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