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UI cleanup, some code cleanup

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efischer
2022-02-20 01:05:28 -06:00
parent 0bebbc7602
commit 837ef7bfe4
5 changed files with 179 additions and 436 deletions
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src/main/java/UserInterface.java
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@@ -256,15 +256,20 @@ public class UserInterface {
// }
// else {
while (!quit) {
System.out.println("\nALPHA/BETA T-CELL RECEPTOR MATCHING SIMULATOR");
System.out.println("");
System.out.println("--------BiGPairSEQ SIMULATOR--------");
System.out.println("ALPHA/BETA T-CELL RECEPTOR MATCHING");
System.out.println(" USING WEIGHTED BIPARTITE GRAPHS ");
System.out.println("------------------------------------");
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 and data");
System.out.println("4) Simulate CDR3 alpha/beta T cell matching");
System.out.println("3) Generate CDR3 alpha/beta occupancy data and overlap graph");
System.out.println("4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ)");
//Need to re-do the CDR3/CDR1 matching to correspond to new pattern
//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("6) Simulate CDR3/CDR1 T cell matching");
System.out.println("9) Acknowledgements");
System.out.println("0) Exit");
try {
input = sc.nextInt();
@@ -273,8 +278,8 @@ public class UserInterface {
case 2 -> makePlate();
case 3 -> makeCDR3Graph();
case 4 -> matchCDR3s();
case 6 -> matchCellsCDR1();
case 7 -> acknowledge();
//case 6 -> matchCellsCDR1();
case 9 -> acknowledge();
case 0 -> quit = true;
default -> throw new InputMismatchException("Invalid input.");
}
@@ -295,7 +300,7 @@ public class UserInterface {
System.out.println("\nSimulated T-Cells consist of integer values representing:\n" +
"* a pair of alpha and beta CDR3 peptides (unique within simulated population)\n" +
"* a pair of alpha and beta CDR1 peptides (not necessarily unique).");
System.out.println("\nThe cells will be written to a file.");
System.out.println("\nThe cells will be written to a CSV file.");
System.out.print("Please enter a file name: ");
filename = sc.next();
System.out.println("CDR3 sequences are more diverse than CDR1 sequences.");
@@ -311,7 +316,6 @@ public class UserInterface {
sc.next();
}
CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
//CellSample sample = Simulator.generateCellSampleExp(numCells, cdr1Freq);
CellFileWriter writer = new CellFileWriter(filename, sample);
writer.writeCellsToFile();
}
@@ -364,10 +368,16 @@ public class UserInterface {
boolean exponential = false;
double lambda = 1.5;
try {
System.out.println("\nSimulated sample plates consist of:");
System.out.println("* a number of wells");
System.out.println(" * separated into one or more sections");
System.out.println(" * each of which has a set quantity of cells per well");
System.out.println(" * selected from a statistical distribution of distinct cells");
System.out.println(" * with a set dropout rate for individual sequences within a cell");
System.out.println("\nMaking a sample plate requires a population of distinct cells");
System.out.println("Please enter name of an existing cell sample file: ");
cellFile = sc.next();
System.out.println("\nThe sample plate will be written to file");
System.out.println("\nThe sample plate will be written to a CSV file");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
System.out.println("Select T-cell frequency distribution function");
@@ -401,7 +411,6 @@ public class UserInterface {
break;
default:
System.out.println("Invalid input. Defaulting to exponential.");
//poisson = true;
exponential = true;
}
System.out.print("Number of wells on plate: ");
@@ -426,7 +435,7 @@ public class UserInterface {
i++;
numSections--;
}
System.out.println("Errors in amplification can induce a well dropout rate for peptides");
System.out.println("Errors in amplification can induce a well dropout rate for sequences");
System.out.print("Enter well dropout rate (0.0 to 1.0): ");
dropOutRate = sc.nextDouble();
if(dropOutRate < 0.0 || dropOutRate > 1.0) {
@@ -462,14 +471,14 @@ public class UserInterface {
Integer lowThreshold = 0;
Integer highThreshold = Integer.MAX_VALUE;
try {
String str = "\nGenerating bipartite weighted graph encoding occupancy data requires ";
str = str.concat("a cell sample file and a sample plate file.");
String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
str = str.concat("\nrequires 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 graph and occupancy data will be written to a file.");
System.out.println("The graph and occupancy data will be written to a serialized binary file.");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
System.out.println("What is the minimum number of CDR3 alpha/beta overlap wells to include in graph?");
@@ -502,7 +511,7 @@ public class UserInterface {
GraphWithMapData data = Simulator.makeGraph(cells, plate, lowThreshold, highThreshold, true);
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
System.out.println("Writing graph and occupancy data to file. This may take some time.");
System.out.println("Time to write file is not included in simulation time data.");
System.out.println("File I/O time is not included in results.");
dataWriter.writeDataToFile();
}
}
@@ -514,14 +523,18 @@ public class UserInterface {
Integer maxOccupancyDiff = Integer.MAX_VALUE;
Integer minOverlapPercent = 0;
try {
System.out.println("\nSimulated matching experiment requires graph and occupancy data file");
System.out.println("\nBiGpairSEQ simulation requires an occupancy data and overlap graph 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();
System.out.println("Bipartite graph can be pre-filtered for relative alpha/beta occupancy.");
System.out.println("(To skip pre-filtering: enter number of wells on the sample plate used to make graph)");
System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
maxOccupancyDiff = sc.nextInt();
System.out.println("Bipartite graph can be pre-filtered for pair well overlap percentage");
System.out.println("(To skip pre-filtering: enter 0");
System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
minOverlapPercent = sc.nextInt();
if (minOverlapPercent < 0 || minOverlapPercent > 100) {
@@ -532,8 +545,8 @@ public class UserInterface {
sc.next();
}
//read object data from file
System.out.println("Reading data from file. This may take some time");
System.out.println("Time to read file is not included in simulation time data");
System.out.println("Reading graph data from file. This may take some time");
System.out.println("File I/O time is not included in results");
GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFile);
GraphWithMapData data = dataReader.getData();
//set source file name
@@ -546,15 +559,26 @@ public class UserInterface {
writer.writeResultsToFile();
}
//old version before I wrote graph data to a file
// private static void matchCells() {
///////
//Rewrite this to fit new matchCDR3 method with file I/O
///////
// 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
// looking at the top two matches for each CDR3. If CDR3s in the same cell simply swap CDR1s, we assume a correct
// match
// */
// String filename = null;
// String preliminaryResultsFilename = 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
// Integer lowThresholdCDR3 = 0;
// Integer highThresholdCDR3 = Integer.MAX_VALUE;
// Integer maxOccupancyDiffCDR3 = 96; //no filtering if max difference is all wells by default
// Integer minOverlapPercentCDR3 = 0; //no filtering if min percentage is zero by default
// Integer lowThresholdCDR1 = 0;
// Integer highThresholdCDR1 = Integer.MAX_VALUE;
// boolean outputCDR3Matches = false;
// 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: ");
@@ -564,20 +588,42 @@ public class UserInterface {
// 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){
// System.out.println("What is the minimum number of CDR3 alpha/beta overlap wells to attempt matching?");
// lowThresholdCDR3 = sc.nextInt();
// if(lowThresholdCDR3 < 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) {
// System.out.println("What is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
// highThresholdCDR3 = sc.nextInt();
// System.out.println("What is the maximum difference in CDR3 alpha/beta occupancy to attempt matching?");
// maxOccupancyDiffCDR3 = sc.nextInt();
// System.out.println("What is the minimum CDR3 overlap percentage to attempt matching? (0 - 100)");
// minOverlapPercentCDR3 = sc.nextInt();
// if (minOverlapPercentCDR3 < 0 || minOverlapPercentCDR3 > 100) {
// throw new InputMismatchException("Value outside range. Minimum percent set to 0");
// }
// System.out.println("What is the minimum number of CDR3/CDR1 overlap wells to attempt matching?");
// lowThresholdCDR1 = sc.nextInt();
// if(lowThresholdCDR1 < 1){
// throw new InputMismatchException("Minimum value for low threshold is 1");
// }
// System.out.println("What is the maximum number of CDR3/CDR1 overlap wells to attempt matching?");
// highThresholdCDR1 = sc.nextInt();
// System.out.println("Matching CDR3s to CDR1s requires first matching CDR3 alpha/betas.");
// System.out.println("Output a file for CDR3 alpha/beta match results as well?");
// System.out.print("Please enter y/n: ");
// String ans = sc.next();
// Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
// Matcher matcher = pattern.matcher(ans);
// if(matcher.matches()){
// outputCDR3Matches = true;
// System.out.println("Please enter filename for CDR3 alpha/beta match results");
// preliminaryResultsFilename = sc.next();
// System.out.println("CDR3 alpha/beta matches will be output to file");
// }
// else{
// System.out.println("CDR3 alpha/beta matches will not be output to file");
// }
// } catch (InputMismatchException ex) {
// System.out.println(ex);
// sc.next();
@@ -592,129 +638,40 @@ 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;
// if(highThresholdCDR3 >= plate.getSize()){
// highThresholdCDR3 = plate.getSize() - 1;
// }
// if(highThresholdCDR1 >= plate.getSize()){
// highThresholdCDR1 = 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);
// MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3,
// maxOccupancyDiffCDR3, minOverlapPercentCDR3, true);
// MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
// highThresholdCDR1, preliminaryResults);
// MatchingFileWriter writer = new MatchingFileWriter(filename + "_FirstPass", results[0]);
// writer.writeResultsToFile();
// writer = new MatchingFileWriter(filename + "_SecondPass", results[1]);
// writer.writeResultsToFile();
// if(outputCDR3Matches){
// writer = new MatchingFileWriter(preliminaryResultsFilename, preliminaryResults);
// 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
looking at the top two matches for each CDR3. If CDR3s in the same cell simply swap CDR1s, we assume a correct
match
*/
String filename = null;
String preliminaryResultsFilename = null;
String cellFile = null;
String plateFile = null;
Integer lowThresholdCDR3 = 0;
Integer highThresholdCDR3 = Integer.MAX_VALUE;
Integer maxOccupancyDiffCDR3 = 96; //no filtering if max difference is all wells by default
Integer minOverlapPercentCDR3 = 0; //no filtering if min percentage is zero by default
Integer lowThresholdCDR1 = 0;
Integer highThresholdCDR1 = Integer.MAX_VALUE;
boolean outputCDR3Matches = false;
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 CDR3 alpha/beta overlap wells to attempt matching?");
lowThresholdCDR3 = sc.nextInt();
if(lowThresholdCDR3 < 1){
throw new InputMismatchException("Minimum value for low threshold is 1");
}
System.out.println("What is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
highThresholdCDR3 = sc.nextInt();
System.out.println("What is the maximum difference in CDR3 alpha/beta occupancy to attempt matching?");
maxOccupancyDiffCDR3 = sc.nextInt();
System.out.println("What is the minimum CDR3 overlap percentage to attempt matching? (0 - 100)");
minOverlapPercentCDR3 = sc.nextInt();
if (minOverlapPercentCDR3 < 0 || minOverlapPercentCDR3 > 100) {
throw new InputMismatchException("Value outside range. Minimum percent set to 0");
}
System.out.println("What is the minimum number of CDR3/CDR1 overlap wells to attempt matching?");
lowThresholdCDR1 = sc.nextInt();
if(lowThresholdCDR1 < 1){
throw new InputMismatchException("Minimum value for low threshold is 1");
}
System.out.println("What is the maximum number of CDR3/CDR1 overlap wells to attempt matching?");
highThresholdCDR1 = sc.nextInt();
System.out.println("Matching CDR3s to CDR1s requires first matching CDR3 alpha/betas.");
System.out.println("Output a file for CDR3 alpha/beta match results as well?");
System.out.print("Please enter y/n: ");
String ans = sc.next();
Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
Matcher matcher = pattern.matcher(ans);
if(matcher.matches()){
outputCDR3Matches = true;
System.out.println("Please enter filename for CDR3 alpha/beta match results");
preliminaryResultsFilename = sc.next();
System.out.println("CDR3 alpha/beta matches will be output to file");
}
else{
System.out.println("CDR3 alpha/beta matches will not be output to file");
}
} 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(highThresholdCDR3 >= plate.getSize()){
highThresholdCDR3 = plate.getSize() - 1;
}
if(highThresholdCDR1 >= plate.getSize()){
highThresholdCDR1 = plate.getSize() - 1;
}
List<Integer[]> cells = cellReader.getCells();
MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3,
maxOccupancyDiffCDR3, minOverlapPercentCDR3, true);
MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
highThresholdCDR1, preliminaryResults);
MatchingFileWriter writer = new MatchingFileWriter(filename + "_FirstPass", results[0]);
writer.writeResultsToFile();
writer = new MatchingFileWriter(filename + "_SecondPass", results[1]);
writer.writeResultsToFile();
if(outputCDR3Matches){
writer = new MatchingFileWriter(preliminaryResultsFilename, preliminaryResults);
writer.writeResultsToFile();
}
}
}
private static void acknowledge(){
System.out.println("Simulation based on:");
System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
System.out.println("");
System.out.println("pairSEQ citation:");
System.out.println("Howie, B., Sherwood, A. M., et. al.");
System.out.println("High-throughput pairing of T cell receptor alpha and beta sequences.");
System.out.println("Sci. Transl. Med. 7, 301ra131 (2015)");
System.out.println("");
System.out.println("Simulation by Eugene Fischer, 2021");
System.out.println("Simulation by Eugene Fischer, 2021-2022");
}
}