Update readme with CLI arguments

readme.md

@@ -12,7 +12,7 @@ Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and c
 against a null distribution, BiGpairSEQ does not do any statistical calculations
 directly.
 
-BiGpairSEQ creates a [weightd bipartite graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
+BiGpairSEQ creates a [weighted bipartite graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
 The distinct TCRA and TCRB sequences form the two sets of vertices. Every TCRA/TCRB pair that share a well
 are connected by an edge, with the edge weight set to the number of wells in which both sequences appear.
 (Sequences present in *all* wells are filtered out prior to creating the graph, as there is no signal in their occupancy pattern.)
@@ -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--------
@@ -66,6 +71,19 @@ Please select an option:
 0) Exit
 ```
 
+By default, the Options menu looks like this:
+```
+--------------OPTIONS---------------
+1) Turn on cell sample file caching
+2) Turn on plate file caching
+3) Turn on graph/data file caching
+4) Turn off serialized binary graph output
+5) Turn on GraphML graph output
+6) Maximum weight matching algorithm options
+0) Return to main menu
+```
+
+
 ### INPUT/OUTPUT
 
 To run the simulation, the program reads and writes 4 kinds of files:
@@ -75,21 +93,25 @@ To run the simulation, the program reads and writes 4 kinds of files:
 * Matching Results files in CSV format
 
 These files are often generated in sequence. When entering filenames, it is not necessary to include the file extension
-(.csv or .ser). When reading or writing files, the program will automatically add the correct extension to any filename without one.
+(.csv or .ser). When reading or writing files, the program will automatically add the correct extension to any filename 
+without one.
 
 To save file I/O time, the most recent instance of each of these four
-files either generated or read from disk can be cached in program memory. This is could be important for Graph/Data files,
-which can be several gigabytes in size. Since some simulations may require running multiple, 
-differently-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached may reduce execution time.
-(The manipulation necessary to re-use a graph incurs its own performance overhead, though, which may scale with graph
-size faster than file I/O does. If so, caching is best for smaller graphs.)
-
-When caching is active, subsequent uses of the same data file won't need to be read in again until another file of that type is used or generated,
+files either generated or read from disk can be cached in program memory. When caching is active, subsequent uses of the 
+same data file won't need to be read in again until another file of that type is used or generated,
 or caching is turned off for that file type. The program checks whether it needs to update its cached data by comparing
 filenames as entered by the user. On encountering a new filename, the program flushes its cache and reads in the new file.
 
+(Note that cached Graph/Data files must be transformed back into their original state after a matching experiment, which
+may take some time. Whether file I/O or graph transformation takes longer for graph/data files is likely to be
+device-specific.)
+
 The program's caching behavior can be controlled in the Options menu. By default, all caching is OFF.
 
+The program can optionally output Graph/Data files in .GraphML format (.graphml) for data portability. This can be 
+turned on in the Options menu. By default, GraphML output is OFF.
+
+---
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
 four sequences: Alpha CDR3, Beta CDR3, Alpha CDR1, Beta CDR1. The sequences are represented by
@@ -107,7 +129,6 @@ Comments are preceded by `#`
 
 Structure:
 
----
     # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
 | Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
 |---|---|---|---|
@@ -131,11 +152,14 @@ Options when making a Sample Plate file:
     * Standard deviation size 
   * Exponential
     * Lambda value
-      * *(Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was exponential with a lambda of approximately 0.6. (Howie, et al. 2015))*
+      * *(Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was approximately exponential with a lambda ~0.6. (Howie, et al. 2015))*
 * Total number of wells on the plate
-* Number of sections on plate
-* Number of T cells per well
-  * per section, if more than one section
+* Well populations random or fixed
+  * If random, minimum and maximum population sizes
+  * If fixed
+    * Number of sections on plate
+    * Number of T cells per well
+      * per section, if more than one section
 * Dropout rate
 
 Files are in CSV format. There are no header labels. Every row represents a well. 
@@ -149,7 +173,6 @@ Dropout sequences are replaced with the value `-1`. Comments are preceded by `#`
 
 Structure:
 
----
 ```
 # Cell source file name:
 # Each row represents one well on the plate
@@ -178,14 +201,19 @@ Options for creating a Graph/Data file:
 * The Cell Sample file to use
 * The Sample Plate file to use. (This must have been generated from the selected Cell Sample file.)
 
-These files do not have a human-readable structure, and are not portable to other programs. (Export of graphs in a 
-portable data format may be implemented in the future. The tricky part is encoding the necessary metadata.)
+These files do not have a human-readable structure, and are not portable to other programs.
+
+(For portability to other software, turn on GraphML output in the Options menu. This will produce a .graphml file
+for the weighted graph, with vertex attributes sequence, type, and occupancy data.)
 
 ---
 
 #### Matching Results Files 
-Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a Graph and 
-Data file. Matching results files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
+Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a serialized
+binary Graph/Data file (.ser). (Because .graphML files are larger than .ser files, BiGpairSEQ_Sim supports .graphML
+output only. Graph/data input must use a serialized binary.)
+
+Matching results files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
 Metadata about the matching simulation is included as comments. Comments are preceded by `#`.
 
 Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
@@ -200,7 +228,6 @@ Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
 
 Example output:
 
----
 ```
 # Source Sample Plate file: 4MilCellsPlate.csv
 # Source Graph and Data file: 4MilCellsPlateGraph.ser
@@ -251,29 +278,31 @@ slightly less time than the simulation itself. Real elapsed time from start to f
 ## TODO
 
 * ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
-* Hold graph data in memory until another graph is read-in? ~~ABANDONED~~ ~~UNABANDONED~~ DONE
+* ~~Hold graph data in memory until another graph is read-in? ABANDONED UNABANDONED~~ DONE
   * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~
   * Might have figured out a way to do it, by taking edges out and then putting them back into the graph. This may actually be possible.
   * It is possible, though the modifications to the graph incur their own performance penalties. Need testing to see which option is best.
-* See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows. 
-  * ~~Problem is variable number of cells in a well~~
-  * ~~Apache Commons CSV library writes entries a row at a time~~ 
-    * _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing._
-* Re-implement command line arguments, to enable scripting and statistical simulation studies
-* Implement sample plates with random numbers of T cells per well.
-  * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not.
-    * preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
-* Enable GraphML output in addition to serialized object binaries, for data portability
-  * Custom vertex type with attribute for sequence occupancy?
-* Re-implement CDR1 matching method
-* Implement Duan and Su's maximum weight matching algorithm
-  * Add controllable algorithm-type parameter?
 * ~~Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm~~ DONE
   * ~~in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage~~
   * ~~Add controllable heap-type parameter?~~
-    * Parameter implemented. For large graphs, Fibonacci heap wins. Now the new default.
-
-
+    * Parameter implemented. Fibonacci heap the current default.
+* ~~Implement sample plates with random numbers of T cells per well.~~ DONE
+  * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not.
+    * preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
+* See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows. 
+  * ~~Problem is variable number of cells in a well~~
+  * ~~Apache Commons CSV library writes entries a row at a time~~ 
+    * _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing.
+* ~~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~~ 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
 * Howie, B., Sherwood, A. M., et al. ["High-throughput pairing of T cell receptor alpha and beta sequences."](https://pubmed.ncbi.nlm.nih.gov/26290413/) Sci. Transl. Med. 7, 301ra131 (2015)

src/main/java/BiGpairSEQ.java

@@ -1,6 +1,6 @@
 import java.util.Random;
 
-//main class. For choosing interface type and caching file data
+//main class. For choosing interface type and holding settings
 public class BiGpairSEQ {
 
     private static final Random rand = new Random();
@@ -14,6 +14,8 @@ public class BiGpairSEQ {
     private static boolean cachePlate = false;
     private static boolean cacheGraph = false;
     private static String priorityQueueHeapType = "FIBONACCI";
+    private static boolean outputBinary = true;
+    private static boolean outputGraphML = false;
 
     public static void main(String[] args) {
         if (args.length == 0) {
@@ -21,8 +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.");
         }
     }
 
@@ -164,4 +166,11 @@ public class BiGpairSEQ {
     public static void setFibonacciHeap() {
         priorityQueueHeapType = "FIBONACCI";
     }
+
+    public static boolean outputBinary() {return outputBinary;}
+    public static void setOutputBinary(boolean b) {outputBinary = b;}
+
+    public static boolean outputGraphML() {return outputGraphML;}
+    public static void setOutputGraphML(boolean b) {outputGraphML = b;}
+
 }

src/main/java/CellSample.java

@@ -1,10 +1,37 @@
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.stream.IntStream;
 
 public class CellSample {
 
     private List<Integer[]> cells;
     private Integer cdr1Freq;
 
+    public CellSample(Integer numDistinctCells, Integer cdr1Freq){
+        this.cdr1Freq = cdr1Freq;
+        List<Integer> numbersCDR3 = new ArrayList<>();
+        List<Integer> numbersCDR1 = new ArrayList<>();
+        Integer numDistCDR3s = 2 * numDistinctCells + 1;
+        IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
+        IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
+        Collections.shuffle(numbersCDR3);
+        Collections.shuffle(numbersCDR1);
+
+        //Each cell represented by 4 values
+        //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
+        List<Integer[]> distinctCells = new ArrayList<>();
+        for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
+            Integer tmpCDR3a = numbersCDR3.get(i);
+            Integer tmpCDR3b = numbersCDR3.get(i+1);
+            Integer tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size());
+            Integer tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size());
+            Integer[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
+            distinctCells.add(tmp);
+        }
+        this.cells = distinctCells;
+    }
+
     public CellSample(List<Integer[]> cells, Integer cdr1Freq){
         this.cells = cells;
         this.cdr1Freq = cdr1Freq;

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){
-        CellSample sample = Simulator.generateCellSample(numCells, 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/GraphMLFileReader.java

@@ -1,35 +0,0 @@
-import org.jgrapht.graph.SimpleWeightedGraph;
-import org.jgrapht.nio.graphml.GraphMLImporter;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-public class GraphMLFileReader {
-
-    private String filename;
-    private SimpleWeightedGraph graph;
-
-    public GraphMLFileReader(String filename, SimpleWeightedGraph graph) {
-        if(!filename.matches(".*\\.graphml")){
-            filename = filename + ".graphml";
-        }
-        this.filename = filename;
-        this.graph = graph;
-
-        try(//don't need to close reader bc of try-with-resources auto-closing
-            BufferedReader reader = Files.newBufferedReader(Path.of(filename));
-        ){
-            GraphMLImporter<SimpleWeightedGraph, BufferedReader> importer = new GraphMLImporter<>();
-            importer.importGraph(graph, reader);
-        }
-        catch (IOException ex) {
-            System.out.println("Graph file " + filename + " not found.");
-            System.err.println(ex);
-        }
-    }
-
-    public SimpleWeightedGraph getGraph() { return graph; }
-
-}

src/main/java/GraphMLFileWriter.java

@@ -1,4 +1,8 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
+import org.jgrapht.nio.Attribute;
+import org.jgrapht.nio.AttributeType;
+import org.jgrapht.nio.DefaultAttribute;
 import org.jgrapht.nio.dot.DOTExporter;
 import org.jgrapht.nio.graphml.GraphMLExporter;
 
@@ -7,25 +11,69 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
 
 public class GraphMLFileWriter {
 
     String filename;
-    SimpleWeightedGraph graph;
+    GraphWithMapData data;
 
 
-    public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) {
+    public GraphMLFileWriter(String filename, GraphWithMapData data) {
         if(!filename.matches(".*\\.graphml")){
             filename = filename + ".graphml";
         }
         this.filename = filename;
-        this.graph = graph;
+        this.data = data;
     }
 
+//    public void writeGraphToFile() {
+//        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+//        ){
+//            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+//            exporter.exportGraph(graph, writer);
+//        } catch(IOException ex){
+//            System.out.println("Could not make new file named "+filename);
+//            System.err.println(ex);
+//        }
+//    }
+
     public void writeGraphToFile() {
+        SimpleWeightedGraph graph = data.getGraph();
+        Map<Integer, Integer> vertexToAlphaMap = data.getPlateVtoAMap();
+        Map<Integer, Integer> vertexToBetaMap = data.getPlateVtoBMap();
+        Map<Integer, Integer> alphaOccs = data.getAlphaWellCounts();
+        Map<Integer, Integer> betaOccs = data.getBetaWellCounts();
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
         ){
-            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+            //create exporter. Let the vertex labels be the unique ids for the vertices
+            GraphMLExporter<Integer, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(v -> v.toString());
+            //set to export weights
+            exporter.setExportEdgeWeights(true);
+            //set type, sequence, and occupancy attributes for each vertex
+            exporter.setVertexAttributeProvider( v -> {
+                Map<String, Attribute> attributes = new HashMap<>();
+                if(vertexToAlphaMap.containsKey(v)) {
+                    attributes.put("type", DefaultAttribute.createAttribute("CDR3 Alpha"));
+                    attributes.put("sequence", DefaultAttribute.createAttribute(vertexToAlphaMap.get(v)));
+                    attributes.put("occupancy", DefaultAttribute.createAttribute(
+                            alphaOccs.get(vertexToAlphaMap.get(v))));
+                }
+                else if(vertexToBetaMap.containsKey(v)) {
+                    attributes.put("type", DefaultAttribute.createAttribute("CDR3 Beta"));
+                    attributes.put("sequence", DefaultAttribute.createAttribute(vertexToBetaMap.get(v)));
+                    attributes.put("occupancy", DefaultAttribute.createAttribute(
+                            betaOccs.get(vertexToBetaMap.get(v))));
+                }
+                return attributes;
+            });
+            //register the attributes
+            exporter.registerAttribute("type", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("sequence", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("occupancy", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            //export the graph
             exporter.exportGraph(graph, writer);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);
@@ -33,3 +81,4 @@ public class GraphMLFileWriter {
         }
     }
 }
+

src/main/java/GraphModificationFunctions.java

@@ -4,7 +4,6 @@ import org.jgrapht.graph.SimpleWeightedGraph;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 public interface GraphModificationFunctions {
 

src/main/java/InteractiveInterface.java

@@ -74,7 +74,7 @@ public class InteractiveInterface {
             System.out.println(ex);
             sc.next();
         }
-        CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
+        CellSample sample = new CellSample(numCells, cdr1Freq);
         assert filename != null;
         System.out.println("Writing cells to file");
         CellFileWriter writer = new CellFileWriter(filename, sample);
@@ -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");
@@ -252,7 +250,6 @@ public class InteractiveInterface {
         String filename = null;
         String cellFile = null;
         String plateFile = null;
-
         try {
             String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
             str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -293,7 +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);
             }
@@ -307,12 +304,18 @@ 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;
-            GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
-            dataWriter.writeDataToFile();
-            System.out.println("Graph and Data file written to: " + filename);
+            if(BiGpairSEQ.outputBinary()) {
+                GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
+                dataWriter.writeDataToFile();
+                System.out.println("Serialized binary graph/data file written to: " + filename);
+            }
+            if(BiGpairSEQ.outputGraphML()) {
+                GraphMLFileWriter graphMLWriter = new GraphMLFileWriter(filename, data);
+                graphMLWriter.writeGraphToFile();
+                System.out.println("GraphML file written to: " + filename);
+            }
             if(BiGpairSEQ.cacheGraph()) {
                 BiGpairSEQ.setGraphInMemory(data, filename);
 
@@ -372,7 +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);
@@ -500,7 +503,9 @@ public class InteractiveInterface {
             System.out.println("1) Turn " + getOnOff(!BiGpairSEQ.cacheCells()) + " cell sample file caching");
             System.out.println("2) Turn " + getOnOff(!BiGpairSEQ.cachePlate()) + " plate file caching");
             System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
-            System.out.println("4) Maximum weight matching algorithm options");
+            System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
+            System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output");
+            System.out.println("6) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {
                 input = sc.nextInt();
@@ -508,7 +513,9 @@ public class InteractiveInterface {
                     case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
                     case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
                     case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
-                    case 4 -> algorithmOptions();
+                    case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
+                    case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
+                    case 6 -> algorithmOptions();
                     case 0 -> backToMain = true;
                     default -> System.out.println("Invalid input");
                 }

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

@@ -23,33 +23,10 @@ public class Simulator implements GraphModificationFunctions {
     private static final int cdr1AlphaIndex = 2;
     private static final int cdr1BetaIndex = 3;
 
-    public static CellSample generateCellSample(Integer numDistinctCells, Integer cdr1Freq) {
-        //In real T cells, CDR1s have about one third the diversity of CDR3s
-        List<Integer> numbersCDR3 = new ArrayList<>();
-        List<Integer> numbersCDR1 = new ArrayList<>();
-        Integer numDistCDR3s = 2 * numDistinctCells + 1;
-        IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
-        IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
-        Collections.shuffle(numbersCDR3);
-        Collections.shuffle(numbersCDR1);
-
-        //Each cell represented by 4 values
-        //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
-        List<Integer[]> distinctCells = new ArrayList<>();
-        for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
-            Integer tmpCDR3a = numbersCDR3.get(i);
-            Integer tmpCDR3b = numbersCDR3.get(i+1);
-            Integer tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size());
-            Integer tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size());
-            Integer[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
-            distinctCells.add(tmp);
-        }
-        return new CellSample(distinctCells, cdr1Freq);
-    }
-
     //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};
 
@@ -137,7 +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;
     }
@@ -260,6 +237,7 @@ public class Simulator implements GraphModificationFunctions {
         }
 
         //Metadata comments for CSV file
+        String algoType = "LEDA book with heap: " + heapType;
         int min = Math.min(alphaCount, betaCount);
         //rate of attempted matching
         double attemptRate = (double) (trueCount + falseCount) / min;
@@ -290,6 +268,7 @@ public class Simulator implements GraphModificationFunctions {
         Map<String, String> metadata = new LinkedHashMap<>();
         metadata.put("sample plate filename", data.getSourceFilename());
         metadata.put("graph filename", dataFilename);
+        metadata.put("algorithm type", algoType);
         metadata.put("well populations", wellPopulationsString);
         metadata.put("total alphas found", alphaCount.toString());
         metadata.put("total betas found", betaCount.toString());
@@ -301,7 +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){
@@ -690,7 +669,7 @@ public class Simulator implements GraphModificationFunctions {
 
     private static Map<Integer, Integer> makeVertexToSequenceMap(Map<Integer, Integer> sequences, Integer startValue) {
         Map<Integer, Integer> map = new LinkedHashMap<>(); //LinkedHashMap to preserve order of entry
-        Integer index = startValue;
+        Integer index = startValue; //is this necessary? I don't think I use this.
         for (Integer k: sequences.keySet()) {
             map.put(index, k);
             index++;

src/main/java/Vertex.java

@@ -1,14 +1,20 @@
+
+
 public class Vertex {
-    private final Integer peptide;
+    private final Integer vertexLabel;
+    private final Integer sequence;
     private final Integer occupancy;
 
-    public Vertex(Integer peptide, Integer occupancy) {
-        this.peptide = peptide;
+    public Vertex(Integer vertexLabel, Integer sequence, Integer occupancy) {
+        this.vertexLabel = vertexLabel;
+        this.sequence = sequence;
         this.occupancy = occupancy;
     }
 
-    public Integer getPeptide() {
-        return peptide;
+    public Integer getVertexLabel() { return vertexLabel; }
+
+    public Integer getSequence() {
+        return sequence;
     }
 
     public Integer getOccupancy() {