package cell_controllers;
public abstract class CellController { 
  	public CellController(int[] dimensions, boolean random) 
	public Map getData() 
	public void increaseData(String type, Color colour) 
	public void decreaseData(String type, Color colour) 
	public abstract void setUpSpecific(Map<String, int[][]> map);
	public abstract void setUpRandom(Map<String, Double> paramMap);
	public void resize(int dimensions) 
	public void truncate(int dimensions) 
	public abstract Cell getDefaultCell();
	public void switchTorroidal() 
	public void enlarge(int dimensions) 
	public void initializeNeighbors() 
	public abstract void setNextStates();
	public void updateCells() 
	public Color[][] getColors() 
	public abstract Map<String, int[][]> makeCellMap();
	public abstract void writeToXML(String filename) throws WriterException;
}
 
package cell_controllers;
public class FireController extends CellController { 
  	public FireController(int[] dimensions, Map<String, int[][]> map, Map<String, Double> paramMap, boolean random) 
	public void initializeData() 
	public void setUpSpecific(Map<String, int[][]> map) 
	public void setUpRandom(Map<String, Double> paramMap) 
	public void setNextStates() 
	public Cell getDefaultCell() 
	public Map<String, int[][]> makeCellMap() 
	public void writeToXML(String filename) throws WriterException 
}
 
package cell_controllers;
public class LifeCellController extends CellController { 
  	public LifeCellController(int[] dimensions, Map<String, int[][]> map, Map<String, Double> paramMap,
	public void setUpRandom(Map<String, Double> paramMap) 
	public void setUpSpecific(Map<String, int[][]> map) 
	public Cell getDefaultCell() 
	public void setNextStates() 
	public Map<String, int[][]> makeCellMap() 
	public void writeToXML(String filename) throws WriterException 
}
 
package cell_controllers;
public class RPSController extends CellController { 
  	public RPSController(int[] dimensions, Map<String, int[][]> map, Map<String, Double> paramMap, boolean random) 
	public void setUpRandom(Map<String, Double> paramMap) 
	public void setUpSpecific(Map<String, int[][]> map) 
	public Cell getDefaultCell() 
	public void setNextStates() 
	public Map<String, int[][]> makeCellMap() 
	public void writeToXML(String filename) throws WriterException 
}
 
package cell_controllers;
public class SegregationController extends CellController { 
  	public SegregationController(int[] dimensions, Map<String, int[][]> map, Map<String, Double> paramMap, 
	public void setUpSpecific(Map<String, int[][]> map) 
	public void initializeData() 
	public void setUpRandom(Map<String, Double> paramMap) 
	public void setNextStates() 
	public Cell getDefaultCell() 
	public Map<String, int[][]> makeCellMap() 
	public void writeToXML(String filename) throws WriterException 
}
 
package cell_controllers;
public class WatorController extends CellController { 
  	public WatorController(int[] dimensions, Map<String, int[][]> map, Map<String, Double> paramMap, boolean random) 
	public void initializeNeighbors() 
	public Cell retrieveCell(int x, int y) 
	public void setNextStates() 
	public void updateFish(WatorCell fishCell) 
	public void updateShark(WatorCell sharkCell) 
	public Cell getDefaultCell() 
	public WatorCell newSpot(WatorCell animal) 
	public void setUpSpecific(Map<String, int[][]> map) 
	public void setUpRandom(Map<String, Double> paramMap) 
	public Map<String, int[][]> makeCellMap() 
	public void writeToXML(String filename) throws WriterException 
	public void initializeData() 
}
 
package cells;
public class Cell { 
  	public Cell(String state) 
	public void setNextState(String state) 
	public void setState(Color newColour) 
	public void setNextStateDefault() 
	public String getState() 
	public Color getColor() 
	public String[] getNeighborStateNames() 
	public Cell[] getNeighbors() 
	public void addNeighbors(Cell[] neighbors) 
}
 
package cells;
public class GameOfLifeCell extends Cell { 
  	public GameOfLifeCell(String onOrOff) 
	public void setNextState() 
}
 
package cells;
public class RPSCell extends Cell { 
  	public RPSCell() 
	public RPSCell(Color color, String colorString) 
	public void infect(RPSCell neighbour) 
	public boolean edible(RPSCell neighbour) 
	public RPSCell retrieveRandomNeighbour() 
	public void changeTo(Color color, String colorString, int level) 
}
 
package front_end;
public class Graph { 
      public Graph() 
    public void addPoint(String cellType, int step, Integer number, Color color) 
    public void updateGraph(Group root) 
}
 
package front_end;
public class Grid { 
      public Grid(int[] dim, int width, int height, Double edges) 
    public void updateGridColors(Group root, CellController control) 
}
 
package front_end;
public class GUI { 
      public void start(Stage stage) 
}
 
package front_end;
public class Main extends Application{ 
      public void start(Stage primaryStage) 
}
 
package front_end;
public class Simulator { 
      public void startSimulation(Stage stage, Group root) 
    public int getDimensions() 
    public void resize(int newDimensions, Group root) 
    public void manualStep(Group root) 
    public void setFile(File file) throws IllegalArgumentException 
    public void turnOn() 
    public void turnOff() 
    public void speedUp() 
    public void speedDown() 
    public void switchToroidal() 
    public void toXML(String filename) throws WriterException 
}
 
package shapes;
public class HexagonNeighborFinder extends NeighborFinder { 
  	public HexagonNeighborFinder(Cell[][] inputCellGrid, boolean torroidal2) 
	public void initializeNeighbors() 
}
 
package shapes;
public abstract class NeighborFinder { 
  	public NeighborFinder(Cell[][] inputCellGrid, Boolean torroidal2) 
	public abstract void initializeNeighbors();
	public Cell[][] getCellGrid()
	public Cell retrieveCell(int x, int y) 
}
 
package shapes;
public class SquareNeighborFinder extends NeighborFinder { 
  	public SquareNeighborFinder(Cell[][] inputCellGrid, Boolean torroidal2) 
	public void initializeNeighbors() 		
}
 
package shapes;
public class TriangleNeighborFinder extends NeighborFinder { 
  	public TriangleNeighborFinder(Cell[][] inputCellGrid, boolean torroidal2) 
	public void initializeNeighbors() 
}
 
package watorCells;
public abstract class Animal { 
  	public void incrementTime() 
	public boolean isDead() 
	public boolean timeToMultiply() 
	public abstract String getType();
	public void decrementHealth() 
	public void replenishHealth() 
}
 
package watorCells;
public class Fish extends Animal{ 
  	public Fish() 
	public String getType() 
}
 
package watorCells;
public class Shark extends Animal { 
  	public Shark() 
	public boolean isDead() 
	public String getType() 
	public void decrementHealth() 
	public void replenishHealth() 
}
 
package watorCells;
public class Water extends Animal { 
  	public Water() 
	public String getType() 
}
 
package watorCells;
public class WatorCell extends Cell{ 
  	public WatorCell(String state, Animal object) 
	public String getAnimalType() 
	public String getState() 
	public Animal getAnimal() 
	public void setToWater()  
	public void updateColor() 
	public void setNewAnimal(Animal newAnimal, String newState) 
	public void decrementAnimalHealth() 
}
 
package xml;
public class ParserXML { 
  	public ParserXML(File file) 
	public void findCellTypes() 
	public int[] getCellInfo(Node cellNode) 
	public boolean isRandom() 
	public Map<String, int[][]> getAllCells() 
	public Map<String, Double> getParameters()
	public String getSimulationType() 
	public int[] getDimensions()
}
 
package xml;
public class WriterException extends Exception { 
  }
 
package xml;
public class WriterXML { 
  	public WriterXML(String fileName, String simType, Map<String, Double> map, Map<String, int[][]> cellMap, int x,
	public void addAuthors() 
	public void addCells(Map<String, int[][]> map) 
	public void addParams(Map<String, Double> map) 
	public void addDimensions(int x, int y) 
	public void convert() throws WriterException 
}