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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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2
src/main/java/CellFileWriter.java
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@@ -10,7 +10,7 @@ import java.util.List;
public class CellFileWriter { public class CellFileWriter {
private String[] headers = {"Alpha", "Beta"}; private String[] headers = {"Alpha CDR3", "Beta CDR3", "Alpha CDR1", "Beta CDR1"};
List<Integer[]> cells; List<Integer[]> cells;
String filename; String filename;

27
src/main/java/Simulator.java
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@@ -46,7 +46,32 @@ public class Simulator {
return new CellSample(distinctCells); 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()); System.out.println("Cells: " + distinctCells.size());
int numWells = samplePlate.getSize(); int numWells = samplePlate.getSize();
System.out.println("Making cell maps"); System.out.println("Making cell maps");

13
src/main/java/UserInterface.java
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@@ -1,6 +1,5 @@
import java.util.List; import java.util.List;
import java.util.Scanner; import java.util.Scanner;
import java.util.ArrayList;
import java.util.InputMismatchException; import java.util.InputMismatchException;
// //
@@ -15,9 +14,10 @@ public class UserInterface {
System.out.println("\nALPHA/BETA T-CELL RECEPTOR MATCHING SIMULATOR"); System.out.println("\nALPHA/BETA T-CELL RECEPTOR MATCHING SIMULATOR");
System.out.println("Please select an option:"); System.out.println("Please select an option:");
System.out.println("1) Generate a population of distinct cells"); System.out.println("1) Generate a population of distinct cells");
System.out.println("2) Generate a sample plate of T-cells"); System.out.println("2) Generate a sample plate of T cells");
System.out.println("3) Simulate T-Cell matching"); System.out.println("3) Simulate CDR3 alpha/beta T cell matching");
System.out.println("4) Acknowledgements"); System.out.println("4) Simulate CDR3/CDR1 T cell matching");
System.out.println("5) Acknowledgements");
System.out.println("0) Exit"); System.out.println("0) Exit");
try { try {
input = sc.nextInt(); input = sc.nextInt();
@@ -25,7 +25,8 @@ public class UserInterface {
case 1 -> makeCells(); case 1 -> makeCells();
case 2 -> makePlate(); case 2 -> makePlate();
case 3 -> matchCells(); case 3 -> matchCells();
case 4 -> acknowledge(); //case 4 -> //method call here
case 5 -> acknowledge();
case 0 -> quit = true; case 0 -> quit = true;
default -> throw new InputMismatchException("Invalid input."); default -> throw new InputMismatchException("Invalid input.");
} }
@@ -186,7 +187,7 @@ public class UserInterface {
highThreshold = plate.getSize() - 1; highThreshold = plate.getSize() - 1;
} }
List<Integer[]> cells = cellReader.getCells(); List<Integer[]> cells = cellReader.getCells();
Simulator.matchCells(filename, cells, plate, lowThreshold, highThreshold); Simulator.matchCDR3s(filename, cells, plate, lowThreshold, highThreshold);
} }
} }