BiGpairSEQ/src/main/java/GraphWithMapData.java

import org.jgrapht.graph.SimpleWeightedGraph;

import java.time.Duration;
import java.util.Map;

//Can't just write the graph, because I need the occupancy data too.
//Makes most sense to serialize object and write that to a file.
//Which means there's no reason to split map data and graph data up.
//Custom vertex class means a lot of the map data can now be encoded in the graph itself
public class GraphWithMapData implements java.io.Serializable {

    private String cellFilename;
    private int cellSampleSize;
    private String plateFilename;
    private final SimpleWeightedGraph graph;
    private final int numWells;
    private final Integer[] wellPopulations;
    private final int alphaCount;
    private final int betaCount;
    private final double dropoutRate;
    private final int readDepth;
    private final double readErrorRate;
    private final double errorCollisionRate;
    private final double realSequenceCollisionRate;
    private final Map<String, String> distCellsMapAlphaKey;
//    private final Map<Integer, Integer> plateVtoAMap;
//    private final Map<Integer, Integer> plateVtoBMap;
//    private final Map<Integer, Integer> plateAtoVMap;
//    private final Map<Integer, Integer> plateBtoVMap;
//    private final Map<Integer, Integer> alphaWellCounts;
//    private final Map<Integer, Integer> betaWellCounts;
    private final Duration time;

    public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
                            Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount,
                            Double dropoutRate, Integer readDepth, Double readErrorRate, Double errorCollisionRate,
                            Double realSequenceCollisionRate, Duration time){

//                            Map<Integer, Integer> plateVtoAMap,
//                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
//                            Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
//                            Map<Integer, Integer> betaWellCounts,) {
        this.graph = graph;
        this.numWells = numWells;
        this.wellPopulations = wellConcentrations;
        this.alphaCount = alphaCount;
        this.betaCount = betaCount;
        this.distCellsMapAlphaKey = distCellsMapAlphaKey;
//        this.plateVtoAMap = plateVtoAMap;
//        this.plateVtoBMap = plateVtoBMap;
//        this.plateAtoVMap = plateAtoVMap;
//        this.plateBtoVMap = plateBtoVMap;
//        this.alphaWellCounts = alphaWellCounts;
//        this.betaWellCounts = betaWellCounts;
        this.dropoutRate = dropoutRate;
        this.readDepth = readDepth;
        this.readErrorRate = readErrorRate;
        this.errorCollisionRate = errorCollisionRate;
        this.realSequenceCollisionRate = realSequenceCollisionRate;
        this.time = time;
    }

    public SimpleWeightedGraph getGraph() {
        return graph;
    }

    public Integer getNumWells() {
        return numWells;
    }

    public Integer[] getWellPopulations() {
        return wellPopulations;
    }

    public Integer getAlphaCount() {
        return alphaCount;
    }

    public Integer getBetaCount() {
        return betaCount;
    }

    public Map<String, String> getDistCellsMapAlphaKey() {
        return distCellsMapAlphaKey;
    }

//    public Map<Integer, Integer> getPlateVtoAMap() {
//        return plateVtoAMap;
//    }
//
//    public Map<Integer, Integer> getPlateVtoBMap() {
//        return plateVtoBMap;
//    }
//
//    public Map<Integer, Integer> getPlateAtoVMap() {
//        return plateAtoVMap;
//    }
//
//    public Map<Integer, Integer> getPlateBtoVMap() {
//        return plateBtoVMap;
//    }
//
//    public Map<Integer, Integer> getAlphaWellCounts() {
//        return alphaWellCounts;
//    }
//
//    public Map<Integer, Integer> getBetaWellCounts() {
//        return betaWellCounts;
//    }

    public Integer getReadDepth() { return readDepth; }

    public Duration getTime() {
        return time;
    }

    public void setCellFilename(String filename) { this.cellFilename = filename; }

    public String getCellFilename() { return this.cellFilename; }

    public Integer getCellSampleSize() { return this.cellSampleSize; }

    public void setCellSampleSize(int size) { this.cellSampleSize = size;}

    public void setPlateFilename(String filename) {
        this.plateFilename = filename;
    }

    public String getPlateFilename() {
        return plateFilename;
    }

    public Double getReadErrorRate() {
        return readErrorRate;
    }

    public Double getErrorCollisionRate() {
        return errorCollisionRate;
    }

    public Double getRealSequenceCollisionRate() { return realSequenceCollisionRate; }

    public Double getDropoutRate() { return dropoutRate; }
}