package agents;
public abstract class Agent extends Circle { 
  	public Agent(double radius) 
	public void updatePos(Cell c) 
	public static double cellWidth(Cell c) 
}
 
package agents;
public class AntAgent extends Agent { 
  	public AntAgent(Cell location) 
			public int compare(Cell o1, Cell o2) 
			public int compare(Cell o1, Cell o2) 
}
 
package agents;
public class AntAgentMover { 
  	public AntAgentMover() 
	public void addAnt(AntAgent a) 
	public void removeAnt(AntAgent a) 
	public void updateAnts() 
}
 
package agents;
public class SugarAgent extends Agent { 
  	public SugarAgent(SugarCell c, int vision, int metabolism, int initSugar) 
	public SugarCell getCell() 
	public void setCell(SugarCell sc) 
			public int compare(Cell o1, Cell o2) 
	public void addSAM(SugarAgentMover samAdd) 
	public boolean isFertile() 
	public boolean isFemale() 
	public void setSugar(int s) 
	public int getSugar() 
	public void reproduce() 
	public int getVision() 
	public int getMetabolism() 
	public int getInitialSugar() 
	public SugarCell findSpot() 
}
 
package agents;
public class SugarAgentMover { 
  	public SugarAgentMover() 
	public void addAgent(SugarAgent sa) 
	public void removeAgent(SugarAgent sa) 
	public void updateAgents() 
}
 
package buttons;
public abstract class ActionButton extends Button{ 
  	public static final ResourceBundle myResources = ResourceBundle.getBundle(DEFAULT_RESOURCE_PACKAGE+RESOURCE_FILE);
	public ActionButton(Color buttonColor) 
	public void setButtonText(String buttonName) 
	public void setPosition(int x, int y ) 
	public String getButtonText() 
	public Boolean getPlayBoolean () 
	public static Boolean setPlayBoolean(Boolean state) 
}
 
package buttons;
public class ChartButton extends ActionButton{ 
  	public ChartButton(Color buttonColor) 
	           public void handle(WindowEvent we) 
}
 
package buttons;
public class CompareButton extends ActionButton{ 
  	public CompareButton(Color buttonColor) 
}
 
package buttons;
public class FileUploadButton extends ActionButton{ 
  	public FileUploadButton(Color buttonColor) 
}
 
package buttons;
public class JumpButton extends ActionButton{ 
  	public JumpButton(Color buttonColor) 
}
 
package buttons;
public class PauseButton extends ActionButton{ 
  	public PauseButton(Color buttonColor) 
}
 
package buttons;
public class PlayButton extends ActionButton{ 
  	public PlayButton(Color buttonColor) 
}
 
package buttons;
public class ResetButton extends ActionButton{ 
  	public ResetButton(Color buttonColor) 
	public static void reset() 
}
 
package buttons;
public class SpeedSlider extends Slider{ 
  	public SpeedSlider(double minsliderspeed, double maxsliderspeed, double defaultsliderspeed) 
	public void setPosition(int x, int y) 
}
 
package buttons;
public class StepButton extends ActionButton{ 
  	public StepButton(Color buttonColor) 
}
 
package buttons;
public class SwitchButton extends Label 
  	public SwitchButton()
	public SimpleBooleanProperty switchOnProperty()  
	public void setPosition(int x, int y ) 
}
 
package buttons;
public class SwitchNeighborButton extends Label 
  	public SwitchNeighborButton()
	public SimpleBooleanProperty switchOnProperty()  
	public void setPosition(int x, int y ) 
}
 
package neighbors;
public class RectFiniteNeighbors { 
  	public void setAllCornerNeighbors(Cell[][] grid, int gridSize) 
	public void setAllSideNeighbors(Cell[][] grid, int gridSize) 
	public void setAllMiddleNeighbors(Cell[][] grid, int gridSize) 
	public void setCardinalCornerNeighbors(Cell[][] grid, int gridSize) 
	public void setCardinalSideNeighbors(Cell[][] grid, int gridSize) 
	public void setCardinalMiddleNeighbors(Cell[][] grid, int gridSize) 
}
 
package neighbors;
public class RectToroidalNeighbors { 
  	public void setCardinalSideToroidalNeighbors(Cell[][] grid, int gridSize) 
	public void setCardinalCornerToroidalNeighbors(Cell[][] grid, int gridSize) 
	public void setAllCornerToroidalNeighbors(Cell[][] grid, int gridSize) 
	public void setAllSideToroidalNeighbors(Cell[][] grid, int gridSize) 
}
 
package neighbors;
public class TriangleFiniteNeighbors { 
  	public void setCardinalNormalNeighbors(Cell[][] grid, int gridSize) 
	public void setCardinalInvertedNeighbors(Cell[][] grid, int gridSize) 
	public void setAllNormalNeighbors(Cell[][] grid, int gridSize) 
	public void setAllInvertedNeighbors(Cell[][] grid, int gridSize) 
}
 
package neighbors;
public class TriangleToroidalNeighbors { 
  	public void setCardinalInvertedToroidalNeighbors(Cell[][] grid, int gridSize) 
	public void setCardinalNormalToroidalNeighbors(Cell[][] grid, int gridSize) 
	public void setAllNormalToroidalNeighbors(Cell[][] grid, int gridSize) 
	public void setAllInvertedToroidalNeighbors(Cell[][] grid, int gridSize) 
}
 
package rectCells;
public class AntCell extends Cell { 
  	public AntCell(int state, double...points) 
	public AntCell(double...points) 
	public void updateFill() 
	public void reduceDurability() 
	public int getMaxState() 
	public void addAnt(AntAgent a) 
	public void removeAnt(AntAgent a) 
	public boolean roomForAnts() 
	public double getNestPheromones() 
	public double getFoodPheromones() 
	public void setNestPheromones(double np) 
	public void setFoodPheromones(double fp) 
}
 
package rectCells;
public class BacteriaCell extends Cell { 
  	public BacteriaCell(int state, double...points) 
	public BacteriaCell(double...points) 
			public void handle(MouseEvent me) 
	public void updateFill() 
	public int getMaxState() 
	public void setLevel(int lvl) 
	public int getLevel() 
}
 
package rectCells;
public abstract class Cell extends Polygon implements IGrid { 
  	public Cell(double...points) 
			public void handle(MouseEvent me) 
	public abstract void updateFill();
	public void updateNeighborStates() 
	public abstract int getMaxState();
	public void setState(int state) 
	public int getState() 
	public void setNeighbor(Cell c) 
	public void setNeighbors(Cell...neighborCells) 
	public List<Integer> getNeighborStates() 
	public List<Cell> getNeighbors() 
	public void setCellMover(CellMover cmNew) 
	public CellMover getCellMover() 
	public void setSwapped(boolean b) 
	public boolean getSwapped() 
}
 
package rectCells;
public class CellMover { 
  	public CellMover() 
	public void addCell(Cell c) 
	public Cell findOpenCell() 
	public void copyState(Cell origin, Cell destination) 
	public double getPercentAlike(int state) 
}
 
package rectCells;
public class FireCell extends Cell { 
  	public FireCell(int state, double...points) 
	public FireCell(double...points) 
	public int getMaxState() 
	public void updateFill() 
}
 
package rectCells;
 public interface IGrid {
  	public void updateNeighborStates();
}
 
package rectCells;
public class LifeCell extends Cell { 
  	public LifeCell(int state, double...points) 
	public LifeCell(double...points) 
	public LifeCell() 
	public int getMaxState() 
	public void updateFill() 
}
 
package rectCells;
public class PredPreyCell extends Cell { 
  	public PredPreyCell(int state, double...points) 
	public PredPreyCell(double...points) 
	public int getReproduce() 
	public void setReproduce(int e) 
	public int getEnergy() 
	public void setEnergy(int e) 
	public int getMaxState() 
	public void updateFill() 
}
 
package rectCells;
public class SegregationCell extends Cell { 
  	public SegregationCell(int state, double...points) 
	public SegregationCell(double...points) 
	public SegregationCell() 
	public int getMaxState() 
	public void updateFill() 
}
 
package rectCells;
public class SugarCell extends Cell { 
  	public SugarCell(int state, double...points) 
	public SugarCell(double...points) 
	public void updateFill() 
	public void setCapacity(int c) 
	public int getMaxState() 
	public SugarAgent getAgent() 
	public void setAgent(SugarAgent sa) 
}
 
package rectGrids;
public class AntGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff)
}
 
package rectGrids;
public class BacteriaGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff)
}
 
package rectGrids;
public class FireGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff) 
}
 
package rectGrids;
public abstract class Grid { 
  	public int[] getGridConfig(String config) 
}
 
package rectGrids;
public class LifeGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff)
}
 
package rectGrids;
public class PredPreyGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff) 
}
 
package rectGrids;
public abstract class RectangleGrid extends Grid{ 
  	public abstract Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff);
	public CellMover getCm() return cm;}
}
 
package rectGrids;
public class SegregationGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff) 
}
 
package rectGrids;
public class SugarGrid extends RectangleGrid { 
  	public Cell[][] createGrid(int offset, int gridSize, int cellWidth, int cellHeight, double cutOff)
}
 
package triangleGrids;
public class FireTriangleGrid extends TriangleGrid{ 
  	public Cell[][] createGrid(double offset, int gridSize, double height, double width, double cutOff) 
}
 
package triangleGrids;
public class LifeTriangleGrid extends TriangleGrid{ 
  	public Cell[][] createGrid(double offset, int gridSize, double height, double width, double cutOff) 
}
 
package triangleGrids;
public class PredPreyTriangleGrid extends TriangleGrid{ 
  	public Cell[][] createGrid(double offset, int gridSize, double height, double width, double cutOff) 
}
 
package triangleGrids;
public class SegregationTriangleGrid extends TriangleGrid{ 
  	public Cell[][] createGrid(double offset, int gridSize, double height, double width, double cutOff) 
}
 
package triangleGrids;
public abstract class TriangleGrid extends Grid{ 
  	public abstract Cell[][] createGrid(double offset, int gridSize, double height, double width, double cutOff);
}
 
package View;
public class ButtonView { 
  	public static ComboBox<File> getFileSelector() 
	public static void setFileSelector(ComboBox<File> fileSelector) 
	public static TextField getJumpField() 
	public static void setJumpField(TextField jumpField) 
	public static void createButtons() 
	public static void arrangeButtons() 
	public static void setTitleAuthor() 
}
 
package View;
public class ChartView { 
  	public ChartView() 
	public Scene initializeStartScene() 
	public static void updateChartAttributes() 
	public void beginAnimationLoop() 
	public void step(double elapsedTime, Cell[][] cellGrid) 
	public static void updateCellCount() 
	public static void updateChartAnimationRate(double rate) 
}
 
package View;
public class Main extends Application { 
  	public void start(Stage primaryStage) throws Exception 
	public static Stage getMainStage() 
}
 
package View;
public class MainView { 
  	public MainView() 
	public static final File LIFE_FILE = new File("data/GameOfLife.xml");
	public static final File FIRE_FILE = new File("data/SpreadingFire.xml");
	public static final File SEGREGATION_FILE = new File("data/Segregation.xml");
	public static final File PRED_PREY_FILE = new File("data/PredPrey.xml");
	public static final File SUGAR_SCAPE_FILE = new File("data/SugarScape.xml");
	public static final File BACTERIA_FILE = new File("data/Bacteria.xml");
	public static final File ANT_FILE = new File("data/Ants.xml");
	public static void setupGrid(String name) 
	public static void setupTriangleGrid(String name) 
	public Scene initializeStartScene() 
			public void handle(MouseEvent mouseEvent) 
	public static void beginAnimationLoop() 
	public static Scene setupScene() 
	public static void removeCells() 
	public static void addCells() 
	public static void step(double elapsedTime, Cell[][] cellGrid) 
	public static void switchSimulation() 
	public static void switchShape() 
	public static void switchNeighborConfig() 
	public static void createDropDownMenu() 
	public static void setAnimationRate(double rate) 
	public static Cell[][] getMyCellGrid() 
	public static String getSimulation() 
	public static boolean isPlaying() 
	public static boolean isCharting() 
	public static void setChartBoolean(boolean b) 
	public static void setPlaying(boolean b) 
	public static Group getGroup() 
	public static void setSimulation(String s) 
	public static Grid getGrid() 
}
 
package XML;
public class AntHolder  extends DataHolder { 
  	public static void setSugarScape(int ratio, double pDiff, Color antColor, String antGrid) 
	public static Color getAntColor() 
	public static String getAntGrid() 
	public static double getPheromoneDiffusion() 
	public static int getSizeRatio() 
}
 
package XML;
public class BacteriaHolder extends DataHolder { 
  	public static String getBacteriaGrid() 
	public static Color getColorA() 
	public static Color getColorB() 
	public static Color getColorC() 
	public static Color getDefaultColor() 
	public static void setBacteria(Color colorA, Color colorB, Color colorC, Color defaultColor, String bacteriaGrid) 
}
 
package XML;
public abstract class DataHolder { 
  	public static XMLReader getFileInput() 
	public static void setFileInput(XMLReader file) 
	public static String getType() 
	public static String getAuthor() 
	public static void clearXMLReader() 
	public static int getDimensions() 
	public static void setType(String type) 
	public static void setAuthor(String author) 
	public static void setDimensions(int dimensions) 
	public static void setInputFile(File in) 
	public static File getInputFile() 
}
 
package XML;
public class FireHolder extends DataHolder { 
  	public static String getFireGrid() 
	public static Color getBurntColor() 
	public static Color getTreeColor() 
	public static Color getBurningColor() 
	public static double getProbCatch() 
	public static void setSpreadingFire(Color burntColor, Color burningColor, Color treeColor, double percent, String fireGrid) 
}
 
package XML;
public class LifeHolder extends DataHolder { 
  	public static double getPercentDead() 
	public static String getLifeGrid() 
	public static Color getDeadColor() 
	public static Color getAliveColor() 
	public static void setGameOfLife(Color aliveColor, Color deadColor, double percent, String lifeGrid) 
}
 
package XML;
public class PredPreyHolder extends DataHolder { 
  	public static Color getPredColor() 
	public static Color getPreyColor() 
	public static Color getWaterColor() 
	public static int getPredReproduction() 
	public static int getPreyReproduction() 
	public static int getPredEnergy() 
	public static int getEnergyGain() 
	public static String getPredGrid() 
	public static void setPredPreyColor(Color predColor, Color preyColor, Color waterColor) 
	public static void setPredPreyParams( int preyProduction, int predEnergy, int energyGain, int predReproduction, String predGrid) 
}
 
package XML;
public class SegregationHolder extends DataHolder { 
  	public static Color getAColor() 
	public static Color getBColor() 
	public static Color getNeutralColor() 
	public static String getSegGrid() 
	public static void setSegregation(Color aColor, Color bColor, Color neutralColor, String segGrid) 
}
 
package XML;
public class SugarHolder extends DataHolder { 
  	public static String getSugarGrid() 
	public static int getColorOne() 
	public static int getColorTwo() 
	public static int getColorThree() 
	public static int getGrowthRate() 
	public static int getGrowthInterval() 
	public static int getMaxFertility() 
	public static int getMinFertility() 
	public static int getMaxAge() 
	public static int getSizeRatio() 
	public static void setSugarScape(int colorOne, int colorTwo, int colorThree, int growthRate, int growthInterval, String sugarGrid) 
	public static void setSugarAgents(int mAge, int minF, int maxF, int ratio) 
}
 
package XML;
public class XMLException extends RuntimeException { 
      public XMLException (String message, Object ... values) 
    public XMLException (Throwable cause, String message, Object ... values) 
    public XMLException (Throwable cause) 
}
 
package XML;
public class XMLReader { 
  	public XMLReader(File inputFile) 
	public static Color hex2Rgb(String colorStr) 
}