Command line arguments working, need better documentation and error handling
This commit is contained in:
@@ -16,42 +16,164 @@ public class UserInterface {
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public static void main(String[] args) {
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if(args.length != 0){
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Options options = new Options();
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Option matchCDR3 = Option.builder("m")
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.longOpt("match")
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Options mainOptions = new Options();
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Option makeCells = Option.builder("cells")
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.longOpt("make-cells")
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.desc("Makes a file of distinct cells")
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.build();
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Option makePlate = Option.builder("plates")
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.longOpt("make-plates")
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.desc("Makes a sample plate file")
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.build();
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Option matchCDR3 = Option.builder("match")
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.longOpt("match-cdr3")
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.desc("Match CDR3s. Requires a cell sample file and any number of plate files.")
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.build();
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options.addOption(matchCDR3);
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OptionGroup mainGroup = new OptionGroup();
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mainGroup.addOption(makeCells);
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mainGroup.addOption(makePlate);
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mainGroup.addOption(matchCDR3);
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mainGroup.setRequired(true);
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mainOptions.addOptionGroup(mainGroup);
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//Reuse clones of this for other options groups, rather than making it lots of times
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Option outputFile = Option.builder("o")
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.longOpt("output-file")
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.hasArg()
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.argName("filename")
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.desc("Name of output file")
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.build();
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mainOptions.addOption(outputFile);
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//Options cellOptions = new Options();
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Option numCells = Option.builder("nc")
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.longOpt("num-cells")
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.desc("The number of distinct cells to generate")
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.hasArg()
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.argName("number")
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.build();
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mainOptions.addOption(numCells);
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Option cdr1Freq = Option.builder("d")
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.longOpt("peptide-diversity-factor")
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.hasArg()
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.argName("number")
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.desc("Number of distinct CDR3s for every CDR1")
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.build();
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mainOptions.addOption(cdr1Freq);
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//Option cellOutput = (Option) outputFile.clone();
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//cellOutput.setRequired(true);
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//mainOptions.addOption(cellOutput);
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//Options plateOptions = new Options();
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Option inputCells = Option.builder("c")
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.longOpt("cellfile")
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.longOpt("cell-file")
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.hasArg()
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.argName("file")
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.desc("The cell sample file used for matching")
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.required().build();
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options.addOption(inputCells);
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.desc("The cell sample file used for filling wells")
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.build();
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mainOptions.addOption(inputCells);
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Option numWells = Option.builder("w")
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.longOpt("num-wells")
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.hasArg()
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.argName("number")
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.desc("The number of wells on each plate")
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.build();
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mainOptions.addOption(numWells);
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Option numPlates = Option.builder("np")
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.longOpt("num-plates")
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.hasArg()
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.argName("number")
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.desc("The number of plate files to output")
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.build();
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mainOptions.addOption(numPlates);
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//Option plateOutput = (Option) outputFile.clone();
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//plateOutput.setRequired(true);
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//plateOutput.setDescription("Prefix for plate output filenames");
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//mainOptions.addOption(plateOutput);
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Option plateErr = Option.builder("err")
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.longOpt("drop-out-rate")
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.hasArg()
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.argName("number")
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.desc("Well drop-out rate. (Probability between 0 and 1)")
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.build();
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mainOptions.addOption(plateErr);
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Option plateConcentrations = Option.builder("t")
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.longOpt("t-cells-per-well")
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.hasArgs()
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.argName("number 1, number 2, ...")
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.desc("Number of T cells per well for each plate section")
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.build();
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mainOptions.addOption(plateConcentrations);
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//different distributions, mutually exclusive
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OptionGroup plateDistributions = new OptionGroup();
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Option plateExp = Option.builder("exponential")
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.desc("Sample from distinct cells with exponential frequency distribution")
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.build();
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plateDistributions.addOption(plateExp);
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Option plateGaussian = Option.builder("gaussian")
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.desc("Sample from distinct cells with gaussain frequency distribution")
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.build();
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plateDistributions.addOption(plateGaussian);
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Option platePoisson = Option.builder("poisson")
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.desc("Sample from distinct cells with poisson frequency distribution")
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.build();
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plateDistributions.addOption(platePoisson);
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mainOptions.addOptionGroup(plateDistributions);
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Option plateStdDev = Option.builder("stddev")
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.desc("Standard deviation for gaussian distribution")
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.hasArg()
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.argName("number")
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.build();
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mainOptions.addOption(plateStdDev);
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Option plateLambda = Option.builder("lambda")
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.desc("Lambda for exponential distribution")
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.hasArg()
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.argName("number")
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.build();
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mainOptions.addOption(plateLambda);
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//
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// String cellFile, String filename, Double stdDev,
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// Integer numWells, Integer numSections,
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// Integer[] concentrations, Double dropOutRate
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//
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//Options matchOptions = new Options();
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inputCells.setDescription("The cell sample file to be used for matching.");
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mainOptions.addOption(inputCells);
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Option lowThresh = Option.builder("low")
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.longOpt("low-threshold")
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.hasArg()
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.argName("number")
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.desc("Sets the minimum occupancy overlap to attempt matching")
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.required().build();
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options.addOption(lowThresh);
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.build();
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mainOptions.addOption(lowThresh);
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Option highThresh = Option.builder("high")
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.longOpt("high-threshold")
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.hasArg()
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.argName("number")
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.desc("Sets the maximum occupancy overlap to attempt matching")
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.required().build();
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options.addOption(highThresh);
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.build();
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mainOptions.addOption(highThresh);
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Option inputPlates = Option.builder("p")
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.longOpt("platefiles")
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.longOpt("plate-files")
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.hasArgs()
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.desc("Plate files to match")
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.required().build();
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options.addOption(inputPlates);
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.build();
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mainOptions.addOption(inputPlates);
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CommandLineParser parser = new DefaultParser();
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try {
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CommandLine line = parser.parse(options, args);
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if(line.hasOption("m")){
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CommandLine line = parser.parse(mainOptions, args);
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if(line.hasOption("match")){
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//line = parser.parse(mainOptions, args);
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String cellFile = line.getOptionValue("c");
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Integer lowThreshold = Integer.valueOf(line.getOptionValue(lowThresh));
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Integer highThreshold = Integer.valueOf(line.getOptionValue(highThresh));
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@@ -59,6 +181,49 @@ public class UserInterface {
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matchCDR3s(cellFile, plate, lowThreshold, highThreshold);
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}
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}
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else if(line.hasOption("cells")){
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//line = parser.parse(mainOptions, args);
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String filename = line.getOptionValue("o");
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Integer numDistCells = Integer.valueOf(line.getOptionValue("nc"));
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Integer freq = Integer.valueOf(line.getOptionValue("d"));
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makeCells(filename, numDistCells, freq);
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}
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else if(line.hasOption("plates")){
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//line = parser.parse(mainOptions, args);
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String cellFile = line.getOptionValue("c");
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String filenamePrefix = line.getOptionValue("o");
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Integer numWellsOnPlate = Integer.valueOf(line.getOptionValue("w"));
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Integer numPlatesToMake = Integer.valueOf(line.getOptionValue("np"));
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String[] concentrationsToUseString = line.getOptionValues("t");
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Integer numSections = concentrationsToUseString.length;
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Integer[] concentrationsToUse = new Integer[numSections];
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for(int i = 0; i <numSections; i++){
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concentrationsToUse[i] = Integer.valueOf(concentrationsToUseString[i]);
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}
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Double dropOutRate = Double.valueOf(line.getOptionValue("err"));
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if(line.hasOption("exponential")){
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Double lambda = Double.valueOf(line.getOptionValue("lambda"));
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for(int i = 1; i <= numPlatesToMake; i++){
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makePlateExp(cellFile, filenamePrefix + i, lambda, numWellsOnPlate,
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concentrationsToUse,dropOutRate);
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}
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}
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else if(line.hasOption("gaussian")){
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Double stdDev = Double.valueOf(line.getOptionValue("std-dev"));
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for(int i = 1; i <= numPlatesToMake; i++){
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makePlate(cellFile, filenamePrefix + i, stdDev, numWellsOnPlate,
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concentrationsToUse,dropOutRate);
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}
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}
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else if(line.hasOption("poisson")){
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for(int i = 1; i <= numPlatesToMake; i++){
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makePlatePoisson(cellFile, filenamePrefix + i, numWellsOnPlate,
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concentrationsToUse,dropOutRate);
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}
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}
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}
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}
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catch (ParseException exp) {
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System.err.println("Parsing failed. Reason: " + exp.getMessage());
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@@ -118,27 +283,47 @@ public class UserInterface {
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sc.next();
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}
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CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
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//CellSample sample = Simulator.generateCellSampleExp(numCells, cdr1Freq);
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CellFileWriter writer = new CellFileWriter(filename, sample);
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writer.writeCellsToFile();
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}
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//for calling from command line
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private static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
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CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
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CellFileWriter writer = new CellFileWriter(filename, sample);
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writer.writeCellsToFile();
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}
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private static void makePlate(String cellFile, String filename, Double stdDev,
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Integer numWells, Integer numSections,
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Integer[] concentrations, Double dropOutRate){
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private static void makePlateExp(String cellFile, String filename, Double lambda,
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Integer numWells, Integer[] concentrations, Double dropOutRate){
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CellFileReader cellReader = new CellFileReader(cellFile);
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
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samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells());
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
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samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
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PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
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writer.writePlateFile();
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}
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//method to output a CSV of
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private static void makePlatePoisson(String cellFile, String filename, Integer numWells,
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Integer[] concentrations, Double dropOutRate){
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CellFileReader cellReader = new CellFileReader(cellFile);
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Double stdDev = Math.sqrt(cellReader.getCellCount());
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
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samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
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PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
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writer.writePlateFile();
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}
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private static void makePlate(String cellFile, String filename, Double stdDev,
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Integer numWells, Integer[] concentrations, Double dropOutRate){
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CellFileReader cellReader = new CellFileReader(cellFile);
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
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samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
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PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
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writer.writePlateFile();
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}
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//method to output a CSV of sample plate
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private static void makePlate() {
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String cellFile = null;
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String filename = null;
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@@ -148,6 +333,8 @@ public class UserInterface {
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Integer[] concentrations = {1};
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Double dropOutRate = 0.0;
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boolean poisson = false;
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boolean exponential = false;
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double lambda = 1.5;
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try {
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System.out.println("\nMaking a sample plate requires a population of distinct cells");
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System.out.println("Please enter name of an existing cell sample file: ");
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@@ -158,6 +345,9 @@ public class UserInterface {
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System.out.println("Select T-cell frequency distribution function");
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System.out.println("1) Poisson");
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System.out.println("2) Gaussian");
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System.out.println("3) Exponential");
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System.out.println("(Note: approximate distribution in original paper is exponential, lambda = 0.6.)");
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System.out.println("(approximated from slope of log-log graph in figure 4c)");
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System.out.println("(Note: wider distributions are more memory intensive to match)");
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System.out.print("Enter selection value: ");
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input = sc.nextInt();
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@@ -173,9 +363,18 @@ public class UserInterface {
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throw new InputMismatchException("Value must be positive.");
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}
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break;
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case 3:
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exponential = true;
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System.out.println("Please enter lambda value for exponential distribution.");
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lambda = sc.nextDouble();
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if(lambda <= 0.0){
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throw new InputMismatchException("Value must be positive.");
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}
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break;
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default:
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System.out.println("Invalid input. Defaulting to Poisson.");
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poisson = true;
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System.out.println("Invalid input. Defaulting to exponential.");
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//poisson = true;
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exponential = true;
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}
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System.out.print("Number of wells on plate: ");
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numWells = sc.nextInt();
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@@ -210,13 +409,21 @@ public class UserInterface {
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sc.next();
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}
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CellFileReader cellReader = new CellFileReader(cellFile);
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if(poisson) {
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stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
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if(exponential){
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
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samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
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PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
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writer.writePlateFile();
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}
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else {
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if (poisson) {
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stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
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}
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
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samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
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PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
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writer.writePlateFile();
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}
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Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
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samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells());
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PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
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writer.writePlateFile();
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}
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private static void matchCDR3s(String cellFile, String plateFile, Integer lowThreshold, Integer highThreshold){
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