) - Method in class pipe.dataLayer.DataLayer
  Creates a Arc object from a Arc DOM Element
createArc - Variable in class pipe.gui.GuiView
createArcElement(Arc, Document) - Method in class pipe.dataLayer.DataLayer
  Creates a Arc Element for a PNML Petri-Net DOM
createArcPoint(String, String, String, Document, int) - Method in class pipe.dataLayer.DataLayer
createBackwardsIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Creates Backwards Incidence Matrix from current Petri-Net
createCurrentMarkupMatrix() - Method in class pipe.dataLayer.DataLayer
  Creates Initial Markup Matrix from current Petri-Net
createFowardIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Creates Foward Incidence Matrix from current Petri-Net
createGrid() - Static method in class pipe.gui.Grid
createIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Creates Incidence Matrix from current Petri-Net
createInitialMarkupMatrix() - Method in class pipe.dataLayer.DataLayer
  Creates Initial Markup Matrix from current Petri-Net
createMatrixes() - Method in class pipe.dataLayer.DataLayer
  Creates all Petri-Net Matrixes from current Petri-Net
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
createPlace(Element) - Method in class pipe.dataLayer.DataLayer
  Creates a Place object from a Place DOM Element
createPlaceElement(Place, Document) - Method in class pipe.dataLayer.DataLayer
  Creates a Place Element for a PNML Petri-Net DOM
createTransition(Element) - Method in class pipe.dataLayer.DataLayer
  Creates a Transition object from a Transition DOM Element
createTransitionElement(Transition, Document) - Method in class pipe.dataLayer.DataLayer
  Creates a Transition Element for a PNML Petri-Net DOM
currCColNum - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
currCRowNum - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
current - Variable in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
currentItem - Variable in class pipe.gui.AnimationHistory
currentMarking - Variable in class pipe.dataLayer.Place
  Current Marking
currentMarkupMatrix - Variable in class pipe.dataLayer.DataLayer
  Initial Markup Matrix
currentPNMLData() - Static method in class pipe.gui.CreateGui
  returns the current dataLayer object - used to get a reference to pass to the modules
currentPoint - Variable in class pipe.dataLayer.ArcPath

## D

DEFAULT_ELEMENT_TYPE - Static variable in interface pipe.gui.Constants
DELETE - Static variable in interface pipe.gui.Constants
DELTOKEN - Static variable in interface pipe.gui.Constants
DIAMETER - Static variable in class pipe.dataLayer.Place
DIAMETER - Static variable in class pipe.dataLayer.Token
DISPLAY_SCALE_FACTORX - Variable in class pipe.dataLayer.DataLayer
  X-Axis Scale Value
DISPLAY_SCALE_FACTORY - Variable in class pipe.dataLayer.DataLayer
  Y-Axis Scale Value
DISPLAY_SHIFT_FACTORX - Variable in class pipe.dataLayer.DataLayer
  X-Axis Shift Value
DISPLAY_SHIFT_FACTORY - Variable in class pipe.dataLayer.DataLayer
  Y-Axis Shift Value
DRAW - Static variable in interface pipe.gui.Constants
DataLayer - class pipe.dataLayer.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
DeletePetriNetObjectAction - class pipe.gui.DeletePetriNetObjectAction.
DeletePetriNetObjectAction(PetriNetObject) - Constructor for class pipe.gui.DeletePetriNetObjectAction
Dnamaca - class pipe.modules.dnamaca.Dnamaca.
Dnamaca() - Constructor for class pipe.modules.dnamaca.Dnamaca
Dnamaca.DnamacaRun - class pipe.modules.dnamaca.Dnamaca.DnamacaRun.
Dnamaca.DnamacaRun() - Constructor for class pipe.modules.dnamaca.Dnamaca.DnamacaRun
Dnamaca.DnamacaRun.ExternalTask - class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask.
Dnamaca.DnamacaRun.ExternalTask() - Constructor for class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
Dnamaca.DnamacaRun.ExternalTask.ActualTask - class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask.ActualTask.
Dnamaca.DnamacaRun.ExternalTask.ActualTask() - Constructor for class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask.ActualTask
Dnamaca.DnamacaRun.TimerListener - class pipe.modules.dnamaca.Dnamaca.DnamacaRun.TimerListener.
Dnamaca.DnamacaRun.TimerListener() - Constructor for class pipe.modules.dnamaca.Dnamaca.DnamacaRun.TimerListener
d - Variable in class pipe.dataLayer.Cubic
data - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
decCount() - Method in class pipe.dataLayer.Token
defaultNet - Variable in class pipe.gui.widgets.PetriNetChooserPanel
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
deleteAction - Variable in class pipe.gui.GuiFrame
deleteColsWithoutMinimalSupport() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
deleteColumn(int[][], int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
deleteExtendedColumn(int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
deletePetriNetObject(PetriNetObject) - Method in class pipe.gui.SelectionObject
deletePoint(ArcPathPoint) - Method in class pipe.dataLayer.ArcPath
deleteSelection() - Method in class pipe.gui.SelectionObject
deleteTokenAction - Variable in class pipe.gui.GuiFrame
deleted - Variable in class pipe.dataLayer.Arc
depth - Variable in class pipe.dataLayer.calculations.myNode
deselect() - Method in class pipe.dataLayer.AnnotationNote
deselect() - Method in class pipe.dataLayer.PetriNetObject
deselectPoint(int) - Method in class pipe.dataLayer.ArcPath
dialog - Variable in class pipe.gui.HelpBox
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
displayName - Variable in class pipe.gui.ModuleClassContainer
displayResults() - Method in class pipe.modules.dnamaca.Dnamaca
divideByGCD(int[][], int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
divideEquals(int) - Method in class pipe.dataLayer.PNMatrix
  Divide a matrix by an int in place, A = s*A
doRandomFiring() - Method in class pipe.gui.Animator
doc - Variable in class pipe.gui.AnimationHistory
done() - Method in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
drag(int, int) - Method in class pipe.dataLayer.AnnotationNote.ResizePoint
dragInit - Variable in class pipe.gui.PetriNetObjectHandler
dragPoints - Variable in class pipe.dataLayer.AnnotationNote
draggable - Variable in class pipe.dataLayer.PetriNetObject
drawAxis(Graphics2D) - Method in class pipe.gui.widgets.GraphPanel
drawBorder - Variable in class pipe.dataLayer.AnnotationNote
drawGrid(Graphics) - Static method in class pipe.gui.Grid
drawPoints(Graphics2D) - Method in class pipe.gui.widgets.GraphPanel

## E

ELEMENT_FILL_COLOUR - Static variable in interface pipe.gui.Constants
ELEMENT_LINE_COLOUR - Static variable in interface pipe.gui.Constants
ENABLED_TRANSITION_COLOUR - Static variable in interface pipe.gui.Constants
EditAnnotationAction - class pipe.gui.EditAnnotationAction.
EditAnnotationAction(AnnotationNote) - Constructor for class pipe.gui.EditAnnotationAction
EditAnnotationBorderAction - class pipe.gui.EditAnnotationBorderAction.
EditAnnotationBorderAction(AnnotationNote) - Constructor for class pipe.gui.EditAnnotationBorderAction
EditRateAction - class pipe.gui.EditRateAction.
  Action object that can be used to add a rate to a transition.
EditRateAction(Container, Component) - Constructor for class pipe.gui.EditRateAction
EditTimedAction - class pipe.gui.EditTimedAction.
  Action object that can be used to add a rate to a transition.
EditTimedAction(Transition) - Constructor for class pipe.gui.EditTimedAction
EditTokenAction - class pipe.gui.EditTokenAction.
  Action object that can be used to effect adding/removing tokens from a place
EditTokenAction(Container, Place) - Constructor for class pipe.gui.EditTokenAction
EditWeightAction - class pipe.gui.EditWeightAction.
EditWeightAction(Container, Arc) - Constructor for class pipe.gui.EditWeightAction
EndNodes - Variable in class pipe.dataLayer.calculations.myTree
Export - class pipe.gui.Export.
  Class for exporting things to other formats, as well as printing.
Export() - Constructor for class pipe.gui.Export
ExtFileManager - class pipe.gui.ExtFileManager.
ExtFileManager() - Constructor for class pipe.gui.ExtFileManager
ExtensionFilter - class pipe.gui.ExtensionFilter.
ExtensionFilter(String, String) - Constructor for class pipe.gui.ExtensionFilter
edit_window - Variable in class pipe.gui.SelectionObject
effectiveSetLength(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
  find the number of non-zero elements in a set
eliminateCol(int) - Method in class pipe.dataLayer.PNMatrix
  Eliminate a column from the matrix, column index is toDelete
emph - Variable in class pipe.gui.AnimationHistory
emptyPNML() - Method in class pipe.dataLayer.DataLayer
  Empty all attributes, turn into empty Petri-Net
enableActions(boolean) - Method in class pipe.gui.GuiFrame
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
enabled - Variable in class pipe.dataLayer.Transition
enabled - Static variable in class pipe.gui.Grid
enabled() - Static method in class pipe.gui.Grid
enabled - Variable in class pipe.gui.SelectionObject
enabledBackwards - Variable in class pipe.dataLayer.Transition
endDocument() - Method in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
endElement(String, String, String) - Method in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
eval(float) - Method in class pipe.dataLayer.Cubic
  evaluate cubic
exCopyCol - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
exCopyRow - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
execute(DataLayer) - Method in class pipe.gui.ModuleMethod
  Executes the Method that this class represents.
executeAlgorithm() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
executeAlgorithm(boolean) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
exitAction - Variable in class pipe.gui.GuiFrame
exportGuiView(GuiView, int) - Static method in class pipe.gui.Export
exportPNGAction - Variable in class pipe.gui.GuiFrame
exportPSAction - Variable in class pipe.gui.GuiFrame
ext - Variable in class pipe.gui.widgets.FileBrowser
extend - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
extendCols - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
extendCopy - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
extendRows - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
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

## F

FIRE - Static variable in interface pipe.gui.Constants
FileBrowser - class pipe.gui.widgets.FileBrowser.
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
Found_An_Omega - Variable in class pipe.dataLayer.calculations.myTree
fSeq - Variable in class pipe.gui.AnimationHistory
  Holds all the transitions in the sequence
file - Variable in class pipe.gui.GuiFrame.ExampleFileAction
fileName - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
filename - Variable in class pipe.gui.HelpBox
fillC() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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.
findSubset(int[], int[]) - Static method in class pipe.modules.classification.Classification
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
fireRandomTransition() - Method in class pipe.dataLayer.DataLayer
  Fire a random transition, takes rate (probability) of Transitions into account
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(int) - 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
fireTransitionBackwards(int) - Method in class pipe.dataLayer.DataLayer
firedTransitions - Variable in class pipe.gui.Animator
firstArc - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
firstNonZeroColumn(int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
firstNonZeroElementIndex(int) - Method in class pipe.dataLayer.PNMatrix
  Find the column index of the first non zero element of row h.
firstNonZeroRowC() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
firstNonZeroRowIndex() - Method in class pipe.dataLayer.PNMatrix
  Find the first non-zero row of a matrix.
forwardsPlaceSet(DataLayer, int) - Method in class pipe.modules.classification.Classification
fowardsIncidenceMatrix - Variable in class pipe.dataLayer.DataLayer
  Foward Incidence Matrix
frame - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
frameTitle - Variable in class pipe.gui.GuiFrame
freeChoiceNet(DataLayer) - Method in class pipe.modules.classification.Classification
  Free choice net detection
freeSpace - Static variable in class pipe.gui.CreateGui

## G

GRID - Static variable in interface pipe.gui.Constants
GSPN - class pipe.modules.gspn.GSPN.
GSPN() - Constructor for class pipe.modules.gspn.GSPN
GraphBottom - Static variable in class pipe.gui.widgets.GraphPanel
GraphLeft - Static variable in class pipe.gui.widgets.GraphPanel
GraphPanel - class pipe.gui.widgets.GraphPanel.
GraphPanel(ArrayList, ArrayList) - Constructor for class pipe.gui.widgets.GraphPanel
GraphPanel() - Constructor for class pipe.gui.widgets.GraphPanel
GraphPanelPane - class pipe.gui.widgets.GraphPanelPane.
GraphPanelPane() - Constructor for class pipe.gui.widgets.GraphPanelPane
GraphPointSize - Static variable in class pipe.gui.widgets.GraphPanel
GraphRight - Static variable in class pipe.gui.widgets.GraphPanel
GraphTop - Static variable in class pipe.gui.widgets.GraphPanel
Grid - class pipe.gui.Grid.
Grid() - Constructor for class pipe.gui.Grid
GuiAction - class pipe.gui.GuiAction.
  GuiAction class
GuiAction(String, String, String) - Constructor for class pipe.gui.GuiAction
GuiAction(String, String, String, boolean) - Constructor for class pipe.gui.GuiAction
GuiFrame - class pipe.gui.GuiFrame.
GuiFrame(String) - Constructor for class pipe.gui.GuiFrame
GuiFrame.AnimateAction - class pipe.gui.GuiFrame.AnimateAction.
GuiFrame.AnimateAction(String, int, String) - Constructor for class pipe.gui.GuiFrame.AnimateAction
GuiFrame.AnimateAction(String, int, String, boolean) - Constructor for class pipe.gui.GuiFrame.AnimateAction
GuiFrame.DeleteAction - class pipe.gui.GuiFrame.DeleteAction.
GuiFrame.DeleteAction(String, String, String) - Constructor for class pipe.gui.GuiFrame.DeleteAction
GuiFrame.ExampleFileAction - class pipe.gui.GuiFrame.ExampleFileAction.
GuiFrame.ExampleFileAction(File) - Constructor for class pipe.gui.GuiFrame.ExampleFileAction
GuiFrame.FileAction - class pipe.gui.GuiFrame.FileAction.
GuiFrame.FileAction(String, String, String) - Constructor for class pipe.gui.GuiFrame.FileAction
GuiFrame.GridAction - class pipe.gui.GuiFrame.GridAction.
GuiFrame.GridAction(String, String, String) - Constructor for class pipe.gui.GuiFrame.GridAction
GuiFrame.ToggleButton - class pipe.gui.GuiFrame.ToggleButton.
  A JToggleButton that watches an Action for selection change
GuiFrame.ToggleButton(Action) - Constructor for class pipe.gui.GuiFrame.ToggleButton
GuiFrame.TypeAction - class pipe.gui.GuiFrame.TypeAction.
GuiFrame.TypeAction(String, int, String, String) - Constructor for class pipe.gui.GuiFrame.TypeAction
GuiFrame.TypeAction(String, int, String, String, boolean) - Constructor for class pipe.gui.GuiFrame.TypeAction
GuiFrame.WindowHandler - class pipe.gui.GuiFrame.WindowHandler.
GuiFrame.WindowHandler() - Constructor for class pipe.gui.GuiFrame.WindowHandler
GuiView - class pipe.gui.GuiView.
  The petrinet is drawn onto this frame.
GuiView() - Constructor for class pipe.gui.GuiView
GuiView.MouseHandler - class pipe.gui.GuiView.MouseHandler.
GuiView.MouseHandler() - Constructor for class pipe.gui.GuiView.MouseHandler
gcd() - Method in class pipe.dataLayer.PNMatrix
  Find the greatest common divisor of a column matrix (vector) of integers.
gcd(int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
gcd2(int, int) - Method in class pipe.dataLayer.PNMatrix
  Find the greatest common divisor of 2 integers.
generateArray(int[][], int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generateCPlusCMinus() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generateCoveredString() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generateExtend() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generateInitialiseZeroArray(int[][], int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generateMod() - Method in class pipe.modules.dnamaca.Dnamaca
generatePinvarDisplay(boolean) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generateTinvarDisplay(boolean) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
generatingDisplay() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
get(int, int) - Method in class pipe.dataLayer.PNMatrix
  Get a single element.
get(int) - Method in class pipe.dataLayer.calculations.StateList
get() - Method in class pipe.modules.dnamaca.SwingWorker.ThreadVar
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
getArcSelection() - Method in class pipe.dataLayer.ArcPath
getArcWithSource(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Return the Arc called arcName from the Petri-Net
getArcWithTarget(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Return the Arc called arcName from the Petri-Net
getArcs() - Method in class pipe.dataLayer.DataLayer
  Get an List of all the Arcs objects in the Petri-Net
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
getControlPoint(Point2D.Float, Point2D.Float, Point2D.Float, Point2D.Float) - Method in class pipe.dataLayer.ArcPath
getCount() - Method in class pipe.dataLayer.Token
getCurrent() - Method in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
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
getDOM(String) - Method in class pipe.dataLayer.DataLayer
  Return a DOM for the PNML file at URI pnmlFileName
getDOM(File) - Method in class pipe.dataLayer.DataLayer
  Return a DOM for the PNML File pnmlFile
getDOM() - Method in class pipe.dataLayer.DataLayer
  Return a DOM for the Petri-Net
getDataLayer() - Method in class pipe.gui.widgets.PetriNetChooserPanel
getDescription() - Method in class pipe.gui.ExtensionFilter
getEmbeddedMarkovChainSteadyStateDistribution(Matrix, Matrix, Matrix, Matrix) - Method in class pipe.modules.gspn.GSPN
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
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
getGCD(int[][], int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
getGraph() - Method in class pipe.gui.widgets.GraphPanelPane
getGridSpacing() - Static method in class pipe.gui.Grid
getID() - Method in class pipe.dataLayer.AnnotationNote
getID() - Method in class pipe.dataLayer.NameLabel
getID() - Method in class pipe.dataLayer.calculations.Marking
getID() - Method in class pipe.dataLayer.calculations.StateList
getID(int) - Method in class pipe.dataLayer.calculations.StateList
getId() - Method in class pipe.dataLayer.Arc
  Get id
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
getIncidenceMatrix() - Method in class pipe.dataLayer.DataLayer
  Return the Incidence Matrix for the Petri-Net
getIndex() - Method in class pipe.dataLayer.ArcPathPoint
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
getIntersectOffset(Point2D) - Method in class pipe.dataLayer.PlaceTransitionObject
getLabels() - Method in class pipe.dataLayer.DataLayer
  Get a List of all the net-level NameLabel objects in the Petri-Net
getListPosition(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Get position of Petri-Net Object in ArrayList of given Petri-Net Object's type
getMarking() - Method in class pipe.dataLayer.calculations.Marking
getMarking(DataLayer) - Method in class pipe.modules.gspn.GSPN
  Get the initial marking of the supplied net
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.
getMessage() - Method in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
getMod(Point2D.Float, Point2D.Float) - Method in class pipe.dataLayer.ArcPath
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 root directory under which the modules will be found.
getModuleName() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
getModuleTree() - Method in class pipe.gui.ModuleManager
getName() - Method in class pipe.dataLayer.PlaceTransitionObject
  Get name
getName() - Method in interface pipe.modules.Module
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.GSPN
getName() - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
getName() - Method in class pipe.modules.matrixes.Matrixes
getName() - Method in class pipe.modules.predatorInvariantAnalysis.PredatorInvariantAnalysis
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
getNumPoints() - Method in class pipe.dataLayer.ArcPath
getNumberSequences() - Method in class pipe.gui.Animator
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
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
getPlaceTransitionObject(String) - Method in class pipe.dataLayer.DataLayer
  Return the PlaceTransitionObject called ptoName from the Petri-Net
getPlaces() - Method in class pipe.dataLayer.DataLayer
  Get an List of all the Place objects in the Petri-Net
getPoint(int) - Method in class pipe.dataLayer.ArcPath
getPoint() - Method in class pipe.dataLayer.ArcPathPoint
getPointPlot(Point2D.Double) - Method in class pipe.gui.widgets.GraphPanel
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.Transition
getRateForSpecificStateChange(DataLayer, int[], int[]) - Method in class pipe.modules.gspn.GSPN
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.
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
getStatusBar() - Method in class pipe.gui.GuiFrame
getSteadyStateDistribution(double[], double[]) - Method in class pipe.modules.gspn.GSPN
getTab() - Static method in class pipe.gui.CreateGui
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
getTimed() - Method in class pipe.dataLayer.Transition
  Get the timed transition attribute (for GSPNs)
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
getTransitionConditions(int) - Method in class pipe.modules.dnamaca.Dnamaca
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
getTransitionProbabilityMatrix(DataLayer, StateList) - Method in class pipe.modules.gspn.GSPN
  Constructs a matrix of probabilities of changing from one marking to another.
getTransitionThroughput(DataLayer, StateList, StateList, Matrix, double[]) - Method in class pipe.modules.gspn.GSPN
getTransitionThroughputSPN(DataLayer, StateList, double[], int) - Method in class pipe.modules.gspn.GSPN
getTransitions() - Method in class pipe.dataLayer.DataLayer
  Get an List of all the Transition objects in the Petri-Net
getTranslated(double, double) - Method in class pipe.gui.widgets.GraphPanel
getURI() - Method in class pipe.dataLayer.DataLayer
  Return a URI for the PNML file for the Petri-Net
getUniqueId() - Method in class pipe.dataLayer.Token
  returns a unique id for an arc of the form to_n
getUrtaPath() - Method in class pipe.modules.dnamaca.Dnamaca
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.
getVanishingAndTangible(DataLayer, StateList, StateList, StateList) - Method in class pipe.modules.gspn.GSPN
  This function takes a reachability set and splits it into subsets of tangible and vanishing states
getVanishingStateThroughput(DataLayer, StateList, int, Matrix) - Method in class pipe.modules.gspn.GSPN
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
getX1() - Method in class pipe.dataLayer.Cubic
getX2() - Method in class pipe.dataLayer.Cubic
getXPosition() - Method in class pipe.dataLayer.NameLabel
getYPosition() - Method in class pipe.dataLayer.NameLabel
go() - Method in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
graph - Variable in class pipe.gui.widgets.GraphPanelPane
gridBagLayout1 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
gridColor - Static variable in class pipe.gui.Grid
gridCount - Static variable in class pipe.gui.Grid
gridDisplay - Static variable in class pipe.gui.Grid
gridHeight - Static variable in class pipe.gui.Grid
gridSpacing - Static variable in class pipe.gui.Grid
gridWidth - Static variable in class pipe.gui.Grid
guiDialog - Variable in class pipe.modules.dnamaca.Dnamaca

## H

HelpBox - class pipe.gui.HelpBox.
HelpBox(String, String, String, String) - Constructor for class pipe.gui.HelpBox
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.
hasTimed() - Method in class pipe.modules.dnamaca.Dnamaca
hasTimedTransitions(DataLayer) - Method in class pipe.modules.gspn.GSPN
  See if the supplied net has any timed transitions.
head - Variable in class pipe.gui.ArrowHead
hidePoints() - Method in class pipe.dataLayer.ArcPath
highlightEnabledTransitions() - Method in class pipe.gui.Animator
highlighted - Variable in class pipe.dataLayer.Transition
history - Variable in class pipe.gui.HelpBox
hyperlinkUpdate(HyperlinkEvent) - Method in class pipe.gui.HelpBox
hyperlinkUpdate(HyperlinkEvent) - Method in class pipe.gui.widgets.ResultsHTMLPane

## I

IMMTRANS - Static variable in interface pipe.gui.Constants
IncidenceMatrix - Variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
InsertOmegas() - Method in class pipe.dataLayer.calculations.myNode
InvariantAnalysis - class pipe.modules.invariantAnalysis.InvariantAnalysis.
InvariantAnalysis() - Constructor for class pipe.modules.invariantAnalysis.InvariantAnalysis
InvariantDialog - class pipe.modules.predatorInvariantAnalysis.InvariantDialog.
  Title: Description: Copyright: Copyright (c) 2001 Company:
InvariantDialog(String, String, String, String) - Constructor for class pipe.modules.predatorInvariantAnalysis.InvariantDialog
InvariantDialog(Frame, String, boolean) - Constructor for class pipe.modules.predatorInvariantAnalysis.InvariantDialog
InvariantDialog() - Constructor for class pipe.modules.predatorInvariantAnalysis.InvariantDialog
InvariantXmlFileReader - class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader.
InvariantXmlFileReader(Analysis) - Constructor for class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
id - Variable in class pipe.dataLayer.NameLabel
id - Variable in class pipe.dataLayer.PetriNetObject
  Id
id - Variable in class pipe.dataLayer.calculations.Marking
identity(int, int) - Static method in class pipe.dataLayer.PNMatrix
  Generate identity matrix]
identityMatrix(int[][]) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
ignoreSelection - Static variable in class pipe.dataLayer.PetriNetObject
ignoreSelection(boolean) - Static method in class pipe.dataLayer.PetriNetObject
imageFileName - Variable in class pipe.gui.GuiFrame.TypeAction
imgPath - Static variable in class pipe.gui.CreateGui
importModule(File) - Static method in class pipe.gui.ModuleLoader
incCount() - Method in class pipe.dataLayer.Token
  Methods used to manipulate the transition count
incidenceMatrix - Variable in class pipe.dataLayer.DataLayer
  Incidence Matrix
increment() - Static method in class pipe.gui.Grid
init() - Static method in class pipe.gui.CreateGui
initExit() - Method in class pipe.gui.GuiFrame
initStyles() - Method in class pipe.gui.AnimationHistory
initText - Variable in class pipe.gui.AnimationHistory
initial() - Method in class pipe.modules.dnamaca.Dnamaca
initialMarking - Variable in class pipe.dataLayer.Place
  Initial Marking
initialMarkupMatrix - Variable in class pipe.dataLayer.DataLayer
  Initial Markup Matrix
initialiseArray(int[], int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
initialiseC(int[][]) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
initialiseExtend() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
initialiseTranspose() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
initialiseZero(int[][]) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
initializeMatrixes() - Method in class pipe.dataLayer.DataLayer
  Initialize Arrays
inscriptionFlag - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
installedModules - Variable in class pipe.gui.ModuleManager
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
invariantDialog - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
isCovered() - Method in class pipe.dataLayer.PNMatrix
  Find if a matrix of invariants is covered.
isDeleteable() - Method in class pipe.dataLayer.ArcPathPoint
isDraggable() - Method in class pipe.dataLayer.PetriNetObject
isDragging - Variable in class pipe.dataLayer.PlaceTransitionObject
  Used in the mouse events to control dragging
isDragging - Variable in class pipe.gui.PetriNetObjectHandler
isEFCGSPN(DataLayer) - Method in class pipe.modules.gspn.GSPN
  Qualitative analysis - see if the supplied GSPN is an EFC-GSPN.
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
isModule(Class) - Static method in class pipe.gui.ModuleLoader
isPointSelected(int) - Method in class pipe.dataLayer.ArcPath
isPressed - Variable in class pipe.dataLayer.AnnotationNote.ResizePoint
isSelectable() - Method in class pipe.dataLayer.PetriNetObject
isSelected() - Method in class pipe.dataLayer.PetriNetObject
isSelected() - Method in class pipe.gui.GuiAction
isSelecting - Variable in class pipe.gui.SelectionObject
isShowingBorder() - Method in class pipe.dataLayer.AnnotationNote
isSubset(int[], int[]) - Static method in class pipe.modules.classification.Classification
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

jButton1 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jLabel1 - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
jLabel1 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jLabel2 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jLabel3 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jLabel4 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jLabel5 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jScrollPane1 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jScrollPane2 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jScrollPane3 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jScrollPane4 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jbInit() - Method in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
jcbCumulative - Variable in class pipe.modules.dnamaca.Dnamaca
jtfCycles - Variable in class pipe.modules.simulation.Simulation
jtfFirings - Variable in class pipe.modules.simulation.Simulation
jtfSourceCondition - Variable in class pipe.modules.dnamaca.Dnamaca
jtfTStart - Variable in class pipe.modules.dnamaca.Dnamaca
jtfTStep - Variable in class pipe.modules.dnamaca.Dnamaca
jtfTStop - Variable in class pipe.modules.dnamaca.Dnamaca
jtfTargetCondition - Variable in class pipe.modules.dnamaca.Dnamaca
justSelected - Static variable in class pipe.gui.PetriNetObjectHandler

## K

keyHandler - Variable in class pipe.gui.PlaceTransitionObjectHandler
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

LEFT - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
LOWEST_LAYER_OFFSET - Static variable in interface pipe.gui.Constants
LabelAction - class pipe.gui.LabelAction.
  Action object that can be used to effect labelling a component.
LabelAction(Container, Component) - Constructor for class pipe.gui.LabelAction
label - Variable in class pipe.gui.EditTokenAction
label - Variable in class pipe.gui.EditWeightAction
label - Variable in class pipe.gui.LabelAction
label - Variable in class pipe.gui.StatusBar
label - Variable in class pipe.gui.widgets.PetriNetChooserPanel
labelsArray - Variable in class pipe.dataLayer.DataLayer
  ArrayList for net-level label objects (as opposed to element-level labels).
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
lengthOfTask - Variable in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
linearCombToNewColumn(int, int, int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
linearCombination(int, int, int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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[].
list - Variable in class pipe.dataLayer.calculations.StateList
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
loadNodeString - Variable in class pipe.gui.ModuleManager
loadPNML(String) - Method in class pipe.dataLayer.DataLayer
  Load PNML file
load_modules - Variable in class pipe.gui.ModuleManager

## M

MODULE_NAME - Static variable in class pipe.modules.classification.Classification
MODULE_NAME - Static variable in class pipe.modules.comparison.Comparison
MODULE_NAME - Static variable in class pipe.modules.dnamaca.Dnamaca
MODULE_NAME - Static variable in class pipe.modules.gspn.GSPN
MODULE_NAME - Static variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
MODULE_NAME - Static variable in class pipe.modules.matrixes.Matrixes
MODULE_NAME - Static variable in class pipe.modules.predatorInvariantAnalysis.PredatorInvariantAnalysis
MODULE_NAME - Static variable in class pipe.modules.simulation.Simulation
MODULE_NAME - Static variable in class pipe.modules.stateSpace.StateSpace
Marking - class pipe.dataLayer.calculations.Marking.
Marking(int[], String) - Constructor for class pipe.dataLayer.calculations.Marking
Markup - Variable in class pipe.dataLayer.calculations.myNode
MarkupCompare(int[]) - Method in class pipe.dataLayer.calculations.myNode
Matrixes - class pipe.modules.matrixes.Matrixes.
Matrixes() - Constructor for class pipe.modules.matrixes.Matrixes
Module - interface pipe.modules.Module.
ModuleClassContainer - class pipe.gui.ModuleClassContainer.
  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 pipe.gui.ModuleLoader.
ModuleLoader() - Constructor for class pipe.gui.ModuleLoader
ModuleManager - class pipe.gui.ModuleManager.
  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.RemoveModuleAction - class pipe.gui.ModuleManager.RemoveModuleAction.
  Action object that can be used to remove a module from the ModuleTree
ModuleManager.RemoveModuleAction(TreePath) - Constructor for class pipe.gui.ModuleManager.RemoveModuleAction
ModuleManager.TreeHandler - class pipe.gui.ModuleManager.TreeHandler.
ModuleManager.TreeHandler() - Constructor for class pipe.gui.ModuleManager.TreeHandler
ModuleMethod - class pipe.gui.ModuleMethod.
  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
m - Variable in class pipe.dataLayer.PNMatrix
  Row and column dimensions.
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 - Variable in class pipe.dataLayer.calculations.Marking
markingFlag - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
markingOffsetX - Variable in class pipe.dataLayer.Place
  Initial Marking X-axis Offset
markingOffsetY - Variable in class pipe.dataLayer.Place
  Initial Marking Y-axis Offset
markupHistoryMatrix - Variable in class pipe.dataLayer.DataLayer
  Markup Storage Array
markupMatrixAnimationStorage - Variable in class pipe.dataLayer.DataLayer
  Markup Matrix Storage used during animation
markupStore - Variable in class pipe.dataLayer.DataLayer
  Markup Matrix Storage
menuBar - Variable in class pipe.gui.GuiFrame
methods - Variable in class pipe.gui.ModuleClassContainer
minus(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  C = A - B
minusEquals(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  A = A - B
modClass - Variable in class pipe.gui.ModuleMethod
modFile - Variable in class pipe.modules.dnamaca.Dnamaca
modMeth - Variable in class pipe.gui.ModuleMethod
modString - Variable in class pipe.modules.dnamaca.Dnamaca
mode - Variable in class pipe.gui.GuiFrame
model() - Method in class pipe.modules.dnamaca.Dnamaca
modify(double, double, double, double) - Method in class pipe.dataLayer.Token
  Modifies start and end X and Y coords - does nothing.
moduleTree - Variable in class pipe.gui.ModuleManager
modulus1_1b(int[], int[]) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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.dataLayer.PlaceTransitionObject
  Implemented the moving of the objects - now done in the handler
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.GuiView.MouseHandler
mouseMoved(MouseEvent) - Method in class pipe.gui.SelectionObject
mousePressed(MouseEvent) - Method in class pipe.dataLayer.AnnotationNote.ResizePointHandler
mousePressed(MouseEvent) - Method in class pipe.dataLayer.PlaceTransitionObject
  Event handler for when the user presses down on the mouse, this is used in conjunction with mouseDragged and mouseReleased to implement the moving action
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.GuiView.MouseHandler
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.dataLayer.PlaceTransitionObject
  Implemented the moving action - now moved into the handler
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.PlaceTransitionObjectHandler
mouseReleased(MouseEvent) - Method in class pipe.gui.SelectionObject
multiplyRow(Matrix, int, double) - Method in class pipe.modules.gspn.GSPN
myAnnotation - Variable in class pipe.dataLayer.AnnotationNote.AnnotationKeyUpdateHandler
myArc - Variable in class pipe.dataLayer.ArcPath
myArc - Variable in class pipe.gui.EditWeightAction
myArcPath - Variable in class pipe.dataLayer.ArcPathPoint
myExtensionDesc - Variable in class pipe.gui.ExtensionFilter
myExtensionString - Variable in class pipe.gui.ExtensionFilter
myNode - class pipe.dataLayer.calculations.myNode.
myNode(int[], myTree, int) - Constructor for class pipe.dataLayer.calculations.myNode
myNode(int[], myNode, myTree, int) - Constructor for class pipe.dataLayer.calculations.myNode
myNote - Variable in class pipe.dataLayer.AnnotationNote.ResizePoint
myObject - Variable in class pipe.gui.PetriNetObjectHandler
myPath - Variable in class pipe.dataLayer.Arc
myPoint - Variable in class pipe.dataLayer.AnnotationNote.ResizePointHandler
myTree - class pipe.dataLayer.calculations.myTree.
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

NOTE_DISABLED_COLOUR - Static variable in interface pipe.gui.Constants
NOTE_EDITING_COLOUR - Static variable in interface pipe.gui.Constants
NameLabel - class pipe.dataLayer.NameLabel.
  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
n - Variable in class pipe.dataLayer.PNMatrix
  Row and column dimensions.
name - Variable in class pipe.gui.ModuleMethod
netChanged - Variable in class pipe.gui.GuiView
newNameCounter - Variable in class pipe.gui.GuiFrame
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
nonZero() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
nonZeroIndices() - Method in class pipe.dataLayer.PNMatrix
  Form a matrix with columns the row indices of non-zero elements.
note - Variable in class pipe.dataLayer.AnnotationNote
noteRect - Variable in class pipe.dataLayer.AnnotationNote
nullModel(int) - Static method in class pipe.gui.CreateGui
nullView(int) - Static method in class pipe.gui.CreateGui
numberSequences - Variable in class pipe.gui.Animator
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
openAction - Variable in class pipe.gui.GuiFrame
openFile() - Method in class pipe.gui.widgets.FileBrowser
outlineTransition() - Method in class pipe.dataLayer.Transition
output(int) - Method in class pipe.dataLayer.calculations.StateList

## P

PInvariants - Variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
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
PNG - Static variable in class pipe.gui.Export
PNMatrix - class pipe.dataLayer.PNMatrix.
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
POSTSCRIPT - Static variable in class pipe.gui.Export
PRINTER - Static variable in class pipe.gui.Export
PROPERTY_FILE_DESC - Static variable in interface pipe.gui.Constants
PROPERTY_FILE_EXTENSION - Static variable in interface pipe.gui.Constants
PetriNetChooserPanel - class pipe.gui.widgets.PetriNetChooserPanel.
  Makes a filebrowser panel which is a JPanel containing the required stuff
PetriNetChooserPanel(String, DataLayer) - Constructor for class pipe.gui.widgets.PetriNetChooserPanel
PetriNetObject - class pipe.dataLayer.PetriNetObject.
  PetriNetObject - Petri-Net Object Class - Abstract
PetriNetObject(String) - Constructor for class pipe.dataLayer.PetriNetObject
  Create PetriNetObject
PetriNetObject() - Constructor for class pipe.dataLayer.PetriNetObject
  Create PetriNetObject
PetriNetObjectHandler - class pipe.gui.PetriNetObjectHandler.
  Class used to implement methods corresponding to mouse events on all PetriNetObjects.
PetriNetObjectHandler(Container, PetriNetObject) - Constructor for class pipe.gui.PetriNetObjectHandler
Place - class pipe.dataLayer.Place.
  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
PlaceHandler - class pipe.gui.PlaceHandler.
  Class used to implement methods corresponding to mouse events on places.
PlaceHandler(Container, Place) - Constructor for class pipe.gui.PlaceHandler
PlaceTransitionObject - class pipe.dataLayer.PlaceTransitionObject.
  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 pipe.gui.PlaceTransitionObjectHandler.
  Class used to implement methods corresponding to mouse events on places.
PlaceTransitionObjectHandler(Container, PlaceTransitionObject) - Constructor for class pipe.gui.PlaceTransitionObjectHandler
PredatorInvariantAnalysis - class pipe.modules.predatorInvariantAnalysis.PredatorInvariantAnalysis.
PredatorInvariantAnalysis() - Constructor for class pipe.modules.predatorInvariantAnalysis.PredatorInvariantAnalysis
pCovered - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
pEquTextArea - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
pInvarTextArea - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
pMinusCombine(int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
pPlusCombine(int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
paintComponent(Graphics) - Method in class pipe.dataLayer.AnnotationNote.ResizePoint
paintComponent(Graphics) - Method in class pipe.dataLayer.AnnotationNote
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
  Implemented in subclasses as involves some tailoring according to the shape
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
panel1 - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
parent - Variable in class pipe.dataLayer.calculations.myNode
parent - Variable in class pipe.gui.ModuleManager
passageTime() - Method in class pipe.modules.dnamaca.Dnamaca
path - Variable in class pipe.dataLayer.ArcPath
pathPoints - Variable in class pipe.dataLayer.ArcPath
pathToDeadlock - Variable in class pipe.dataLayer.calculations.myTree
performance() - Method in class pipe.modules.dnamaca.Dnamaca
phase2() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
phase2(boolean) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
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.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.invariantAnalysis - package pipe.modules.invariantAnalysis
pipe.modules.matrixes - package pipe.modules.matrixes
pipe.modules.predatorInvariantAnalysis - package pipe.modules.predatorInvariantAnalysis
pipe.modules.simulation - package pipe.modules.simulation
pipe.modules.stateSpace - package pipe.modules.stateSpace
place - Static variable in class pipe.dataLayer.Place
  Ellipse2D.Double place
placeAction - Variable in class pipe.gui.GuiFrame
placeMarkings - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
placeNames - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
placeNum - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
places - Variable in class pipe.modules.dnamaca.Dnamaca
placesArray - Variable in class pipe.dataLayer.DataLayer
  List containing all the Place objects in the Petri-Net
plus(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  C = A + B
plusEquals(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  A = A + B
pnName - Variable in class pipe.dataLayer.PetriNetObject
  Name Label for displaying name
pnObject - Variable in class pipe.gui.GuiView.MouseHandler
pnmlName - Variable in class pipe.dataLayer.DataLayer
  PNML File Name
pnmldata - Variable in class pipe.modules.dnamaca.Dnamaca
point - Static variable in class pipe.dataLayer.Arc
point - Variable in class pipe.dataLayer.ArcPathPoint
pointLock - Variable in class pipe.dataLayer.ArcPath
pointSelection - Variable in class pipe.dataLayer.ArcPath
pointTo - Variable in class pipe.gui.ArrowHead
pointType - Variable in class pipe.dataLayer.ArcPathPoint
position - Variable in class pipe.dataLayer.DataLayer
  Markup Matrix Storage Position
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
prev_mode - Variable in class pipe.gui.GuiFrame
previousInstance - Variable in class pipe.dataLayer.calculations.myNode
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() - Method in class pipe.dataLayer.calculations.StateList
print(int[]) - Method in class pipe.dataLayer.calculations.StateList
print(boolean[]) - Method in class pipe.dataLayer.calculations.myNode
print(Graphics, PageFormat, int) - Method in class pipe.gui.GuiView
print(boolean[]) - Method in class pipe.modules.gspn.GSPN
print2DArray(int[][]) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
print2DArray(int[][], int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
printAction - Variable in class pipe.gui.GuiFrame
printArray(int[]) - Method in class pipe.dataLayer.PNMatrix
  Used to display intermediate results for checking
printMarking(int[]) - Method in class pipe.modules.gspn.GSPN
printMatrix(double[][]) - Method in class pipe.modules.gspn.GSPN
printMatrix(int[][]) - Method in class pipe.modules.gspn.GSPN
printString(int, int) - Method in class pipe.dataLayer.PNMatrix
  Print the matrix to a string.
probMarkingAToMarkingB(DataLayer, int[], int[]) - Method in class pipe.modules.gspn.GSPN
  Calculate the probability of changing from one marking to another Works out the intersection of transitions enabled to fire at a particular marking, transitions that can be reached from a particular marking and the intersection of the two.
probabilityMatrix(DataLayer, StateList, StateList) - Method in class pipe.modules.gspn.GSPN
processSelection(MouseEvent) - Method in class pipe.gui.SelectionObject
processWindowEvent(WindowEvent) - Method in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
progressMonitor - Variable in class pipe.modules.dnamaca.Dnamaca.DnamacaRun
propertyChange(PropertyChangeEvent) - Method in class pipe.gui.GuiFrame.ToggleButton
proximityContains(Point2D) - Method in class pipe.dataLayer.ArcPath
proximityIntersects(Rectangle2D) - Method in class pipe.dataLayer.ArcPath
proximityPlace - Static variable in class pipe.dataLayer.Place
proximityShape - Variable in class pipe.dataLayer.ArcPath
proximityStroke - Static variable in class pipe.dataLayer.ArcPath
proximityTransition - Variable in class pipe.dataLayer.Transition
purgePathPoints() - Method in class pipe.dataLayer.ArcPath

## R

RANDOM - Static variable in interface pipe.gui.Constants
RESERVED_BORDER - Static variable in interface pipe.gui.Constants
RESIZE_POINT_DOWN_COLOUR - Static variable in interface pipe.gui.Constants
RIGHT - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
ROTATE_ANGLE - Static variable in class pipe.gui.TransitionHandler
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.
Repeated_Node - Variable in class pipe.dataLayer.calculations.myNode
ResultsHTMLPane - class pipe.gui.widgets.ResultsHTMLPane.
ResultsHTMLPane() - Constructor for class pipe.gui.widgets.ResultsHTMLPane
RotateTransitionAction - class pipe.gui.RotateTransitionAction.
RotateTransitionAction(Container, Transition, int, String) - Constructor for class pipe.gui.RotateTransitionAction
randomAction - Variable in class pipe.gui.GuiFrame
randomAnimateAction - Variable in class pipe.gui.GuiFrame
randomNumber - Static variable in class pipe.dataLayer.DataLayer
rate - Variable in class pipe.dataLayer.Transition
  The transition rate
rateMatrix(DataLayer, StateList, StateList) - Method in class pipe.modules.gspn.GSPN
reduce(int[]) - Static method in class pipe.modules.classification.Classification
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.
regular - Variable in class pipe.gui.AnimationHistory
removeAnimationHistory() - Static method in class pipe.gui.CreateGui
removeArc(String) - Method in class pipe.dataLayer.DataLayer
  Remove first Arc that has an id equal to idInput
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
removeNode - Variable in class pipe.gui.ModuleManager.RemoveModuleAction
removePetriNetObject(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Removes the specified object from the appropriate ArrayList of objects.
removePlace(String) - Method in class pipe.dataLayer.DataLayer
  Remove first Place that has an id equal to idInput
removeTab(int) - Static method in class pipe.gui.CreateGui
removeToArc(Arc) - Method in class pipe.dataLayer.PlaceTransitionObject
removeTransition(String) - Method in class pipe.dataLayer.DataLayer
  Remove first Transition that has an id equal to idInput
renderIncidenceMatrix(DataLayer, int[][]) - Method in class pipe.modules.matrixes.Matrixes
renderLists(double[], StateList) - Method in class pipe.modules.gspn.GSPN
renderMarkingMatrices(DataLayer) - Method in class pipe.modules.matrixes.Matrixes
renderProbabilities(double[][], StateList, StateList) - Method in class pipe.modules.gspn.GSPN
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
renderTransitionStates(DataLayer) - Method in class pipe.modules.matrixes.Matrixes
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.
resetArray(int[]) - Method in class pipe.modules.invariantAnalysis.InvariantAnalysis
resetEnabledTransitions() - Method in class pipe.dataLayer.DataLayer
restoreInitialMarking() - Method in class pipe.dataLayer.DataLayer
  Restores Initial Markup Matrix to current Petri-Net Markup
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
resultText - Variable in class pipe.modules.dnamaca.Dnamaca
results - Variable in class pipe.gui.widgets.ResultsHTMLPane
results - Variable in class pipe.modules.classification.Classification
results - Variable in class pipe.modules.comparison.Comparison
results - Variable in class pipe.modules.gspn.GSPN
results - Variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
results - Variable in class pipe.modules.matrixes.Matrixes
results - Variable in class pipe.modules.simulation.Simulation
results - Variable in class pipe.modules.stateSpace.StateSpace
resultsButton - Variable in class pipe.modules.dnamaca.Dnamaca
resultsGraph - Variable in class pipe.modules.dnamaca.Dnamaca
resultsX - Variable in class pipe.modules.dnamaca.Dnamaca
resultsY - Variable in class pipe.modules.dnamaca.Dnamaca
returnClass() - Method in class pipe.gui.ModuleClassContainer
  Returns the class object that the ModuleClass encapsulates
returnTransitions() - Method in class pipe.dataLayer.DataLayer
root - Variable in class pipe.dataLayer.calculations.myTree
rootThreeOverTwo - Static variable in class pipe.dataLayer.Transition
rotate(int) - Method in class pipe.dataLayer.Transition
  Rotates the Transition through the specified angle around the midpoint
rowWithNegativeElement() - Method in class pipe.dataLayer.PNMatrix
  Find the first row with a negative element in a matrix.
rowWithNegativeElementB() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
rowWithNegativeElementBNumber() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
run(DataLayer) - Method in interface pipe.modules.Module
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.GSPN
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 class pipe.modules.predatorInvariantAnalysis.PredatorInvariantAnalysis
run(DataLayer) - Method in class pipe.modules.simulation.Simulation
run(DataLayer) - Method in class pipe.modules.stateSpace.StateSpace
runAnalysis - Variable in class pipe.modules.gspn.GSPN
  Analyse button click handler
runDnamacaAction - Variable in class pipe.modules.dnamaca.Dnamaca
runFileReader() - Method in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
runModule() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
runResultsAction - Variable in class pipe.modules.dnamaca.Dnamaca

## S

SELECT - Static variable in interface pipe.gui.Constants
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
SIZE - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
SIZE - Static variable in class pipe.dataLayer.ArcPathPoint
SIZE_OFFSET - Static variable in class pipe.dataLayer.ArcPathPoint
SOURCE - Static variable in class pipe.dataLayer.Transition.ArcAngleCompare
START - Static variable in interface pipe.gui.Constants
STEPBACKWARD - Static variable in interface pipe.gui.Constants
STEPFORWARD - Static variable in interface pipe.gui.Constants
STOP - Static variable in interface pipe.gui.Constants
STRAIGHT - Static variable in class pipe.dataLayer.ArcPathPoint
SaveHandler - Variable in class pipe.gui.widgets.ResultsHTMLPane
SelectionObject - class pipe.gui.SelectionObject.
SelectionObject(GuiView) - Constructor for class pipe.gui.SelectionObject
SelectionObject() - Constructor for class pipe.gui.SelectionObject
Simulation - class pipe.modules.simulation.Simulation.
Simulation() - Constructor for class pipe.modules.simulation.Simulation
StateList - class pipe.dataLayer.calculations.StateList.
StateList() - Constructor for class pipe.dataLayer.calculations.StateList
StateSpace - class pipe.modules.stateSpace.StateSpace.
StateSpace() - Constructor for class pipe.modules.stateSpace.StateSpace
StatusBar - class pipe.gui.StatusBar.
StatusBar() - Constructor for class pipe.gui.StatusBar
SwingWorker - class pipe.modules.dnamaca.SwingWorker.
  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.
SwingWorker.ThreadVar - class pipe.modules.dnamaca.SwingWorker.ThreadVar.
  Class to maintain reference to current worker thread under separate synchronization control.
SwingWorker.ThreadVar(Thread) - Constructor for class pipe.modules.dnamaca.SwingWorker.ThreadVar
saveAction - Variable in class pipe.gui.GuiFrame
saveAsAction - Variable in class pipe.gui.GuiFrame
saveButtonClick - Variable in class pipe.gui.widgets.GraphPanelPane
saveFile() - Method in class pipe.gui.widgets.FileBrowser
saveNet(File) - Method in class pipe.gui.GuiFrame
saveOperation(boolean) - Method in class pipe.gui.GuiFrame
savePNML(String) - Method in class pipe.dataLayer.DataLayer
  Save the Petri-Net
savePNML(File) - Method in class pipe.dataLayer.DataLayer
  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
selectAction - Variable in class pipe.gui.GuiFrame
selectPoint(int) - Method in class pipe.dataLayer.ArcPath
selectable - Variable in class pipe.dataLayer.PetriNetObject
selected - Variable in class pipe.dataLayer.PetriNetObject
selected - Variable in class pipe.gui.DeletePetriNetObjectAction
selected - Variable in class pipe.gui.EditAnnotationAction
selected - Variable in class pipe.gui.EditAnnotationBorderAction
selected - Variable in class pipe.gui.EditRateAction
selected - Variable in class pipe.gui.EditTimedAction
selected - Variable in class pipe.gui.EditTokenAction
selected - Variable in class pipe.gui.LabelAction
selected - Variable in class pipe.gui.RotateTransitionAction
selected - Variable in class pipe.gui.ToggleArcPointAction
selectedFileName - Variable in class pipe.gui.GuiFrame.TypeAction
selection - Variable in class pipe.gui.GuiView
selectionBorderColour - Variable in class pipe.dataLayer.PetriNetObject
selectionColor - Static variable in class pipe.gui.SelectionObject
selectionColorOutline - Static variable in class pipe.gui.SelectionObject
selectionInit - Variable in class pipe.gui.SelectionObject
selectionRectangle - Variable in class pipe.gui.SelectionObject
set(int, int, int) - Method in class pipe.dataLayer.PNMatrix
  Set a single element.
setAnimationMode(boolean) - Method in class pipe.gui.GuiFrame
setArcConnectionMap() - Method in class pipe.dataLayer.DataLayer
  Function populates the arcsMap hashtable enabling easier cross referencing of places, transitions and the arcs connected to them.
setBackwardsIncidenceMatrix(int[][]) - Method in class pipe.dataLayer.DataLayer
  Set the Backward Incidence Matrix
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
setControlPoints() - Method in class pipe.dataLayer.ArcPath
setCurrentMarking(int) - Method in class pipe.dataLayer.Place
  Set current marking
setCurveControlPoints() - Method in class pipe.dataLayer.ArcPath
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
setEnabledTransitionsBackwards() - Method in class pipe.dataLayer.DataLayer
  Determines whether all transitions are enabled and sets the correct value of the enabled boolean
setEndControlPoints() - Method in class pipe.dataLayer.ArcPath
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
setFowardIncidenceMatrix(int[][]) - Method in class pipe.dataLayer.DataLayer
  Set the Foward Incidence Matrix
setGridSpacing(double) - Static method in class pipe.gui.Grid
setID(String) - Method in class pipe.dataLayer.AnnotationNote
setID(String) - Method in class pipe.dataLayer.NameLabel
setID(String) - Method in class pipe.dataLayer.calculations.Marking
setId(String) - Method in class pipe.dataLayer.Arc
  Set id
setId(String) - Method in class pipe.dataLayer.PetriNetObject
  Set id
setId(String) - Method in class pipe.dataLayer.PlaceTransitionObject
  Set id
setIncidenceMatrix(int[][]) - Method in class pipe.dataLayer.DataLayer
  Set the Incidence Matrix
setInitalMarkupMatrix(int[][]) - Method in class pipe.dataLayer.DataLayer
  Set the Initial Markup Matrix
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
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
setPPlusAndPMinus(int[][], int, int[], int[]) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
setPage(String) - Method in class pipe.gui.HelpBox
  Sets the page to the given non-absolute filename assumed to be in the Docs directory
setPage(URL, boolean) - Method in class pipe.gui.HelpBox
setPathToTransitionAngle(int) - Method in class pipe.dataLayer.Arc
setPetriNetObjectArrayList(PetriNetObject) - Method in class pipe.dataLayer.DataLayer
  Sets an internal ArrayList according to the class of the object passed in.
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.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
setStraightControlPoints() - Method in class pipe.dataLayer.ArcPath
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
setUpVariables() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
setValue(Object) - Method in class pipe.modules.dnamaca.SwingWorker
  Set the value produced by worker thread
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
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
shape - Variable in class pipe.dataLayer.AnnotationNote.ResizePoint
shape - Variable in class pipe.dataLayer.ArcPath
shape - Static variable in class pipe.dataLayer.ArcPathPoint
shiftDown - Static variable in class pipe.gui.ArcKeyboardEventHandler
shiftDown - Variable in class pipe.gui.GuiView
showBorder(boolean) - Method in class pipe.dataLayer.AnnotationNote
showControlPoints - Variable in class pipe.dataLayer.ArcPath
showPoints() - Method in class pipe.dataLayer.ArcPath
showPopupMenu(MouseEvent) - Method in class pipe.gui.ModuleManager.TreeHandler
sign(int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
simpleNet(DataLayer) - Method in class pipe.modules.classification.Classification
  Simple net (SPL-net) detection
simulate(DataLayer, int, int) - Method in class pipe.modules.simulation.Simulation
simulateButtonClick - Variable in class pipe.modules.simulation.Simulation
  Simulate button click handler
size() - Method in class pipe.dataLayer.calculations.StateList
someArc - Static variable in class pipe.dataLayer.PlaceTransitionObject
source - Variable in class pipe.dataLayer.Arc
  references to the objects this arc connects
sourceFilePanel - Variable in class pipe.modules.classification.Classification
sourceFilePanel - Variable in class pipe.modules.comparison.Comparison
sourceFilePanel - Variable in class pipe.modules.gspn.GSPN
sourceFilePanel - Variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
sourceFilePanel - Variable in class pipe.modules.matrixes.Matrixes
sourceFilePanel - Variable in class pipe.modules.simulation.Simulation
sourceFilePanel - Variable in class pipe.modules.stateSpace.StateSpace
sourceOrTarget() - Method in class pipe.dataLayer.Transition.ArcAngleCompare
start() - Method in class pipe.modules.dnamaca.SwingWorker
  Start the worker thread.
startAction - Variable in class pipe.gui.GuiFrame
startDocument() - Method in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
startElement(String, String, String, Attributes) - Method in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
startRandomFiring() - Method in class pipe.gui.Animator
startX - Variable in class pipe.dataLayer.AnnotationNote.ResizePointHandler
startY - Variable in class pipe.dataLayer.AnnotationNote.ResizePointHandler
statMessage - Variable in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
stateMachine(DataLayer) - Method in class pipe.modules.classification.Classification
  State machine detection
stateVector() - Method in class pipe.modules.dnamaca.Dnamaca
statusBar - Variable in class pipe.gui.GuiFrame
stepBack() - Method in class pipe.gui.Animator
stepBackwards() - Method in class pipe.gui.AnimationHistory
stepForward() - Method in class pipe.gui.AnimationHistory
stepForward() - Method in class pipe.gui.Animator
stepbackwardAction - Variable in class pipe.gui.GuiFrame
stepforwardAction - Variable in class pipe.gui.GuiFrame
stop() - Method in class pipe.modules.dnamaca.Dnamaca.DnamacaRun.ExternalTask
stopRandomFiring() - Method in class pipe.gui.Animator
storeInitialMarking() - Method in class pipe.dataLayer.DataLayer
  Stores Initial Markup Matrix from current Petri-Net Markup
storeModel() - Method in class pipe.gui.Animator
storeState() - Method in class pipe.dataLayer.DataLayer
  Stores Current Markup
stroke - Static variable in class pipe.dataLayer.ArcPath
subnetArcSource - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
subnetArcTarget - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
subnetArcWeight - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
subnetFlag - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
subnetLevel - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
substituteColumns1(int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
substituteColumns2(int, int) - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
subtractRow(Matrix, int, int) - Method in class pipe.modules.gspn.GSPN
swapRows(Matrix, int, int) - Method in class pipe.modules.gspn.GSPN

## T

TARGET - Static variable in class pipe.dataLayer.Transition.ArcAngleCompare
TIMEDTRANS - Static variable in interface pipe.gui.Constants
TInvariants - Variable in class pipe.modules.invariantAnalysis.InvariantAnalysis
TOP - Static variable in class pipe.dataLayer.AnnotationNote.ResizePoint
TRANSITION_HEIGHT - Static variable in class pipe.dataLayer.Transition
  Place Width
TRANSITION_WIDTH - Static variable in class pipe.dataLayer.Transition
  Place Width
ToggleArcPointAction - class pipe.gui.ToggleArcPointAction.
ToggleArcPointAction(ArcPathPoint) - Constructor for class pipe.gui.ToggleArcPointAction
Token - class pipe.dataLayer.Token.
  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
Transition - class pipe.dataLayer.Transition.
  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.ArcAngleCompare - class pipe.dataLayer.Transition.ArcAngleCompare.
Transition.ArcAngleCompare(Arc, Transition) - Constructor for class pipe.dataLayer.Transition.ArcAngleCompare
TransitionEnabled(int) - Method in class pipe.dataLayer.calculations.myNode
TransitionHandler - class pipe.gui.TransitionHandler.
  Class used to implement methods corresponding to mouse events on transitions.
TransitionHandler(Container, Transition) - Constructor for class pipe.gui.TransitionHandler
TreeTooBigException - exception pipe.dataLayer.calculations.TreeTooBigException.
TreeTooBigException() - Constructor for class pipe.dataLayer.calculations.TreeTooBigException
tCovered - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
tHeight - Static variable in class pipe.dataLayer.Place
  Token Height
tInvarTextArea - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantDialog
tWidth - Static variable in class pipe.dataLayer.Place
  Token Width
tabs - Static variable in class pipe.gui.CreateGui
target - Variable in class pipe.dataLayer.Arc
task - Variable in class pipe.modules.dnamaca.Dnamaca.DnamacaRun
tempBounds - Variable in class pipe.gui.SelectionObject
testAlgorithm() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
testEqualConflict(DataLayer) - Method in class pipe.modules.gspn.GSPN
  Test for condition Equal Conflict.
textField - Variable in class pipe.gui.widgets.PetriNetChooserPanel
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
theFileName - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
thisClass - Variable in class pipe.gui.ModuleClassContainer
thread - Variable in class pipe.modules.dnamaca.SwingWorker.ThreadVar
thread - Variable in class pipe.modules.dnamaca.SwingWorker
threadVar - Variable in class pipe.modules.dnamaca.SwingWorker
timed - Variable in class pipe.dataLayer.Transition
  Is this a timed transition or not?
timedtransAction - Variable in class pipe.gui.GuiFrame
timer - Variable in class pipe.gui.Animator
timer - Variable in class pipe.modules.dnamaca.Dnamaca.DnamacaRun
timesEquals(int) - Method in class pipe.dataLayer.PNMatrix
  Multiply a matrix by an int in place, A = s*A
tinvars - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
tinvars() - Method in class pipe.modules.predatorInvariantAnalysis.Analysis
toPNG(JComponent, String) - Static method in class pipe.gui.Export
toPostScript(Object, String) - Static method in class pipe.gui.Export
toPrinter(Object) - Static method in class pipe.gui.Export
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
toggleGrid - Variable in class pipe.gui.GuiFrame
togglePointType(int) - Method in class pipe.dataLayer.ArcPath
togglePointType() - Method in class pipe.dataLayer.ArcPathPoint
token - Variable in class pipe.dataLayer.Token
  Ellipse2D.Double token
tokenAction - Variable in class pipe.gui.GuiFrame
tokenDistribution() - Method in class pipe.modules.dnamaca.Dnamaca
tokensArray - Variable in class pipe.dataLayer.DataLayer
  ArrayList containing all the Token objects in the Petri-Net
tooBig - Variable in class pipe.dataLayer.calculations.myTree
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
tranNum - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
tranTarget - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
transAction - Variable in class pipe.gui.GuiFrame
trans_array - Variable in class pipe.dataLayer.calculations.myNode
transition - Variable in class pipe.dataLayer.Transition.ArcAngleCompare
transition - Variable in class pipe.dataLayer.Transition
  Transition is of Rectangle2D.Double
transitionAngle - Variable in class pipe.dataLayer.ArcPath
transitionMeasures() - Method in class pipe.modules.dnamaca.Dnamaca
transitionNames - Variable in class pipe.modules.predatorInvariantAnalysis.Analysis
transitions - Variable in class pipe.dataLayer.calculations.myTree
transitions - Variable in class pipe.modules.dnamaca.Dnamaca
transitions() - Method in class pipe.modules.dnamaca.Dnamaca
transitionsArray - Variable in class pipe.dataLayer.DataLayer
  ArrayList containing all the Transition objects in the Petri-Net
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.
tree - Variable in class pipe.dataLayer.calculations.myNode
treeModel - Variable in class pipe.gui.ModuleManager
type - Static variable in class pipe.dataLayer.Arc
type - Static variable in class pipe.dataLayer.Place
type - Static variable in class pipe.dataLayer.Transition
typeID - Variable in class pipe.gui.GuiFrame.AnimateAction
typeID - Variable in class pipe.gui.GuiFrame.TypeAction
typeMask - Variable in class pipe.dataLayer.AnnotationNote.ResizePoint

## 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
updateGraph(Graphics2D) - Method in class pipe.gui.widgets.GraphPanel
updateLabelLocation() - Method in class pipe.dataLayer.PlaceTransitionObject
updatePointLocation() - Method in class pipe.dataLayer.ArcPathPoint
updatePointLocations() - Method in class pipe.dataLayer.AnnotationNote
updatePosition() - Method in class pipe.dataLayer.NameLabel
updatePreferredSize() - Method in class pipe.gui.GuiView
updateSize() - Method in class pipe.dataLayer.NameLabel
updateSize(MouseEvent) - Method in class pipe.dataLayer.Token
updateSize(Container) - Static method in class pipe.gui.Grid
updateText() - Method in class pipe.gui.AnimationHistory
  Method reinserts the text highlighting the currentItem
urtaExecutablePath - Variable in class pipe.modules.dnamaca.Dnamaca
urtaStrings - Static variable in class pipe.modules.dnamaca.Dnamaca
useCurrent - Variable in class pipe.gui.widgets.PetriNetChooserPanel
useCurrentClick - Variable in class pipe.gui.widgets.PetriNetChooserPanel
userPath - Static variable in class pipe.gui.CreateGui

## V

value - Variable in class pipe.modules.dnamaca.SwingWorker
valueFlag - Variable in class pipe.modules.predatorInvariantAnalysis.InvariantXmlFileReader
vectorTimes(PNMatrix) - Method in class pipe.dataLayer.PNMatrix
  Multiply a row matrix by a column matrix, A = s*A

## W

weight - Variable in class pipe.dataLayer.Arc
  Current Marking
weightLabel - Variable in class pipe.dataLayer.Arc
weightOffsetX - Variable in class pipe.dataLayer.Arc
  Initial Marking X-axis Offset
weightOffsetY - Variable in class pipe.dataLayer.Arc
  Initial Marking Y-axis Offset
windowClosing(WindowEvent) - Method in class pipe.gui.GuiFrame.WindowHandler

## X

xCoord - Variable in class pipe.dataLayer.NameLabel
xHat(double[], double[]) - Method in class pipe.modules.gspn.GSPN
xMax - Variable in class pipe.gui.widgets.GraphPanel
xMin - Variable in class pipe.gui.widgets.GraphPanel
xValues - Variable in class pipe.gui.widgets.GraphPanel

## Y

yCoord - Variable in class pipe.dataLayer.NameLabel
yMax - Variable in class pipe.gui.widgets.GraphPanel
yMin - Variable in class pipe.gui.widgets.GraphPanel
yValues - Variable in class pipe.gui.widgets.GraphPanel

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