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Refactor to read/write files of graph and map data

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efischer
2022-02-19 21:46:01 -06:00
parent 568a6be3c7
commit 13fb7168bf
9 changed files with 281 additions and 204 deletions
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233
src/main/java/UserInterface.java
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@@ -1,5 +1,6 @@
import org.apache.commons.cli.*;
import java.io.IOException;
import java.util.List;
import java.util.Scanner;
import java.util.InputMismatchException;
@@ -259,9 +260,9 @@ public class UserInterface {
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) Generate CDR3 alpha/beta occupancy graph");
//System.out.println("4) Generate CDR3/CDR1 occupancy graph");
System.out.println("5) Simulate CDR3 alpha/beta T cell matching");
System.out.println("3) Generate CDR3 alpha/beta occupancy graph and data");
System.out.println("4) Simulate CDR3 alpha/beta T cell matching");
//System.out.println("5) Generate CDR3/CDR1 occupancy graph");
System.out.println("6) Simulate CDR3/CDR1 T cell matching");
System.out.println("7) Acknowledgements");
System.out.println("0) Exit");
@@ -271,13 +272,13 @@ public class UserInterface {
case 1 -> makeCells();
case 2 -> makePlate();
case 3 -> makeCDR3Graph();
case 5 -> matchCells();
case 4 -> matchCDR3s();
case 6 -> matchCellsCDR1();
case 7 -> acknowledge();
case 0 -> quit = true;
default -> throw new InputMismatchException("Invalid input.");
}
} catch (InputMismatchException ex) {
} catch (InputMismatchException | IOException ex) {
System.out.println(ex);
sc.next();
}
@@ -315,40 +316,40 @@ public class UserInterface {
writer.writeCellsToFile();
}
//for calling from command line
private static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
CellFileWriter writer = new CellFileWriter(filename, sample);
writer.writeCellsToFile();
}
private static void makePlateExp(String cellFile, String filename, Double lambda,
Integer numWells, Integer[] concentrations, Double dropOutRate){
CellFileReader cellReader = new CellFileReader(cellFile);
Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
writer.writePlateFile();
}
private static void makePlatePoisson(String cellFile, String filename, Integer numWells,
Integer[] concentrations, Double dropOutRate){
CellFileReader cellReader = new CellFileReader(cellFile);
Double stdDev = Math.sqrt(cellReader.getCellCount());
Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
writer.writePlateFile();
}
private static void makePlate(String cellFile, String filename, Double stdDev,
Integer numWells, Integer[] concentrations, Double dropOutRate){
CellFileReader cellReader = new CellFileReader(cellFile);
Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
writer.writePlateFile();
}
// //for calling from command line
// private static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
// CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
// CellFileWriter writer = new CellFileWriter(filename, sample);
// writer.writeCellsToFile();
// }
//
// private static void makePlateExp(String cellFile, String filename, Double lambda,
// Integer numWells, Integer[] concentrations, Double dropOutRate){
// CellFileReader cellReader = new CellFileReader(cellFile);
// Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
// samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
// PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
// writer.writePlateFile();
// }
//
// private static void makePlatePoisson(String cellFile, String filename, Integer numWells,
// Integer[] concentrations, Double dropOutRate){
// CellFileReader cellReader = new CellFileReader(cellFile);
// Double stdDev = Math.sqrt(cellReader.getCellCount());
// Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
// samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
// PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
// writer.writePlateFile();
// }
//
// private static void makePlate(String cellFile, String filename, Double stdDev,
// Integer numWells, Integer[] concentrations, Double dropOutRate){
// CellFileReader cellReader = new CellFileReader(cellFile);
// Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
// samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
// PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
// writer.writePlateFile();
// }
//method to output a CSV of sample plate
private static void makePlate() {
@@ -453,69 +454,30 @@ public class UserInterface {
}
}
private static void matchCDR3s(String cellFile, String plateFile, Integer lowThreshold, Integer highThreshold,
Integer maxOccupancyDifference, Integer minOverlapPercent){
CellFileReader cellReader = new CellFileReader(cellFile);
PlateFileReader plateReader = new PlateFileReader(plateFile);
Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
if (cellReader.getCells().size() == 0){
System.exit(0);
}
else if(plate.getWells().size() == 0){
System.exit(0);
}
else{
if(highThreshold >= plate.getSize()){
highThreshold = plate.getSize() - 1;
}
List<Integer[]> cells = cellReader.getCells();
MatchingResult results = Simulator.matchCDR3s(cells, plate, lowThreshold, highThreshold, maxOccupancyDifference, minOverlapPercent, false);
//result writer
MatchingFileWriter writer = new MatchingFileWriter("", results);
writer.writeErrorRateToTerminal();
}
}
private static void makeCDR3Graph() {
String filename = null;
String cellFile = null;
String plateFile = null;
}
private static void matchCells() {
String filename = null;
String cellFile = null;
String plateFile = null;
Integer lowThreshold = 0;
Integer highThreshold = Integer.MAX_VALUE;
Integer maxOccupancyDiff = 96; //no filtering if max difference is all wells by default
Integer minOverlapPercent = 0; //no filtering if min percentage is zero by default
try {
System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
String str = "\nGenerating bipartite weighted graph encoding occupancy data requires ";
str.concat("a cell sample file and a sample plate file.");
System.out.println(str);
System.out.print("Please enter name of an existing cell sample file: ");
cellFile = sc.next();
System.out.print("Please enter name of an existing sample plate file: ");
plateFile = sc.next();
System.out.println("The matching results will be written to a file.");
System.out.println("The graph and occupancy data will be written to a file.");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
System.out.println("What is the minimum number of alpha/beta overlap wells to attempt matching?");
System.out.println("What is the minimum number of CDR3 alpha/beta overlap wells to include in graph?");
lowThreshold = sc.nextInt();
if(lowThreshold < 1){
throw new InputMismatchException("Minimum value for low threshold is 1");
throw new InputMismatchException("Minimum value for low threshold set to 1");
}
System.out.println("What is the maximum number of alpha/beta overlap wells to attempt matching?");
System.out.println("What is the maximum number of CDR3 alpha/beta overlap wells to include in graph?");
highThreshold = sc.nextInt();
System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
maxOccupancyDiff = sc.nextInt();
System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
minOverlapPercent = sc.nextInt();
if (minOverlapPercent < 0 || minOverlapPercent > 100) {
throw new InputMismatchException("Value outside range. Minimum percent set to 0");
}
} catch (InputMismatchException ex) {
System.out.println(ex);
sc.next();
@@ -530,23 +492,108 @@ public class UserInterface {
else if(plate.getWells().size() == 0){
System.out.println("No sample plate found.");
System.out.println("Returning to main menu.");
}
else{
if(highThreshold >= plate.getSize()){
highThreshold = plate.getSize() - 1;
}
List<Integer[]> cells = cellReader.getCells();
MapData maps = Simulator.makeMaps(cells, plate, lowThreshold, true);
GraphWithMapData data = Simulator.makeGraph(plate, maps, lowThreshold, highThreshold, true);
MatchingResult results = Simulator.matchCDR3s(plate, data, lowThreshold, highThreshold,
maxOccupancyDiff,minOverlapPercent, true);
//result writer
MatchingFileWriter writer = new MatchingFileWriter(filename, results);
writer.writeResultsToFile();
GraphWithMapData data = Simulator.makeGraph(cells, plate, lowThreshold, highThreshold, true);
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
dataWriter.writeDataToFile();
}
}
private static void matchCDR3s() throws IOException {
String filename = null;
String dataFile = null;
Integer maxOccupancyDiff = Integer.MAX_VALUE;
Integer minOverlapPercent = 0;
try {
System.out.println("\nSimulated matching experiment requires graph and occupancy data file");
System.out.println("Please enter name of an existing graph and occupancy data file: ");
dataFile = sc.next();
System.out.println("The matching results will be written to a file.");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
} catch (InputMismatchException ex) {
System.out.println(ex);
sc.next();
}
//read object data from file
GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFile);
GraphWithMapData data = dataReader.getData();
//set source file name
data.setSourceFilename(dataFile);
//simulate matching
MatchingResult results = Simulator.matchCDR3s(data, maxOccupancyDiff, minOverlapPercent, true);
//write results to file
MatchingFileWriter writer = new MatchingFileWriter(filename, results);
writer.writeResultsToFile();
}
//old version before I wrote graph data to a file
// private static void matchCells() {
// String filename = null;
// String cellFile = null;
// String plateFile = null;
// Integer lowThreshold = 0;
// Integer highThreshold = Integer.MAX_VALUE;
// Integer maxOccupancyDiff = 96; //no filtering if max difference is all wells by default
// Integer minOverlapPercent = 0; //no filtering if min percentage is zero by default
// try {
// System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
// System.out.print("Please enter name of an existing cell sample file: ");
// cellFile = sc.next();
// System.out.print("Please enter name of an existing sample plate file: ");
// plateFile = sc.next();
// System.out.println("The matching results will be written to a file.");
// System.out.print("Please enter a name for the output file: ");
// filename = sc.next();
// System.out.println("What is the minimum number of alpha/beta overlap wells to attempt matching?");
// lowThreshold = sc.nextInt();
// if(lowThreshold < 1){
// throw new InputMismatchException("Minimum value for low threshold is 1");
// }
// System.out.println("What is the maximum number of alpha/beta overlap wells to attempt matching?");
// highThreshold = sc.nextInt();
// System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
// maxOccupancyDiff = sc.nextInt();
// System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
// minOverlapPercent = sc.nextInt();
// if (minOverlapPercent < 0 || minOverlapPercent > 100) {
// throw new InputMismatchException("Value outside range. Minimum percent set to 0");
// }
// } catch (InputMismatchException ex) {
// System.out.println(ex);
// sc.next();
// }
// CellFileReader cellReader = new CellFileReader(cellFile);
// PlateFileReader plateReader = new PlateFileReader(plateFile);
// Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
// if (cellReader.getCells().size() == 0){
// System.out.println("No cell sample found.");
// System.out.println("Returning to main menu.");
// }
// else if(plate.getWells().size() == 0){
// System.out.println("No sample plate found.");
// System.out.println("Returning to main menu.");
// }
// else{
// if(highThreshold >= plate.getSize()){
// highThreshold = plate.getSize() - 1;
// }
// List<Integer[]> cells = cellReader.getCells();
// GraphWithMapData data = Simulator.makeGraph(cells, plate, lowThreshold, highThreshold, true);
// //write data to a file
//
// MatchingResult results = Simulator.matchCDR3s(data, maxOccupancyDiff,minOverlapPercent, true);
// //result writer
// MatchingFileWriter writer = new MatchingFileWriter(filename, results);
// writer.writeResultsToFile();
// }
// }
public static void matchCellsCDR1(){
/*
The idea here is that we'll get the CDR3 alpha/beta matches first. Then we'll try to match CDR3s to CDR1s by