efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

Refactor to read/write files of graph and map data

Browse Source
This commit is contained in:
efischer
2022-02-19 21:46:01 -06:00
parent 568a6be3c7
commit 13fb7168bf
9 changed files with 281 additions and 204 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
out/artifacts/TCellSim_jar/TCellSim.jar
View File

Binary file not shown.

32
src/main/java/GraphDataObjectReader.java Normal file
View File

@@ -0,0 +1,32 @@
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.ObjectInputStream;
public class GraphDataObjectReader {
private GraphWithMapData data;
private String filename;
public GraphDataObjectReader(String filename) throws IOException {
if(!filename.matches(".*\\.ser")){
filename = filename + ".ser";
}
this.filename = filename;
try(//don't need to close these because of try-with-resources
FileInputStream fileIn = new FileInputStream(filename);
ObjectInputStream in = new ObjectInputStream(fileIn))
{
data = (GraphWithMapData) in.readObject();
} catch (FileNotFoundException | ClassNotFoundException ex) {
ex.printStackTrace();
}
}
public GraphWithMapData getData() {
return data;
}
public String getFilename() {
return filename;
}
}

27
src/main/java/GraphDataObjectWriter.java Normal file
View File

@@ -0,0 +1,27 @@
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectOutputStream;
public class GraphDataObjectWriter {
private GraphWithMapData data;
private String filename;
public GraphDataObjectWriter(String filename, GraphWithMapData data) {
if(!filename.matches(".*\\.ser")){
filename = filename + ".ser";
}
this.filename = filename;
this.data = data;
}
public void writeDataToFile() {
try (FileOutputStream fileOut = new FileOutputStream(filename);
ObjectOutputStream out = new ObjectOutputStream(fileOut);
){
out.writeObject(data);
} catch (IOException ex) {
ex.printStackTrace();
}
}
}

7
src/main/java/GraphFileReader.java → src/main/java/GraphMLFileReader.java
View File

@@ -6,12 +6,15 @@ import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
public class GraphFileReader {
public class GraphMLFileReader {
private String filename;
private SimpleWeightedGraph graph;
public GraphFileReader(String filename, SimpleWeightedGraph graph) {
public GraphMLFileReader(String filename, SimpleWeightedGraph graph) {
if(!filename.matches(".*\\.graphml")){
filename = filename + ".graphml";
}
this.filename = filename;
this.graph = graph;

9
src/main/java/GraphFileWriter.java → src/main/java/GraphMLFileWriter.java
View File

@@ -8,14 +8,15 @@ import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardOpenOption;
public class GraphFileWriter {
public class GraphMLFileWriter {
String filename;
SimpleWeightedGraph graph;
public GraphFileWriter(String filename, SimpleWeightedGraph graph) {
if(!filename.matches(".*\\.gv")){
filename = filename + ".gv";
public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) {
if(!filename.matches(".*\\.graphml")){
filename = filename + ".graphml";
}
this.filename = filename;
this.graph = graph;

71
src/main/java/GraphWithMapData.java
View File

@@ -3,52 +3,91 @@ import org.jgrapht.graph.SimpleWeightedGraph;
import java.time.Duration;
import java.util.Map;
public class GraphWithMapData {
//Can't just write the graph, because I need the occupancy data too.
//Makes most sense to serialize object and write that to a file.
//Which means there's no reason to split map data and graph data up.
public class GraphWithMapData implements java.io.Serializable {
private String sourceFilename;
private final SimpleWeightedGraph graph;
private final MapData maps;
private Integer numWells;
private Integer lowThreshold;
private Integer highThreshold;
private final Map<Integer, Integer> distCellsMapAlphaKey;
private final Map<Integer, Integer> allAlphas;
private final Map<Integer, Integer> allBetas;
private final Map<Integer, Integer> plateVtoAMap;
private final Map<Integer, Integer> plateVtoBMap;
private final Map<Integer, Integer> plateAtoVMap;
private final Map<Integer, Integer> plateBtoVMap;
private final Map<Integer, Integer> alphaWellCounts;
private final Map<Integer, Integer> betaWellCounts;
private final Duration time;
public GraphWithMapData(SimpleWeightedGraph graph, MapData maps, Map<Integer, Integer> alphaWellCounts,
public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer lowThreshold, Integer highThreshold,
Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> allAlphas,
Map<Integer, Integer> allBetas, Map<Integer, Integer> plateVtoAMap,
Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts, Duration time) {
this.graph = graph;
this.maps = maps;
this.numWells = numWells;
this.lowThreshold = lowThreshold;
this.highThreshold = highThreshold;
this.distCellsMapAlphaKey = distCellsMapAlphaKey;
this.allAlphas = allAlphas;
this.allBetas = allBetas;
this.plateVtoAMap = plateVtoAMap;
this.plateVtoBMap = plateVtoBMap;
this.plateAtoVMap = plateAtoVMap;
this.plateBtoVMap = plateBtoVMap;
this.alphaWellCounts = alphaWellCounts;
this.betaWellCounts = betaWellCounts;
this.time = time.plus(maps.getTime());
this.time = time;
}
public SimpleWeightedGraph getGraph() {
return graph;
}
public Integer getNumWells() {
return numWells;
}
public Integer getLowThreshold() {
return lowThreshold;
}
public Integer getHighThreshold() {
return highThreshold;
}
public Map<Integer, Integer> getDistCellsMapAlphaKey() {
return maps.getDistCellsMapAlphaKey();
return distCellsMapAlphaKey;
}
public Map<Integer, Integer> getAllAlphas() {
return maps.getAllAlphas();
return allAlphas;
}
public Map<Integer, Integer> getAllBetas() {
return maps.getAllBetas();
return allBetas;
}
public Map<Integer, Integer> getPlateVtoAMap() {
return maps.getPlateVtoAMap();
return plateVtoAMap;
}
public Map<Integer, Integer> getPlateVtoBMap() {
return maps.getPlateVtoBMap();
return plateVtoBMap;
}
public Map<Integer, Integer> getPlateAtoVMap() {
return maps.getPlateAtoVMap();
return plateAtoVMap;
}
public Map<Integer, Integer> getPlateBtoVMap() {
return maps.getPlateBtoVMap();
return plateBtoVMap;
}
public Map<Integer, Integer> getAlphaWellCounts() {
@@ -62,4 +101,12 @@ public class GraphWithMapData {
public Duration getTime() {
return time;
}
public void setSourceFilename(String filename) {
this.sourceFilename = filename;
}
public String getSourceFilename() {
return sourceFilename;
}
}

64
src/main/java/MapData.java
View File

@@ -1,64 +0,0 @@
import org.jgrapht.graph.SimpleWeightedGraph;
import java.time.Duration;
import java.util.Map;
public class MapData {
private final Map<Integer, Integer> distCellsMapAlphaKey;
private final Map<Integer, Integer> allAlphas;
private final Map<Integer, Integer> allBetas;
private final Map<Integer, Integer> plateVtoAMap;
private final Map<Integer, Integer> plateVtoBMap;
private final Map<Integer, Integer> plateAtoVMap;
private final Map<Integer, Integer> plateBtoVMap;
private final Duration time;
public MapData(Map<Integer, Integer> distCellsMapAlphaKey,
Map<Integer, Integer> allAlphas, Map<Integer, Integer> allBetas,
Map<Integer, Integer> plateVtoAMap, Map<Integer, Integer> plateVtoBMap,
Map<Integer, Integer> plateAtoVMap, Map<Integer, Integer> plateBtoVMap,
Duration time) {
this.distCellsMapAlphaKey = distCellsMapAlphaKey;
this.allAlphas = allAlphas;
this.allBetas = allBetas;
this.plateVtoAMap = plateVtoAMap;
this.plateVtoBMap = plateVtoBMap;
this.plateAtoVMap = plateAtoVMap;
this.plateBtoVMap = plateBtoVMap;
this.time = time;
}
public Map<Integer, Integer> getDistCellsMapAlphaKey() {
return distCellsMapAlphaKey;
}
public Map<Integer, Integer> getAllAlphas() {
return allAlphas;
}
public Map<Integer, Integer> getAllBetas() {
return allBetas;
}
public Map<Integer, Integer> getPlateVtoAMap() {
return plateVtoAMap;
}
public Map<Integer, Integer> getPlateVtoBMap() {
return plateVtoBMap;
}
public Map<Integer, Integer> getPlateAtoVMap() {
return plateAtoVMap;
}
public Map<Integer, Integer> getPlateBtoVMap() {
return plateBtoVMap;
}
public Duration getTime() {
return time;
}
}

42
src/main/java/Simulator.java
View File

@@ -55,13 +55,13 @@ public class Simulator {
// }
//Make the maps needed for matching CDR3s
public static MapData makeMaps(List<Integer[]> distinctCells,
Plate samplePlate, Integer lowThreshold, boolean verbose) {
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold,
Integer highThreshold, boolean verbose) {
Instant start = Instant.now();
int numWells = samplePlate.getSize();
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
int numWells = samplePlate.getSize();
if(verbose){System.out.println("Making cell maps");}
//HashMap keyed to Alphas, values Betas
@@ -109,24 +109,6 @@ public class Simulator {
//keys are betas, values are sequential integer vertices from previous map
Map<Integer, Integer> plateBtoVMap = invertVertexMap(plateVtoBMap);
if(verbose){System.out.println("Vertex maps made");}
Instant stop = Instant.now();
Duration time = Duration.between(start, stop);
return new MapData(distCellsMapAlphaKey, allAlphas, allBetas, plateVtoAMap, plateVtoBMap, plateAtoVMap,
plateBtoVMap, time);
}
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(Plate samplePlate, MapData maps, Integer lowThreshold,
Integer highThreshold, boolean verbose) {
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
Instant start = Instant.now();
Map<Integer, Integer> plateVtoAMap = maps.getPlateVtoAMap();
Map<Integer, Integer> plateVtoBMap = maps.getPlateVtoBMap();
Map<Integer, Integer> plateAtoVMap = maps.getPlateAtoVMap();
Map<Integer, Integer> plateBtoVMap = maps.getPlateBtoVMap();
Map<Integer, Integer> allAlphas = maps.getAllAlphas();
Map<Integer, Integer> allBetas = maps.getAllBetas();
if(verbose){System.out.println("Creating adjacency matrix");}
//Count how many wells each alpha appears in
@@ -160,16 +142,18 @@ public class Simulator {
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
Instant stop = Instant.now();
Duration time = Duration.between(start, stop);
time = time.plus(maps.getTime());
return new GraphWithMapData(graph, maps, alphaWellCounts, betaWellCounts, time);
return new GraphWithMapData(graph, numWells, lowThreshold, highThreshold, distCellsMapAlphaKey, allAlphas,
allBetas, plateVtoAMap, plateVtoBMap, plateAtoVMap, plateBtoVMap, alphaWellCounts, betaWellCounts,
time);
}
//match CDR3s
public static MatchingResult matchCDR3s(Plate samplePlate, GraphWithMapData data, Integer lowThreshold,
Integer highThreshold, Integer maxOccupancyDifference,
public static MatchingResult matchCDR3s(GraphWithMapData data, Integer maxOccupancyDifference,
Integer minOverlapPercent, boolean verbose) {
Instant start = Instant.now();
int numWells = samplePlate.getSize();
int numWells = data.getNumWells();
Integer highThreshold = data.getHighThreshold();
Integer lowThreshold = data.getLowThreshold();
Map<Integer, Integer> distCellsMapAlphaKey = data.getDistCellsMapAlphaKey();
Map<Integer, Integer> plateVtoAMap = data.getPlateVtoAMap();
Map<Integer, Integer> plateVtoBMap = data.getPlateVtoBMap();
@@ -280,7 +264,7 @@ public class Simulator {
System.out.println(s);
}
}
return new MatchingResult(samplePlate.getSourceFileName(), comments, header, allResults, matchMap, time);
return new MatchingResult(data.getSourceFilename(), comments, header, allResults, matchMap, time);
}
public static MatchingResult matchCDR3s(List<Integer[]> distinctCells,
@@ -371,7 +355,7 @@ public class Simulator {
if(verbose){System.out.println("Graph created");}
//write graph to file
GraphFileWriter writer = new GraphFileWriter("graph", graph);
GraphMLFileWriter writer = new GraphMLFileWriter("graph", graph);
writer.writeGraphToFile();
if(verbose){System.out.println("Eliminating edges with weights outside threshold values");}

233
src/main/java/UserInterface.java
View File

@@ -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