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Expanding simulation to attempt CDR3/CDR1 matching - doubles size of cells

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efischer
2021-11-15 11:24:46 -06:00
parent b612d65bda
commit c425b05d8c
3 changed files with 34 additions and 8 deletions
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27
src/main/java/Simulator.java
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@@ -46,7 +46,32 @@ public class Simulator {
return new CellSample(distinctCells);
}
public static void matchCells(String filename, List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold, Integer highThreshold){
public static CellSample generateExpandedCellSample(Integer numDistinctCells) {
//In real T cells, CDR1s have about one third the diversity of CDR3s
//previous sim was only CDR3s
List<Integer> numbersCDR3 = new ArrayList<>();
List<Integer> numbersCDR1 = new ArrayList<>();
Integer numDistCDR3s = 2 * numDistinctCells + 1;
IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / 3) + 1).forEach(i -> numbersCDR1.add(i));
Collections.shuffle(numbersCDR3);
Collections.shuffle(numbersCDR1);
//Each cell represented by 4 values
//two CDR3s, and two CDR1s. First two values are CDR3s, second two are CDR1s
List<Integer[]> distinctCells = new ArrayList<>();
for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
Integer tmpCDR3a = numbersCDR3.get(i);
Integer tmpCDR3b = numbersCDR3.get(i+1);
Integer tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size());
Integer tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size());
Integer[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
distinctCells.add(tmp);
}
return new CellSample(distinctCells);
}
public static void matchCDR3s(String filename, List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold, Integer highThreshold){
System.out.println("Cells: " + distinctCells.size());
int numWells = samplePlate.getSize();
System.out.println("Making cell maps");