BiGpairSEQ/src/main/java/BiGpairSEQ.java

import java.util.Random;

//main class. For choosing interface type and holding settings
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 = false;
    private static AlgorithmType matchingAlgorithmType = AlgorithmType.HUNGARIAN;
    private static HeapType priorityQueueHeapType = HeapType.PAIRING;
    private static DistributionType distributionType = DistributionType.ZIPF;
    private static boolean outputBinary = true;
    private static boolean outputGraphML = false;
    private static boolean calculatePValue = false;
    private static final String version = "version 4.2";

    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 cellSample, String filename) {
        if(cellSampleInMemory != null) {
            clearCellSampleInMemory();
        }
        cellSampleInMemory = cellSample;
        cellFilename = filename;
        System.out.println("Cell sample file " + filename + " cached.");
    }

    public static void clearCellSampleInMemory() {
        cellSampleInMemory = null;
        cellFilename = null;
        System.gc();
        System.out.println("Cell sample file cache cleared.");

    }

    public static String getCellFilename() {
        return cellFilename;
    }

    public static DistributionType getDistributionType() {return distributionType;}

    public static void setDistributionType(DistributionType type) {distributionType = type;}

    public static Plate getPlateInMemory() {
        return plateInMemory;
    }

    public static void setPlateInMemory(Plate plate, String filename) {
        if(plateInMemory != null) {
            clearPlateInMemory();
        }
        plateInMemory = plate;
        plateFilename = filename;
        System.out.println("Sample plate file " + filename + " cached.");
    }

    public static void clearPlateInMemory() {
        plateInMemory = null;
        plateFilename = null;
        System.gc();
        System.out.println("Sample plate file cache cleared.");

    }

    public static String getPlateFilename() {
        return plateFilename;
    }


    public static GraphWithMapData getGraphInMemory() {return graphInMemory;
    }

    public static void setGraphInMemory(GraphWithMapData g, String filename) {
        if (graphInMemory != null) {
            clearGraphInMemory();
        }
        graphInMemory = g;
        graphFilename = filename;
        System.out.println("Graph and data file " + filename + " cached.");
    }

    public static void clearGraphInMemory() {
        graphInMemory = null;
        graphFilename = null;
        System.gc();
        System.out.println("Graph and data file cache cleared.");
    }

    public static String getGraphFilename() {
        return graphFilename;
    }

    public static boolean cacheCells() {
        return cacheCells;
    }

    public static void setCacheCells(boolean cacheCells) {
        //if not caching, clear the memory
        if(!cacheCells){
            BiGpairSEQ.clearCellSampleInMemory();
            System.out.println("Cell sample file caching: OFF.");
        }
        else {
            System.out.println("Cell sample file caching: ON.");
        }
        BiGpairSEQ.cacheCells = cacheCells;
    }

    public static boolean cachePlate() {
        return cachePlate;
    }

    public static void setCachePlate(boolean cachePlate) {
        //if not caching, clear the memory
        if(!cachePlate) {
            BiGpairSEQ.clearPlateInMemory();
            System.out.println("Sample plate file caching: OFF.");
        }
        else {
            System.out.println("Sample plate file caching: ON.");
        }
        BiGpairSEQ.cachePlate = cachePlate;
    }

    public static boolean cacheGraph() {
        return cacheGraph;
    }

    public static void setCacheGraph(boolean cacheGraph) {
        //if not caching, clear the memory
        if(!cacheGraph) {
            BiGpairSEQ.clearGraphInMemory();
            System.out.println("Graph/data file caching: OFF.");
        }
        else {
            System.out.println("Graph/data file caching: ON.");
        }
        BiGpairSEQ.cacheGraph = cacheGraph;
    }

    public static HeapType getPriorityQueueHeapType() {
        return priorityQueueHeapType;
    }

    public static AlgorithmType getMatchingAlgorithmType() { return matchingAlgorithmType; }

    public static void setHungarianAlgorithm() { matchingAlgorithmType = AlgorithmType.HUNGARIAN; }

    public static void setIntegerWeightScalingAlgorithm() { matchingAlgorithmType = AlgorithmType.INTEGER_WEIGHT_SCALING; }

    public static void setAuctionAlgorithm() { matchingAlgorithmType = AlgorithmType.AUCTION; }

    public static void setPairingHeap() {
        priorityQueueHeapType = HeapType.PAIRING;
    }

    public static void setFibonacciHeap() {
        priorityQueueHeapType = HeapType.FIBONACCI;
    }

    public static boolean outputBinary() {return outputBinary;}
    public static void setOutputBinary(boolean b) {outputBinary = b;}

    public static boolean outputGraphML() {return outputGraphML;}
    public static void setOutputGraphML(boolean b) {outputGraphML = b;}

    public static boolean calculatePValue() {return calculatePValue; }
    public static void setCalculatePValue(boolean b) {calculatePValue = b; }

    public static String getVersion() { return version; }
}