Refactoring to allow graphs from file
This commit is contained in:
@@ -14,261 +14,266 @@ public class UserInterface {
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static boolean quit = false;
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public static void main(String[] args) {
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//for now, commenting out all the command line argument stuff.
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// Refactoring to output files of graphs, so it would all need to change anyway.
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if(args.length != 0){
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//These command line options are a big mess
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//Really, I don't think command line tools are expected to work in this many different modes
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//making cells, making plates, and matching are the sort of thing that UNIX philosophy would say
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//should be three separate programs.
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//There might be a way to do it with option parameters?
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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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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("cell-file")
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.hasArg()
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.argName("file")
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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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// if(args.length != 0){
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// //These command line options are a big mess
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// //Really, I don't think command line tools are expected to work in this many different modes
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// //making cells, making plates, and matching are the sort of thing that UNIX philosophy would say
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// //should be three separate programs.
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// //There might be a way to do it with option parameters?
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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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// 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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// 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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//
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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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.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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.build();
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mainOptions.addOption(highThresh);
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Option occDiff = Option.builder("occdiff")
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.longOpt("occupancy-difference")
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.hasArg()
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.argName("Number")
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.desc("Maximum difference in alpha/beta occupancy to attempt matching")
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.build();
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mainOptions.addOption(occDiff);
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Option overlapPer = Option.builder("ovper")
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.longOpt("overlap-percent")
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.hasArg()
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.argName("Percent")
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.desc("Minimum overlap percent to attempt matching (0 -100)")
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.build();
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mainOptions.addOption(overlapPer);
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Option inputPlates = Option.builder("p")
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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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.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(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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Integer occupancyDifference = Integer.valueOf(line.getOptionValue(occDiff));
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Integer overlapPercent = Integer.valueOf(line.getOptionValue(overlapPer));
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for(String plate: line.getOptionValues("p")) {
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matchCDR3s(cellFile, plate, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
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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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}
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}
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else {
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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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//
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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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//
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// //Options plateOptions = new Options();
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// Option inputCells = Option.builder("c")
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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 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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//
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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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//
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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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//
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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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//
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//
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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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//
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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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// .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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// .build();
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// mainOptions.addOption(highThresh);
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// Option occDiff = Option.builder("occdiff")
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// .longOpt("occupancy-difference")
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// .hasArg()
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// .argName("Number")
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// .desc("Maximum difference in alpha/beta occupancy to attempt matching")
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// .build();
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// mainOptions.addOption(occDiff);
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// Option overlapPer = Option.builder("ovper")
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// .longOpt("overlap-percent")
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// .hasArg()
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// .argName("Percent")
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// .desc("Minimum overlap percent to attempt matching (0 -100)")
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// .build();
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// mainOptions.addOption(overlapPer);
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// Option inputPlates = Option.builder("p")
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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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// .build();
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// mainOptions.addOption(inputPlates);
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//
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//
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//
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// CommandLineParser parser = new DefaultParser();
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// try {
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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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// Integer occupancyDifference = Integer.valueOf(line.getOptionValue(occDiff));
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// Integer overlapPercent = Integer.valueOf(line.getOptionValue(overlapPer));
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// for(String plate: line.getOptionValues("p")) {
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// matchCDR3s(cellFile, plate, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
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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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//
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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")){
|
||||
// Double lambda = Double.valueOf(line.getOptionValue("lambda"));
|
||||
// for(int i = 1; i <= numPlatesToMake; i++){
|
||||
// makePlateExp(cellFile, filenamePrefix + i, lambda, numWellsOnPlate,
|
||||
// concentrationsToUse,dropOutRate);
|
||||
// }
|
||||
// }
|
||||
// else if(line.hasOption("gaussian")){
|
||||
// Double stdDev = Double.valueOf(line.getOptionValue("std-dev"));
|
||||
// for(int i = 1; i <= numPlatesToMake; i++){
|
||||
// makePlate(cellFile, filenamePrefix + i, stdDev, numWellsOnPlate,
|
||||
// concentrationsToUse,dropOutRate);
|
||||
// }
|
||||
//
|
||||
// }
|
||||
// else if(line.hasOption("poisson")){
|
||||
// for(int i = 1; i <= numPlatesToMake; i++){
|
||||
// makePlatePoisson(cellFile, filenamePrefix + i, numWellsOnPlate,
|
||||
// concentrationsToUse,dropOutRate);
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// catch (ParseException exp) {
|
||||
// System.err.println("Parsing failed. Reason: " + exp.getMessage());
|
||||
// }
|
||||
// }
|
||||
// else {
|
||||
while (!quit) {
|
||||
System.out.println("\nALPHA/BETA T-CELL RECEPTOR MATCHING SIMULATOR");
|
||||
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) Simulate CDR3 alpha/beta T cell matching");
|
||||
System.out.println("4) Simulate CDR3/CDR1 T cell matching");
|
||||
System.out.println("5) Acknowledgements");
|
||||
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("6) Simulate CDR3/CDR1 T cell matching");
|
||||
System.out.println("7) Acknowledgements");
|
||||
System.out.println("0) Exit");
|
||||
try {
|
||||
input = sc.nextInt();
|
||||
switch (input) {
|
||||
case 1 -> makeCells();
|
||||
case 2 -> makePlate();
|
||||
case 3 -> matchCells();
|
||||
case 4 -> matchCellsCDR1();
|
||||
case 5 -> acknowledge();
|
||||
case 3 -> makeCDR3Graph();
|
||||
case 5 -> matchCells();
|
||||
case 6 -> matchCellsCDR1();
|
||||
case 7 -> acknowledge();
|
||||
case 0 -> quit = true;
|
||||
default -> throw new InputMismatchException("Invalid input.");
|
||||
}
|
||||
@@ -278,7 +283,7 @@ public class UserInterface {
|
||||
}
|
||||
}
|
||||
sc.close();
|
||||
}
|
||||
// }
|
||||
}
|
||||
|
||||
private static void makeCells() {
|
||||
@@ -448,6 +453,8 @@ public class UserInterface {
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
private static void matchCDR3s(String cellFile, String plateFile, Integer lowThreshold, Integer highThreshold,
|
||||
Integer maxOccupancyDifference, Integer minOverlapPercent){
|
||||
CellFileReader cellReader = new CellFileReader(cellFile);
|
||||
@@ -472,6 +479,11 @@ public class UserInterface {
|
||||
}
|
||||
}
|
||||
|
||||
private static void makeCDR3Graph() {
|
||||
String filename = null;
|
||||
String cellFile = null;
|
||||
String plateFile = null;
|
||||
}
|
||||
|
||||
private static void matchCells() {
|
||||
String filename = null;
|
||||
@@ -525,7 +537,10 @@ public class UserInterface {
|
||||
highThreshold = plate.getSize() - 1;
|
||||
}
|
||||
List<Integer[]> cells = cellReader.getCells();
|
||||
MatchingResult results = Simulator.matchCDR3s(cells, plate, lowThreshold, highThreshold, maxOccupancyDiff, minOverlapPercent, true);
|
||||
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();
|
||||
|
||||
Reference in New Issue
Block a user