import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.IntStream;

public class CellSample {

    private List<String[]> cells;
    private Integer cdr1Freq;

    public CellSample(Integer numDistinctCells, Integer cdr1Freq){
        this.cdr1Freq = cdr1Freq;
        List<Integer> numbersCDR3 = new ArrayList<>();
        List<Integer> numbersCDR1 = new ArrayList<>();
        Integer numDistCDR3s = 2 * numDistinctCells + 1;
        //Assign consecutive integers for each CDR3. This ensures they are all unique.
        IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
        //After all CDR3s are assigned, start assigning consecutive integers to CDR1s
        //There will usually be fewer integers in the CDR1 list, which will allow repeats below
        IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
        //randomize the order of the numbers in the lists
        Collections.shuffle(numbersCDR3);
        Collections.shuffle(numbersCDR1);

        //Each cell represented by 4 values
        //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
        List<String[]> distinctCells = new ArrayList<>();
        for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
            //Go through entire CDR3 list once, make pairs of alphas and betas
            String tmpCDR3a = numbersCDR3.get(i).toString();
            String tmpCDR3b = numbersCDR3.get(i+1).toString();
            //Go through the (likely shorter) CDR1 list as many times as necessary, make pairs of alphas and betas
            String tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size()).toString();
            String tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size()).toString();
            //Make the array representing the cell
            String[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
            //Add the cell to the list of distinct cells
            distinctCells.add(tmp);
        }
        this.cells = distinctCells;
    }

    public CellSample(List<String[]> cells, Integer cdr1Freq){
        this.cells = cells;
        this.cdr1Freq = cdr1Freq;
    }

    public List<String[]> getCells(){
        return cells;
    }

    public Integer getCdr1Freq() {
        return cdr1Freq;
    }

    public Integer getCellCount(){
        return cells.size();
    }

}