BiGpairSEQ/src/main/java/BiGpairSEQ.java

import java.util.Random;

//main class. For choosing interface type and caching file data
public class BiGpairSEQ {

    private static final Random rand = new Random();
    private static CellSample cellSampleInMemory = null;
    private static String cellFilename = null;
    private static Plate plateInMemory = null;
    private static String plateFilename = null;
    private static GraphWithMapData graphInMemory = null;
    private static String graphFilename = null;
    private static boolean cacheCells = false;
    private static boolean cachePlate = false;
    private static boolean cacheGraph = true;

    public static void main(String[] args) {
        if (args.length == 0) {
            InteractiveInterface.startInteractive();
        }
        else {
            //This will be uncommented when command line arguments are re-implemented.
            //CommandLineInterface.startCLI(args);
            System.out.println("Command line arguments are still being re-implemented.");
        }
    }

    public static Random getRand() {
        return rand;
    }

    public static CellSample getCellSampleInMemory() {
        return cellSampleInMemory;
    }

    public static void setCellSampleInMemory(CellSample cellSampleInMemory) {
        BiGpairSEQ.cellSampleInMemory = cellSampleInMemory;
    }

    public static void clearCellSampleInMemory() {
        cellSampleInMemory = null;
        System.gc();
    }

    public static String getCellFilename() {
        return cellFilename;
    }

    public static void setCellFilename(String cellFilename) {
        BiGpairSEQ.cellFilename = cellFilename;
    }

    public static Plate getPlateInMemory() {
        return plateInMemory;
    }

    public static void setPlateInMemory(Plate plateInMemory) {
        BiGpairSEQ.plateInMemory = plateInMemory;
    }

    public static void clearPlateInMemory() {
        plateInMemory = null;
        System.gc();
    }

    public static String getPlateFilename() {
        return plateFilename;
    }

    public static void setPlateFilename(String plateFilename) {
        BiGpairSEQ.plateFilename = plateFilename;
    }

    public static GraphWithMapData getGraphInMemory() {
        return graphInMemory;
    }

    public static void setGraphInMemory(GraphWithMapData g) {
        if (graphInMemory != null) {
            clearGraphInMemory();
        }
        graphInMemory = g;
    }

    public static void clearGraphInMemory() {
        graphInMemory = null;
        System.gc();
    }

    public static String getGraphFilename() {
        return graphFilename;
    }

    public static void setGraphFilename(String filename) {
        graphFilename = filename;
    }

    public static boolean cacheCells() {
        return cacheCells;
    }

    public static void setCacheCells(boolean cacheCells) {
        BiGpairSEQ.cacheCells = cacheCells;
    }

    public static boolean cachePlate() {
        return cachePlate;
    }

    public static void setCachePlate(boolean cachePlate) {
        BiGpairSEQ.cachePlate = cachePlate;
    }

    public static boolean cacheGraph() {
        return cacheGraph;
    }

    public static void setCacheGraph(boolean cacheGraph) {
        BiGpairSEQ.cacheGraph = cacheGraph;
    }
}