Update readme with CLI arguments

readme.md

@@ -48,8 +48,13 @@ For example, to run the program with 32 gigabytes of memory, use the command:
 
 `java -Xmx32G -jar BiGpairSEQ_Sim.jar`
 
-Once running, BiGpairSEQ_Sim has an interactive, menu-driven CLI for generating files and simulating TCR pairing. The
-main menu looks like this:
+There are a number of command line options, to allow the program to be used in shell scripts. For a full list,
+use the -help flag:
+
+`java -jar BiGpairSEQ_Sim.jar -help`
+
+If no command line arguments are given, BiGpairSEQ_Sim will launch with an interactive, menu-driven CLI for 
+generating files and simulating TCR pairing. The main menu looks like this:
 
 ```
 --------BiGPairSEQ SIMULATOR--------
@@ -78,6 +83,7 @@ By default, the Options menu looks like this:
 0) Return to main menu
 ```
 
+
 ### INPUT/OUTPUT
 
 To run the simulation, the program reads and writes 4 kinds of files:
@@ -290,11 +296,12 @@ slightly less time than the simulation itself. Real elapsed time from start to f
 * ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
   * ~~Custom vertex type with attribute for sequence occupancy?~~ ABANDONED
     * Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.
-* Re-implement command line arguments, to enable scripting and statistical simulation studies
+* ~~Re-implement command line arguments, to enable scripting and statistical simulation studies~~ DONE
 * Re-implement CDR1 matching method
 * Implement Duan and Su's maximum weight matching algorithm
     * Add controllable algorithm-type parameter?
     * This would be fun and valuable, but probably take more time than I have for a hobby project.
+* Implement Vose's alias method for arbitrary statistical distributions of cells
   
   
 ## CITATIONS

src/main/java/BiGpairSEQ.java

@@ -23,8 +23,8 @@ public class BiGpairSEQ {
         }
         else {
             //This will be uncommented when command line arguments are re-implemented.
-            //CommandLineInterface.startCLI(args);
-            System.out.println("Command line arguments are still being re-implemented.");
+            CommandLineInterface.startCLI(args);
+            //System.out.println("Command line arguments are still being re-implemented.");
         }
     }
 

src/main/java/CommandLineInterface.java

@@ -1,5 +1,9 @@
 import org.apache.commons.cli.*;
 
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.stream.Stream;
+
 /*
  * Class for parsing options passed to program from command line
  *
@@ -29,6 +33,8 @@ import org.apache.commons.cli.*;
  * cellfile : name of the cell sample file to use as input
  * platefile : name of the sample plate file to use as input
  * output : name of the output file
+ * graphml : output a graphml file
+ * binary : output a serialized binary object file
  *
  * Match flags:
  * graphFile : name of graph and data file to use as input
@@ -43,286 +49,379 @@ import org.apache.commons.cli.*;
 public class CommandLineInterface {
 
     public static void startCLI(String[] args) {
-        //These command line options are a big mess
-        //Really, I don't think command line tools are expected to work in this many different modes
-        //making cells, making plates, and matching are the sort of thing that UNIX philosophy would say
-        //should be three separate programs.
-        //There might be a way to do it with option parameters?
-
-        //main options set
-        Options mainOptions = new Options();
-        Option makeCells = Option.builder("cells")
-                .longOpt("make-cells")
-                .desc("Makes a file of distinct cells")
-                .build();
-        Option makePlate = Option.builder("plates")
-                .longOpt("make-plates")
-                .desc("Makes a sample plate file")
-                .build();
-        Option makeGraph = Option.builder("graph")
-                .longOpt("make-graph")
-                .desc("Makes a graph and data file")
-                .build();
-        Option matchCDR3 = Option.builder("match")
-                .longOpt("match-cdr3")
-                .desc("Match CDR3s. Requires a cell sample file and any number of plate files.")
-                .build();
-        OptionGroup mainGroup = new OptionGroup();
-        mainGroup.addOption(makeCells);
-        mainGroup.addOption(makePlate);
-        mainGroup.addOption(makeGraph);
-        mainGroup.addOption(matchCDR3);
-        mainGroup.setRequired(true);
-        mainOptions.addOptionGroup(mainGroup);
-
-        //Reuse clones of this for other options groups, rather than making it lots of times
-        Option outputFile = Option.builder("o")
-                .longOpt("output-file")
-                .hasArg()
-                .argName("filename")
-                .desc("Name of output file")
-                .build();
-        mainOptions.addOption(outputFile);
-
-        //Options cellOptions = new Options();
-        Option numCells = Option.builder("nc")
-                .longOpt("num-cells")
-                .desc("The number of distinct cells to generate")
-                .hasArg()
-                .argName("number")
-                .build();
-        mainOptions.addOption(numCells);
-        Option cdr1Freq = Option.builder("d")
-                .longOpt("peptide-diversity-factor")
-                .hasArg()
-                .argName("number")
-                .desc("Number of distinct CDR3s for every CDR1")
-                .build();
-        mainOptions.addOption(cdr1Freq);
-        //Option cellOutput = (Option) outputFile.clone();
-        //cellOutput.setRequired(true);
-        //mainOptions.addOption(cellOutput);
-
-        //Options plateOptions = new Options();
-        Option inputCells = Option.builder("c")
-                .longOpt("cell-file")
-                .hasArg()
-                .argName("file")
-                .desc("The cell sample file used for filling wells")
-                .build();
-        mainOptions.addOption(inputCells);
-        Option numWells = Option.builder("w")
-                .longOpt("num-wells")
-                .hasArg()
-                .argName("number")
-                .desc("The number of wells on each plate")
-                .build();
-        mainOptions.addOption(numWells);
-        Option numPlates = Option.builder("np")
-                .longOpt("num-plates")
-                .hasArg()
-                .argName("number")
-                .desc("The number of plate files to output")
-                .build();
-        mainOptions.addOption(numPlates);
-        //Option plateOutput = (Option) outputFile.clone();
-        //plateOutput.setRequired(true);
-        //plateOutput.setDescription("Prefix for plate output filenames");
-        //mainOptions.addOption(plateOutput);
-        Option plateErr = Option.builder("err")
-                .longOpt("drop-out-rate")
-                .hasArg()
-                .argName("number")
-                .desc("Well drop-out rate. (Probability between 0 and 1)")
-                .build();
-        mainOptions.addOption(plateErr);
-        Option plateConcentrations = Option.builder("t")
-                .longOpt("t-cells-per-well")
-                .hasArgs()
-                .argName("number 1, number 2, ...")
-                .desc("Number of T cells per well for each plate section")
-                .build();
-        mainOptions.addOption(plateConcentrations);
-
-//different distributions, mutually exclusive
-        OptionGroup plateDistributions = new OptionGroup();
-        Option plateExp = Option.builder("exponential")
-                .desc("Sample from distinct cells with exponential frequency distribution")
-                .build();
-        plateDistributions.addOption(plateExp);
-        Option plateGaussian = Option.builder("gaussian")
-                .desc("Sample from distinct cells with gaussain frequency distribution")
-                .build();
-        plateDistributions.addOption(plateGaussian);
-        Option platePoisson = Option.builder("poisson")
-                .desc("Sample from distinct cells with poisson frequency distribution")
-                .build();
-        plateDistributions.addOption(platePoisson);
-        mainOptions.addOptionGroup(plateDistributions);
-
-        Option plateStdDev = Option.builder("stddev")
-                .desc("Standard deviation for gaussian distribution")
-                .hasArg()
-                .argName("number")
-                .build();
-        mainOptions.addOption(plateStdDev);
-
-        Option plateLambda = Option.builder("lambda")
-                .desc("Lambda for exponential distribution")
-                .hasArg()
-                .argName("number")
-                .build();
-        mainOptions.addOption(plateLambda);
-
-
-
-//
-//            String cellFile, String filename, Double stdDev,
-//                    Integer numWells, Integer numSections,
-//                    Integer[] concentrations, Double dropOutRate
-//
-
-        //Options matchOptions = new Options();
-        inputCells.setDescription("The cell sample file to be used for matching.");
-        mainOptions.addOption(inputCells);
-        Option lowThresh = Option.builder("low")
-                .longOpt("low-threshold")
-                .hasArg()
-                .argName("number")
-                .desc("Sets the minimum occupancy overlap to attempt matching")
-                .build();
-        mainOptions.addOption(lowThresh);
-        Option highThresh = Option.builder("high")
-                .longOpt("high-threshold")
-                .hasArg()
-                .argName("number")
-                .desc("Sets the maximum occupancy overlap to attempt matching")
-                .build();
-        mainOptions.addOption(highThresh);
-        Option occDiff = Option.builder("occdiff")
-                .longOpt("occupancy-difference")
-                .hasArg()
-                .argName("Number")
-                .desc("Maximum difference in alpha/beta occupancy to attempt matching")
-                .build();
-        mainOptions.addOption(occDiff);
-        Option overlapPer = Option.builder("ovper")
-                .longOpt("overlap-percent")
-                .hasArg()
-                .argName("Percent")
-                .desc("Minimum overlap percent to attempt matching (0 -100)")
-                .build();
-        mainOptions.addOption(overlapPer);
-        Option inputPlates = Option.builder("p")
-                .longOpt("plate-files")
-                .hasArgs()
-                .desc("Plate files to match")
-                .build();
-        mainOptions.addOption(inputPlates);
-
-
+        //Options sets for the different modes
+        Options mainOptions = buildMainOptions();
+        Options cellOptions = buildCellOptions();
+        Options plateOptions = buildPlateOptions();
+        Options graphOptions = buildGraphOptions();
+        Options matchOptions = buildMatchCDR3options();
 
         CommandLineParser parser = new DefaultParser();
-        try {
-            CommandLine line = parser.parse(mainOptions, args);
-            if(line.hasOption("match")){
-                //line = parser.parse(mainOptions, args);
-                //String cellFile = line.getOptionValue("c");
-                String graphFile = line.getOptionValue("g");
-                Integer lowThreshold = Integer.valueOf(line.getOptionValue(lowThresh));
-                Integer highThreshold = Integer.valueOf(line.getOptionValue(highThresh));
-                Integer occupancyDifference = Integer.valueOf(line.getOptionValue(occDiff));
-                Integer overlapPercent = Integer.valueOf(line.getOptionValue(overlapPer));
-                for(String plate: line.getOptionValues("p")) {
-                    matchCDR3s(graphFile, lowThreshold, highThreshold, occupancyDifference, overlapPercent);
-                }
+        try{
+            CommandLine line = parser.parse(mainOptions, Arrays.copyOfRange(args, 0, 1));
+
+            if (line.hasOption("help")) {
+                HelpFormatter formatter = new HelpFormatter();
+                formatter.printHelp("BiGpairSEQ_Sim", mainOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_SIM -cells", cellOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim -plate", plateOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim -graph", graphOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim -match", matchOptions);
             }
-            else if(line.hasOption("cells")){
-                //line = parser.parse(mainOptions, args);
+            else if (line.hasOption("cells")) {
+                line = parser.parse(cellOptions, Arrays.copyOfRange(args, 1, args.length));
+                Integer number = Integer.valueOf(line.getOptionValue("n"));
+                Integer diversity = Integer.valueOf(line.getOptionValue("d"));
                 String filename = line.getOptionValue("o");
-                Integer numDistCells = Integer.valueOf(line.getOptionValue("nc"));
-                Integer freq = Integer.valueOf(line.getOptionValue("d"));
-                makeCells(filename, numDistCells, freq);
+                makeCells(filename, number, diversity);
             }
-            else if(line.hasOption("plates")){
-                //line = parser.parse(mainOptions, args);
-                String cellFile = line.getOptionValue("c");
-                String filenamePrefix = line.getOptionValue("o");
-                Integer numWellsOnPlate = Integer.valueOf(line.getOptionValue("w"));
-                Integer numPlatesToMake = Integer.valueOf(line.getOptionValue("np"));
-                String[] concentrationsToUseString = line.getOptionValues("t");
-                Integer numSections = concentrationsToUseString.length;
 
-                Integer[] concentrationsToUse = new Integer[numSections];
-                for(int i = 0; i <numSections; i++){
-                    concentrationsToUse[i] = Integer.valueOf(concentrationsToUseString[i]);
+            else if (line.hasOption("plate")) {
+                line = parser.parse(plateOptions, Arrays.copyOfRange(args, 1, args.length));
+                //get the cells
+                String cellFilename = line.getOptionValue("c");
+                CellSample cells = getCells(cellFilename);
+                //get the rest of the parameters
+                Integer[] populations;
+                String outputFilename = line.getOptionValue("o");
+                Integer numWells = Integer.parseInt(line.getOptionValue("w"));
+                Double dropoutRate = Double.parseDouble(line.getOptionValue("err"));
+                if (line.hasOption("random")) {
+                    //Array holding values of minimum and maximum populations
+                   Integer[] min_max = Stream.of(line.getOptionValues("random"))
+                           .mapToInt(Integer::parseInt)
+                           .boxed()
+                           .toArray(Integer[]::new);
+                   populations = BiGpairSEQ.getRand().ints(min_max[0], min_max[1] + 1)
+                            .limit(numWells)
+                            .boxed()
+                            .toArray(Integer[]::new);
                 }
-                Double dropOutRate = Double.valueOf(line.getOptionValue("err"));
-                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("pop")) {
+                    populations = Stream.of(line.getOptionValues("pop"))
+                            .mapToInt(Integer::parseInt)
+                            .boxed()
+                            .toArray(Integer[]::new);
                 }
-                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{
+                    populations = new Integer[1];
+                    populations[0] = 1;
+                }
+                //make the plate
+                Plate plate;
+                if (line.hasOption("poisson")) {
+                    Double stdDev = Math.sqrt(numWells);
+                    plate = new Plate(cells, cellFilename, numWells, populations, dropoutRate, stdDev, false);
+                }
+                else if (line.hasOption("gaussian")) {
+                    Double stdDev = Double.parseDouble(line.getOptionValue("stddev"));
+                    plate = new Plate(cells, cellFilename, numWells, populations, dropoutRate, stdDev, false);
+                }
+                else {
+                    assert line.hasOption("exponential");
+                    Double lambda = Double.parseDouble(line.getOptionValue("lambda"));
+                    plate = new Plate(cells, cellFilename, numWells, populations, dropoutRate, lambda, true);
+                }
+                PlateFileWriter writer = new PlateFileWriter(outputFilename, plate);
+                writer.writePlateFile();
+            }
 
+            else if (line.hasOption("graph")) { //Making a graph
+                line = parser.parse(graphOptions, Arrays.copyOfRange(args, 1, args.length));
+                String cellFilename = line.getOptionValue("c");
+                String plateFilename = line.getOptionValue("p");
+                String outputFilename = line.getOptionValue("o");
+                //get cells
+                CellSample cells = getCells(cellFilename);
+                //get plate
+                Plate plate = getPlate(plateFilename);
+                GraphWithMapData graph = Simulator.makeGraph(cells, plate, false);
+                if (!line.hasOption("no-binary")) { //output binary file unless told not to
+                    GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
+                    writer.writeDataToFile();
                 }
-                else if(line.hasOption("poisson")){
-                    for(int i = 1; i <= numPlatesToMake; i++){
-                        makePlatePoisson(cellFile, filenamePrefix + i, numWellsOnPlate,
-                                concentrationsToUse,dropOutRate);
-                    }
+                if (line.hasOption("graphml")) { //if told to, output graphml file
+                    GraphMLFileWriter gmlwriter = new GraphMLFileWriter(outputFilename, graph);
+                    gmlwriter.writeGraphToFile();
                 }
             }
+
+            else if (line.hasOption("match")) { //can add a flag for which match type in future, spit this in two
+                line = parser.parse(matchOptions, Arrays.copyOfRange(args, 1, args.length));
+                String graphFilename = line.getOptionValue("g");
+                String outputFilename = line.getOptionValue("o");
+                Integer minThreshold = Integer.parseInt(line.getOptionValue("min"));
+                Integer maxThreshold = Integer.parseInt(line.getOptionValue("max"));
+                Integer minOverlapPct;
+                if (line.hasOption("minpct")) { //see if this filter is being used
+                    minOverlapPct = Integer.parseInt(line.getOptionValue("minpct"));
+                }
+                else {
+                    minOverlapPct = 0;
+                }
+                Integer maxOccupancyDiff;
+                if (line.hasOption("maxdiff")) { //see if this filter is being used
+                    maxOccupancyDiff = Integer.parseInt(line.getOptionValue("maxdiff"));
+                }
+                else {
+                    maxOccupancyDiff = Integer.MAX_VALUE;
+                }
+                GraphWithMapData graph = getGraph(graphFilename);
+                MatchingResult result = Simulator.matchCDR3s(graph, graphFilename, minThreshold, maxThreshold,
+                        maxOccupancyDiff, minOverlapPct, false);
+                MatchingFileWriter writer = new MatchingFileWriter(outputFilename, result);
+                writer.writeResultsToFile();
+                //can put a bunch of ifs for outputting various things from the MatchingResult to System.out here
+                //after I put those flags in the matchOptions
+            }
         }
         catch (ParseException exp) {
             System.err.println("Parsing failed.  Reason: " + exp.getMessage());
         }
     }
 
+    private static Option outputFileOption() {
+        Option outputFile = Option.builder("o")
+                .longOpt("output-file")
+                .hasArg()
+                .argName("filename")
+                .desc("Name of output file")
+                .required()
+                .build();
+        return outputFile;
+    }
+
+    private static Options buildMainOptions() {
+        Options mainOptions = new Options();
+        Option help = Option.builder("help")
+                .desc("Displays this help menu")
+                .build();
+        Option makeCells = Option.builder("cells")
+                .longOpt("make-cells")
+                .desc("Makes a cell sample file of distinct T cells")
+                .build();
+        Option makePlate = Option.builder("plate")
+                .longOpt("make-plate")
+                .desc("Makes a sample plate file. Requires a cell sample file.")
+                .build();
+        Option makeGraph = Option.builder("graph")
+                .longOpt("make-graph")
+                .desc("Makes a graph/data file. Requires a cell sample file and a sample plate file")
+                .build();
+        Option matchCDR3 = Option.builder("match")
+                .longOpt("match-cdr3")
+                .desc("Matches CDR3s. Requires a graph/data file.")
+                .build();
+        OptionGroup mainGroup = new OptionGroup();
+        mainGroup.addOption(help);
+        mainGroup.addOption(makeCells);
+        mainGroup.addOption(makePlate);
+        mainGroup.addOption(makeGraph);
+        mainGroup.addOption(matchCDR3);
+        mainGroup.setRequired(true);
+        mainOptions.addOptionGroup(mainGroup);
+        return mainOptions;
+    }
+
+    private static Options buildCellOptions() {
+        Options cellOptions = new Options();
+        Option numCells = Option.builder("n")
+                .longOpt("num-cells")
+                .desc("The number of distinct cells to generate")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option cdr3Diversity = Option.builder("d")
+                .longOpt("diversity-factor")
+                .desc("The factor by which unique CDR3s outnumber unique CDR1s")
+                .hasArg()
+                .argName("factor")
+                .required().build();
+        cellOptions.addOption(numCells);
+        cellOptions.addOption(cdr3Diversity);
+        cellOptions.addOption(outputFileOption());
+        return cellOptions;
+    }
+
+    private static Options buildPlateOptions() {
+        Options plateOptions = new Options();
+        Option cellFile = Option.builder("c") // add this to plate options
+                .longOpt("cell-file")
+                .desc("The cell sample file to use")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option numWells = Option.builder("w")// add this to plate options
+                .longOpt("wells")
+                .desc("The number of wells on the sample plate")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        //options group for choosing with distribution to use
+        OptionGroup distributions = new OptionGroup();// add this to plate options
+        distributions.setRequired(true);
+        Option poisson = Option.builder("poisson")
+                .desc("Use a Poisson distribution for cell sample")
+                .build();
+        Option gaussian = Option.builder("gaussian")
+                .desc("Use a Gaussian distribution for cell sample")
+                .build();
+        Option exponential = Option.builder("exponential")
+                .desc("Use an exponential distribution for cell sample")
+                .build();
+        distributions.addOption(poisson);
+        distributions.addOption(gaussian);
+        distributions.addOption(exponential);
+        //options group for statistical distribution parameters
+        OptionGroup statParams = new OptionGroup();// add this to plate options
+        Option stdDev = Option.builder("stddev")
+                .desc("If using -gaussian flag, standard deviation for distrbution")
+                .hasArg()
+                .argName("value")
+                .build();
+        Option lambda = Option.builder("lambda")
+                .desc("If using -exponential flag, lambda value for distribution")
+                .hasArg()
+                .argName("value")
+                .build();
+        statParams.addOption(stdDev);
+        statParams.addOption(lambda);
+        //Option group for random plate or set populations
+        OptionGroup wellPopOptions = new OptionGroup(); // add this to plate options
+        wellPopOptions.setRequired(true);
+        Option randomWellPopulations = Option.builder("random")
+                .desc("Randomize well populations on sample plate. Takes two arguments: the minimum possible population and the maximum possible population.")
+                .hasArgs()
+                .numberOfArgs(2)
+                .argName("minimum maximum")
+                .build();
+        Option specificWellPopulations = Option.builder("pop")
+                .desc("The well populations for each section of the sample plate. There will be as many sections as there are populations given.")
+                .hasArgs()
+                .argName("number [number]...")
+                .build();
+        Option dropoutRate = Option.builder("err") //add this to plate options
+                .hasArg()
+                .desc("The sequence dropout rate due to amplification error. (0.0 - 1.0)")
+                .argName("rate")
+                .required()
+                .build();
+        wellPopOptions.addOption(randomWellPopulations);
+        wellPopOptions.addOption(specificWellPopulations);
+        plateOptions.addOption(cellFile);
+        plateOptions.addOption(numWells);
+        plateOptions.addOptionGroup(distributions);
+        plateOptions.addOptionGroup(statParams);
+        plateOptions.addOptionGroup(wellPopOptions);
+        plateOptions.addOption(dropoutRate);
+        plateOptions.addOption(outputFileOption());
+        return plateOptions;
+    }
+
+    private static Options buildGraphOptions() {
+        Options graphOptions = new Options();
+        Option cellFilename = Option.builder("c")
+                .longOpt("cell-file")
+                .desc("Cell sample file to use for checking accuracy")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option plateFilename = Option.builder("p")
+                .longOpt("plate-filename")
+                .desc("Sample plate file (made from given cell sample file) to construct graph from")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option outputGraphML = Option.builder("graphml")
+                .desc("Output GraphML file")
+                .build();
+        Option outputSerializedBinary = Option.builder("nb")
+                .longOpt("no-binary")
+                .desc("Don't output serialized binary file")
+                .build();
+        graphOptions.addOption(cellFilename);
+        graphOptions.addOption(plateFilename);
+        graphOptions.addOption(outputFileOption());
+        graphOptions.addOption(outputGraphML);
+        graphOptions.addOption(outputSerializedBinary);
+        return graphOptions;
+    }
+
+    private static Options buildMatchCDR3options() {
+        Options matchCDR3options = new Options();
+        Option graphFilename = Option.builder("g")
+                .longOpt("graph-file")
+                .desc("The graph/data file to use")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option minOccupancyOverlap = Option.builder("min")
+                .desc("The minimum number of shared wells to attempt to match a sequence pair")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option maxOccupancyOverlap = Option.builder("max")
+                .desc("The maximum number of shared wells to attempt to match a sequence pair")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option minOverlapPercent = Option.builder("minpct")
+                .desc("(Optional) The minimum percentage of a sequence's total occupancy shared by another sequence to attempt matching. (0 - 100) ")
+                .hasArg()
+                .argName("percent")
+                .build();
+        Option maxOccupancyDifference = Option.builder("maxdiff")
+                .desc("(Optional) The maximum difference in total occupancy between two sequences to attempt matching.")
+                .hasArg()
+                .argName("number")
+                .build();
+        matchCDR3options.addOption(graphFilename);
+        matchCDR3options.addOption(minOccupancyOverlap);
+        matchCDR3options.addOption(maxOccupancyOverlap);
+        matchCDR3options.addOption(minOverlapPercent);
+        matchCDR3options.addOption(maxOccupancyDifference);
+        matchCDR3options.addOption(outputFileOption());
+        //options for output to System.out
+       //Option printPairingErrorRate = Option.builder()
+
+        return matchCDR3options;
+    }
+
+
+
+    private static CellSample getCells(String cellFilename) {
+        assert cellFilename != null;
+        CellFileReader reader = new CellFileReader(cellFilename);
+        return reader.getCellSample();
+    }
+
+    private static Plate getPlate(String plateFilename) {
+        assert plateFilename != null;
+        PlateFileReader reader = new PlateFileReader(plateFilename);
+        return reader.getSamplePlate();
+    }
+
+    private static GraphWithMapData getGraph(String graphFilename) {
+        assert graphFilename != null;
+        try{
+            GraphDataObjectReader reader = new GraphDataObjectReader(graphFilename, false);
+            return reader.getData();
+
+        }
+        catch (IOException ex) {
+            ex.printStackTrace();
+            return null;
+        }
+    }
+
     //for calling from command line
-    public static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
+    public static void makeCells(String filename, Integer numCells, Integer cdr1Freq) {
         CellSample sample = new CellSample(numCells, cdr1Freq);
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
     }
-
-    public 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.getListOfDistinctCellsDEPRECATED(), 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.getCellCountDEPRECATED());
-        Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
-        samplePlate.fillWells(cellReader.getFilename(), cellReader.getListOfDistinctCellsDEPRECATED(), 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.getListOfDistinctCellsDEPRECATED(), stdDev);
-        PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
-        writer.writePlateFile();
-    }
-
-    private static void matchCDR3s(String graphFile, Integer lowThreshold, Integer highThreshold,
-                                   Integer occupancyDifference, Integer overlapPercent) {
-
-    }
 }

src/main/java/GraphDataObjectReader.java

@@ -1,10 +1,12 @@
 import java.io.*;
 
 public class GraphDataObjectReader {
+
     private GraphWithMapData data;
     private String filename;
+    private boolean verbose = true;
 
-    public GraphDataObjectReader(String filename) throws IOException {
+    public GraphDataObjectReader(String filename, boolean verbose) throws IOException {
         if(!filename.matches(".*\\.ser")){
             filename = filename + ".ser";
         }

src/main/java/GraphDataObjectWriter.java

@@ -1,3 +1,5 @@
+import org.jgrapht.Graph;
+
 import java.io.BufferedOutputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -7,6 +9,7 @@ public class GraphDataObjectWriter {
 
     private GraphWithMapData data;
     private String filename;
+    private boolean verbose = true;
 
     public GraphDataObjectWriter(String filename, GraphWithMapData data) {
         if(!filename.matches(".*\\.ser")){
@@ -16,13 +19,24 @@ public class GraphDataObjectWriter {
         this.data = data;
     }
 
+    public GraphDataObjectWriter(String filename, GraphWithMapData data, boolean verbose) {
+        this.verbose = verbose;
+        if(!filename.matches(".*\\.ser")){
+            filename = filename + ".ser";
+        }
+        this.filename = filename;
+        this.data = data;
+    }
+
     public void writeDataToFile() {
         try (BufferedOutputStream bufferedOut = new BufferedOutputStream(new FileOutputStream(filename));
 
              ObjectOutputStream out = new ObjectOutputStream(bufferedOut);
         ){
-            System.out.println("Writing graph and occupancy data to file. This may take some time.");
-            System.out.println("File I/O time is not included in results.");
+            if(verbose) {
+                System.out.println("Writing graph and occupancy data to file. This may take some time.");
+                System.out.println("File I/O time is not included in results.");
+            }
             out.writeObject(data);
         } catch (IOException ex) {
             ex.printStackTrace();

src/main/java/InteractiveInterface.java

@@ -227,16 +227,14 @@ public class InteractiveInterface {
         Plate samplePlate;
         PlateFileWriter writer;
         if(exponential){
-            samplePlate = new Plate(numWells, dropOutRate, populations);
-            samplePlate.fillWellsExponential(cellFile, cells.getCells(), lambda);
+            samplePlate = new Plate(cells, cellFile, numWells, populations, dropOutRate, lambda, true);
             writer = new PlateFileWriter(filename, samplePlate);
         }
         else {
             if (poisson) {
                 stdDev = Math.sqrt(cells.getCellCount()); //gaussian with square root of elements approximates poisson
             }
-            samplePlate = new Plate(numWells, dropOutRate, populations);
-            samplePlate.fillWells(cellFile, cells.getCells(), stdDev);
+            samplePlate = new Plate(cells, cellFile, numWells, populations, dropOutRate, stdDev, false);
             writer = new PlateFileWriter(filename, samplePlate);
         }
         System.out.println("Writing Sample Plate to file");
@@ -292,7 +290,7 @@ public class InteractiveInterface {
         else {
             System.out.println("Reading Sample Plate file: " + plateFile);
             PlateFileReader plateReader = new PlateFileReader(plateFile);
-            plate = new Plate(plateReader.getFilename(), plateReader.getWells());
+            plate = plateReader.getSamplePlate();
             if(BiGpairSEQ.cachePlate()) {
                 BiGpairSEQ.setPlateInMemory(plate, plateFile);
             }
@@ -306,8 +304,7 @@ public class InteractiveInterface {
             System.out.println("Returning to main menu.");
         }
         else{
-            List<Integer[]> cells = cellSample.getCells();
-            GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
+            GraphWithMapData data = Simulator.makeGraph(cellSample, plate, true);
             assert filename != null;
             if(BiGpairSEQ.outputBinary()) {
                 GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
@@ -378,7 +375,7 @@ public class InteractiveInterface {
             data = BiGpairSEQ.getGraphInMemory();
         }
         else {
-            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
+            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename, true);
             data = dataReader.getData();
             if(BiGpairSEQ.cacheGraph()) {
                 BiGpairSEQ.setGraphInMemory(data, graphFilename);

src/main/java/MatchingResult.java

@@ -21,15 +21,15 @@ public class MatchingResult {
          * well populations *
          * total alphas found *
          * total betas found *
-         * high overlap threshold
-         * low overlap threshold
-         * maximum occupancy difference
-         * minimum overlap percent
-         * pairing attempt rate
-         * correct pairing count
-         * incorrect pairing count
-         * pairing error rate
-         * simulation time
+         * high overlap threshold *
+         * low overlap threshold *
+         * maximum occupancy difference *
+         * minimum overlap percent *
+         * pairing attempt rate *
+         * correct pairing count *
+         * incorrect pairing count *
+         * pairing error rate *
+         * simulation time (seconds)
          */
         this.metadata = metadata;
         this.comments = new ArrayList<>();
@@ -91,6 +91,22 @@ public class MatchingResult {
         return Integer.parseInt(metadata.get("total beta count"));
     }
 
-    //put in the rest of these methods following the same pattern
+    public Integer getHighOverlapThreshold() { return Integer.parseInt(metadata.get("high overlap threshold"));}
+
+    public Integer getLowOverlapThreshold() { return Integer.parseInt(metadata.get("low overlap threshold"));}
+
+    public Integer getMaxOccupancyDifference() { return Integer.parseInt(metadata.get("maximum occupancy difference"));}
+
+    public Integer getMinOverlapPercent() { return Integer.parseInt(metadata.get("minimum overlap percent"));}
+
+    public Double getPairingAttemptRate() { return Double.parseDouble(metadata.get("pairing attempt rate"));}
+
+    public Integer getCorrectPairingCount() { return Integer.parseInt(metadata.get("correct pairing count"));}
+
+    public Integer getIncorrectPairingCount() { return Integer.parseInt(metadata.get("incorrect pairing count"));}
+
+    public Double getPairingErrorRate() { return Double.parseDouble(metadata.get("pairing error rate"));}
+
+    public String getSimulationTime() { return metadata.get("simulation time (seconds)"); }
 
 }

src/main/java/Plate.java

@@ -8,7 +8,9 @@ TODO: Implement discrete frequency distributions using Vose's Alias Method
 import java.util.*;
 
 public class Plate {
+    private CellSample cells;
     private String sourceFile;
+    private String filename;
     private List<List<Integer[]>> wells;
     private final Random rand = BiGpairSEQ.getRand();
     private int size;
@@ -18,6 +20,25 @@ public class Plate {
     private double lambda;
     boolean exponential = false;
 
+    public Plate(CellSample cells, String cellFilename, int numWells, Integer[] populations,
+                 double dropoutRate, double stdDev_or_lambda, boolean exponential){
+        this.cells = cells;
+        this.sourceFile = cellFilename;
+        this.size = numWells;
+        this.wells = new ArrayList<>();
+        this.error = dropoutRate;
+        this.populations = populations;
+        this.exponential = exponential;
+        if (this.exponential) {
+            this.lambda = stdDev_or_lambda;
+            fillWellsExponential(cells.getCells(), this.lambda);
+        }
+        else {
+            this.stdDev = stdDev_or_lambda;
+            fillWells(cells.getCells(), this.stdDev);
+        }
+    }
+
 
     public Plate(int size, double error, Integer[] populations) {
         this.size = size;
@@ -26,8 +47,9 @@ public class Plate {
         wells = new ArrayList<>();
     }
 
-    public Plate(String sourceFileName, List<List<Integer[]>> wells) {
-        this.sourceFile = sourceFileName;
+    //constructor for returning a Plate from a PlateFileReader
+    public Plate(String filename, List<List<Integer[]>> wells) {
+        this.filename = filename;
         this.wells = wells;
         this.size = wells.size();
 
@@ -43,10 +65,9 @@ public class Plate {
         }
     }
 
-    public void fillWellsExponential(String sourceFileName, List<Integer[]> cells, double lambda){
+    private void fillWellsExponential(List<Integer[]> cells, double lambda){
         this.lambda = lambda;
         exponential = true;
-        sourceFile = sourceFileName;
         int numSections = populations.length;
         int section = 0;
         double m;
@@ -74,9 +95,8 @@ public class Plate {
         }
     }
 
-    public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
+    private void fillWells( List<Integer[]> cells, double stdDev) {
         this.stdDev = stdDev;
-        sourceFile = sourceFileName;
         int numSections = populations.length;
         int section = 0;
         double m;
@@ -159,4 +179,6 @@ public class Plate {
     public String getSourceFileName() {
         return sourceFile;
     }
+
+    public String getFilename() { return filename; }
 }

src/main/java/PlateFileReader.java

@@ -56,11 +56,8 @@ public class PlateFileReader {
 
     }
 
-    public List<List<Integer[]>> getWells() {
-        return wells;
+    public Plate getSamplePlate() {
+        return new Plate(filename, wells);
     }
 
-    public String getFilename() {
-        return filename;
-    }
 }

src/main/java/Simulator.java

@@ -24,8 +24,9 @@ public class Simulator implements GraphModificationFunctions {
     private static final int cdr1BetaIndex = 3;
 
     //Make the graph needed for matching CDR3s
-    public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) {
+    public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
         Instant start = Instant.now();
+        List<Integer[]> distinctCells = cellSample.getCells();
         int[] alphaIndex = {cdr3AlphaIndex};
         int[] betaIndex = {cdr3BetaIndex};
 
@@ -113,7 +114,7 @@ public class Simulator implements GraphModificationFunctions {
                 distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
                 plateBtoVMap, alphaWellCounts, betaWellCounts, time);
         //Set source file name in graph to name of sample plate
-        output.setSourceFilename(samplePlate.getSourceFileName());
+        output.setSourceFilename(samplePlate.getFilename());
         //return GraphWithMapData object
         return output;
     }
@@ -279,7 +280,7 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("correct pairing count", Integer.toString(trueCount));
         metadata.put("incorrect pairing count", Integer.toString(falseCount));
         metadata.put("pairing error rate", pairingErrorRateTrunc.toString());
-        metadata.put("simulation time", nf.format(time.toSeconds()));
+        metadata.put("simulation time (seconds)", nf.format(time.toSeconds()));
         //create MatchingResult object
         MatchingResult output = new MatchingResult(metadata, header, allResults, matchMap, time);
         if(verbose){