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Refactor to make CellSample class more self-contained

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efischer
2022-02-24 16:03:49 -06:00
parent 7f18311054
commit 373a5e02f9
4 changed files with 29 additions and 26 deletions
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27
src/main/java/CellSample.java
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@@ -1,10 +1,37 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.IntStream;
public class CellSample {
private List<Integer[]> 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;
IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 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 (alpha, beta), second two are CDR1s (alpha, beta)
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);
}
this.cells = distinctCells;
}
public CellSample(List<Integer[]> cells, Integer cdr1Freq){
this.cells = cells;
this.cdr1Freq = cdr1Freq;

2
src/main/java/CommandLineInterface.java
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@@ -288,7 +288,7 @@ public class CommandLineInterface {
//for calling from command line
public static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
CellSample sample = new CellSample(numCells, cdr1Freq);
CellFileWriter writer = new CellFileWriter(filename, sample);
writer.writeCellsToFile();
}

2
src/main/java/InteractiveInterface.java
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@@ -74,7 +74,7 @@ public class InteractiveInterface {
System.out.println(ex);
sc.next();
}
CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
CellSample sample = new CellSample(numCells, cdr1Freq);
assert filename != null;
System.out.println("Writing cells to file");
CellFileWriter writer = new CellFileWriter(filename, sample);

24
src/main/java/Simulator.java
View File

@@ -23,30 +23,6 @@ public class Simulator implements GraphModificationFunctions {
private static final int cdr1AlphaIndex = 2;
private static final int cdr1BetaIndex = 3;
public static CellSample generateCellSample(Integer numDistinctCells, Integer cdr1Freq) {
//In real T cells, CDR1s have about one third the diversity of 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 / cdr1Freq) + 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 (alpha, beta), second two are CDR1s (alpha, beta)
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, cdr1Freq);
}
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) {
Instant start = Instant.now();