update readme

.gitignore

@@ -0,0 +1 @@
+/out/

.idea/artifacts/BiGpairSEQ_Sim_jar.xml

@@ -1,11 +1,11 @@
 <component name="ArtifactManager">
-  <artifact type="jar" name="TCellSim:jar">
-    <output-path>$PROJECT_DIR$/out/artifacts/TCellSim_jar</output-path>
-    <root id="archive" name="TCellSim.jar">
+  <artifact type="jar" build-on-make="true" name="BiGpairSEQ_Sim:jar">
+    <output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path>
+    <root id="archive" name="BiGpairSEQ_Sim.jar">
       <element id="directory" name="META-INF">
         <element id="file-copy" path="$PROJECT_DIR$/src/main/java/META-INF/MANIFEST.MF" />
       </element>
-      <element id="module-output" name="TCellSim" />
+      <element id="module-output" name="BigPairSEQ" />
       <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar" path-in-jar="/" />
       <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar" path-in-jar="/" />
       <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar" path-in-jar="/" />

.idea/compiler.xml

@@ -6,7 +6,7 @@
         <sourceOutputDir name="target/generated-sources/annotations" />
         <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
         <outputRelativeToContentRoot value="true" />
-        <module name="TCellSim" />
+        <module name="BigPairSEQ" />
       </profile>
     </annotationProcessing>
   </component>

.idea/libraries/jgrapht_io.xml

@@ -0,0 +1,15 @@
+<component name="libraryTable">
+  <library name="jgrapht.io" type="repository">
+    <properties maven-id="org.jgrapht:jgrapht-io:1.5.1" />
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.1/jgrapht-io-1.5.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.8-1/antlr4-runtime-4.8-1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.8/commons-text-1.8.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.9/commons-lang3-3.9.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>

.idea/libraries/jheaps.xml

@@ -0,0 +1,10 @@
+<component name="libraryTable">
+  <library name="jheaps" type="repository">
+    <properties maven-id="org.jheaps:jheaps:0.14" />
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>

out/artifacts/TCellSim_jar/readme.md

@@ -1,4 +0,0 @@
-Executable .jar file with interactive, command line UI
-Usage: java -jar TCellSim.jar
-
-Requires Java11 or higher (Openjdk-17 recommended)

readme.md

@@ -0,0 +1,293 @@
+# BiGpairSEQ SIMULATOR
+
+
+## ABOUT
+
+This program simulates BiGpairSEQ (Bipartite Graph pairSEQ), a graph theory-based adaptation
+of the pairSEQ algorithm (Howie, et al. 2015) for pairing T cell receptor sequences.
+
+## THEORY
+
+Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and compares
+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.
+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.)
+The problem of pairing TCRA/TCRB sequences thus reduces to the "assignment problem" of finding a maximum weight
+matching on a bipartite graph--the subset of vertex-disjoint edges whose weights sum to the maximum possible value.
+
+This is a well-studied combinatorial optimization problem, with many known solutions.
+The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral weights
+is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 
+their algorithm runs in **O(m sqrt(n) log(N))** time. As the graph representation of a pairSEQ experiment is 
+bipartite with integer weights, this algorithm is ideal for BiGpairSEQ.
+
+Unfortunately, it's a fairly new algorithm, and not yet implemented by the graph theory library used in this simulator.
+So this program instead uses the Fibonacci heap-based algorithm of Fredman and Tarjan (1987), which has a worst-case
+runtime of **O(n (n log(n) + m))**. The algorithm is implemented as described in Melhorn and Näher (1999).
+
+The current version of the program uses a pairing heap instead of a Fibonacci heap for its priority queue,
+which has lower theoretical efficiency but also lower complexity overhead, and is often equivalently performant
+in practice.
+
+## USAGE
+
+### RUNNING THE PROGRAM
+
+[Download the current version of BiGpairSEQ_Sim.](https://gitea.ejsf.synology.me/efischer/BiGpairSEQ/releases)
+
+BiGpairSEQ_Sim is an executable .jar file. Requires Java 11 or higher. [OpenJDK 17](https://jdk.java.net/17/)
+recommended.
+
+Run with the command:
+
+`java -jar BiGpairSEQ_Sim.jar`
+
+Processing sample plates with tens of thousands of sequences may require large amounts 
+of RAM. It is often desirable to increase the JVM maximum heap allocation with the -Xmx flag.
+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:
+
+```
+--------BiGPairSEQ SIMULATOR--------
+ALPHA/BETA T CELL RECEPTOR MATCHING
+  USING WEIGHTED BIPARTITE GRAPHS
+------------------------------------
+Please select an option:
+1) Generate a population of distinct cells
+2) Generate a sample plate of T cells
+3) Generate CDR3 alpha/beta occupancy data and overlap graph
+4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ)
+9) About/Acknowledgments
+0) Exit
+```
+
+### INPUT/OUTPUT
+
+To run the simulation, the program reads and writes 4 kinds of files:
+* Cell Sample files in CSV format
+* Sample Plate files in CSV format
+* Graph/Data files in binary object serialization format
+* Matching Results files in CSV format
+
+These files are often generated in sequence. To save file I/O time, the most recent instance of each of these four
+files either generated or read from disk is cached in program memory. This is especially important for Graph/Data files,
+which can be several gigabytes in size. Since some simulations may require running multiple, 
+differntly-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached drastically reduces 
+execution time. 
+
+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.
+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.
+
+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. 
+
+#### 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
+random integers. CDR3 Alpha and Beta sequences are all unique within a given Cell Sample file. CDR1 Alpha and Beta sequences
+are not necessarily unique; the relative diversity can be set when making the file.
+
+(Note: though cells still have CDR1 sequences, matching of CDR1s is currently awaiting re-implementation.)
+
+Options when making a Cell Sample file:
+* Number of T cells to generate
+* Factor by which CDR3s are more diverse than CDR1s
+
+Files are in CSV format. Rows are distinct T cells, columns are sequences within the cells.
+Comments are preceded by `#`
+
+Structure:
+
+---
+    # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
+| Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
+|---|---|---|---|
+|unique number|unique number|number|number|
+
+---
+
+#### Sample Plate Files
+Sample Plate files consist of any number of "wells" containing any number of T cells (as 
+described above). The wells are filled randomly from a Cell Sample file, according to a selected
+frequency distribution. Additionally, every individual sequence within each cell may, with some
+given dropout probability, be omitted from the file; this simulates the effect of amplification errors
+prior to sequencing. Plates can also be partitioned into any number of sections, each of which can have a 
+different concentration of T cells per well.
+
+Options when making a Sample Plate file:
+* Cell Sample file to use
+* Statistical distribution to apply to Cell Sample file
+  * Poisson
+  * Gaussian
+    * 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))*
+* 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
+* Dropout rate
+
+Files are in CSV format. There are no header labels. Every row represents a well. 
+Every value represents an individual cell, containing four sequences, depicted as an array string:
+`[CDR3A, CDR3B, CDR1A, CDR1B]`. So a representative cell might look like this: 
+
+`[525902, 791533, -1, 866282]`
+
+Notice that the CDR1 Alpha is missing in the cell above--sequence dropout from simulated amplification error.
+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
+# Plate size:
+# Concentrations:
+# Lambda -or- StdDev: 
+```
+| Well 1, cell 1 | Well 1, cell 2 | Well 1, cell 3| ... |
+|---|---|---|---|
+| **Well 2, cell 1** | **Well 2, cell 2** | **Well 2, cell 3**| **...** |
+| **Well 3, cell 1** | **Well 3, cell 2** | **Well 3, cell 3**| **...** |
+| **...** | **...** | **...** | **...** |
+
+---
+
+#### Graph/Data Files
+Graph/Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
+Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file 
+(to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a 
+Sample Plate file (to construct the associated occupancy graph).
+
+These files can be several gigabytes in size. Writing them to a file lets us generate a graph and its metadata once,
+then use it for multiple different BiGpairSEQ simulations.
+
+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.)
+
+---
+
+#### 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.
+Metadata about the matching simulation is included as comments. Comments are preceded by `#`.
+
+Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
+* The minimum number of alpha/beta overlap wells to attempt to match
+  * (must be >= 1)
+* The maximum number of alpha/beta overlap wells to attempt to match
+  * (must be <= the number of wells on the plate - 1)
+* The maximum difference in alpha/beta occupancy to attempt to match
+  * (Optional. To skip using this filter, enter a value >= the number of wells on the plate)
+* The minimum overlap percentage--the percentage of a sequence's occupied wells shared by another sequence--to attempt to match. Given as value in range 0 - 100.
+  * (Optional. To skip using this filter, enter 0)
+
+Example output:
+
+---
+```
+# Source Sample Plate file: 4MilCellsPlate.csv
+# Source Graph and Data file: 4MilCellsPlateGraph.ser
+# T cell counts in sample plate wells: 30000
+# Total alphas found: 11813
+# Total betas found: 11808
+# High overlap threshold: 94
+# Low overlap threshold: 3
+# Minimum overlap percent: 0
+# Maximum occupancy difference: 96
+# Pairing attempt rate: 0.438
+# Correct pairings: 5151
+# Incorrect pairings: 18
+# Pairing error rate: 0.00348
+# Simulation time: 862 seconds
+```
+
+| Alpha | Alpha well count | Beta | Beta well count | Overlap count | Matched Correctly? | P-value |
+|---|---|---|---|---|---|---|
+|5242972|17|1571520|18|17|true|1.41E-18|
+|5161027|18|2072219|18|18|true|7.31E-20|
+|4145198|33|1064455|30|29|true|2.65E-21|
+|7700582|18|112748|18|18|true|7.31E-20|
+|...|...|...|...|...|...|...|
+
+---
+
+**NOTE: The p-values in the output are not used for matching**—they aren't part of the BiGpairSEQ algorithm at all. 
+P-values are calculated *after* BiGpairSEQ matching is completed, for purposes of comparison only, 
+using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et al. 2015)
+
+### PERFORMANCE
+Performance details of the example excerpted above:
+
+On a home computer with a Ryzen 5600X CPU, 64GB of 3200MHz DDR4 RAM (half of which was allocated to the Java Virtual Machine), and a PCIe 3.0 SSD, running Linux Mint 20.3 Edge (5.13 kernel), 
+the author ran a BiGpairSEQ simulation of a 96-well sample plate with 30,000 T cells/well comprising ~11,800 alphas and betas,
+taken from a sample of 4,000,000 distinct cells with an exponential frequency distribution.
+
+With min/max occupancy threshold of 3 and 94 wells for matching, and no other pre-filtering, BiGpairSEQ identified 5,151 
+correct pairings and 18 incorrect pairings, for an accuracy of 99.652%.
+
+The simulation time was 14'22". If intermediate results were held in memory, this would be equivalent to the total elapsed time.
+
+Since this implementation of BiGpairSEQ writes intermediate results to disk (to improve the efficiency of *repeated* simulations
+with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took 
+slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes.
+
+## 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
+  * ~~*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. If so, awesome.
+* 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
+  * in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage
+  * Add controllable heap-type parameter?
+
+
+  
+## 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)
+* Duan, R., Su H. ["A Scaling Algorithm for Maximum Weight Matching in Bipartite Graphs."](https://web.eecs.umich.edu/~pettie/matching/Duan-Su-scaling-bipartite-matching.pdf) Proceedings of the Twenty-Third Annual ACM-SIAM Symposium on Discrete Algorithms, p. 1413-1424. (2012)
+* Melhorn, K., Näher, St. [The LEDA Platform of Combinatorial and Geometric Computing.](https://people.mpi-inf.mpg.de/~mehlhorn/LEDAbook.html) Cambridge University Press. Chapter 7, Graph Algorithms; p. 132-162 (1999)
+* Fredman, M., Tarjan, R. ["Fibonacci heaps and their uses in improved network optimization algorithms."](https://www.cl.cam.ac.uk/teaching/1011/AlgorithII/1987-FredmanTar-fibonacci.pdf) J. ACM, 34(3):596–615 (1987))
+
+## EXTERNAL LIBRARIES USED
+* [JGraphT](https://jgrapht.org) -- Graph theory data structures and algorithms
+* [JHeaps](https://www.jheaps.org) -- For pairing heap priority queue used in maximum weight matching algorithm
+* [Apache Commons CSV](https://commons.apache.org/proper/commons-csv/) -- For CSV file output
+* [Apache Commons CLI](https://commons.apache.org/proper/commons-cli/) -- To enable command line arguments for scripting. (**Awaiting re-implementation**.)
+
+## ACKNOWLEDGEMENTS
+BiGpairSEQ was conceived in collaboration with Dr. Alice MacQueen, who brought the original 
+pairSEQ paper to the author's attention and explained all the biology terms he didn't know.
+
+## AUTHOR
+BiGpairSEQ algorithm and simulation by Eugene Fischer, 2021. UI improvements and documentation, 2022.

src/main/java/BiGpairSEQ.java

@@ -0,0 +1,95 @@
+import java.util.Random;
+
+//main class. For choosing interface type and caching file data
+public class BiGpairSEQ {
+
+    private static final Random rand = new Random();
+    private static CellSample cellSampleInMemory = null;
+    private static String cellFilename = null;
+    private static Plate plateInMemory = null;
+    private static String plateFilename = null;
+    private static GraphWithMapData graphInMemory = null;
+    private static String graphFilename = null;
+
+    public static void main(String[] args) {
+        if (args.length == 0) {
+            InteractiveInterface.startInteractive();
+        }
+        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.");
+        }
+    }
+
+    public static Random getRand() {
+        return rand;
+    }
+
+    public static CellSample getCellSampleInMemory() {
+        return cellSampleInMemory;
+    }
+
+    public static void setCellSampleInMemory(CellSample cellSampleInMemory) {
+        BiGpairSEQ.cellSampleInMemory = cellSampleInMemory;
+    }
+
+    public static void clearCellSampleInMemory() {
+        cellSampleInMemory = null;
+        System.gc();
+    }
+
+    public static String getCellFilename() {
+        return cellFilename;
+    }
+
+    public static void setCellFilename(String cellFilename) {
+        BiGpairSEQ.cellFilename = cellFilename;
+    }
+
+    public static Plate getPlateInMemory() {
+        return plateInMemory;
+    }
+
+    public static void setPlateInMemory(Plate plateInMemory) {
+        BiGpairSEQ.plateInMemory = plateInMemory;
+    }
+
+    public static void clearPlateInMemory() {
+        plateInMemory = null;
+        System.gc();
+    }
+
+    public static String getPlateFilename() {
+        return plateFilename;
+    }
+
+    public static void setPlateFilename(String plateFilename) {
+        BiGpairSEQ.plateFilename = plateFilename;
+    }
+
+    public static GraphWithMapData getGraphInMemory() {
+        return graphInMemory;
+    }
+
+    public static void setGraphInMemory(GraphWithMapData g) {
+        if (graphInMemory != null) {
+            clearGraphInMemory();
+        }
+        graphInMemory = g;
+    }
+
+    public static void clearGraphInMemory() {
+        graphInMemory = null;
+        System.gc();
+    }
+
+    public static String getGraphFilename() {
+        return graphFilename;
+    }
+
+    public static void setGraphFilename(String filename) {
+        graphFilename = filename;
+    }
+
+}

src/main/java/CellFileReader.java

@@ -13,6 +13,7 @@ public class CellFileReader {
 
     private String filename;
     private List<Integer[]> distinctCells = new ArrayList<>();
+    private Integer cdr1Freq;
 
     public CellFileReader(String filename) {
         if(!filename.matches(".*\\.csv")){
@@ -38,19 +39,37 @@ public class CellFileReader {
                 cell[3] = Integer.valueOf(record.get("Beta CDR1"));
                 distinctCells.add(cell);
             }
+
+
         } catch(IOException ex){
             System.out.println("cell file " + filename + " not found.");
             System.err.println(ex);
         }
+
+        //get CDR1 frequency
+        ArrayList<Integer> cdr1Alphas = new ArrayList<>();
+        for (Integer[] cell : distinctCells) {
+            cdr1Alphas.add(cell[3]);
+        }
+        double count = cdr1Alphas.stream().distinct().count();
+        count = Math.ceil(distinctCells.size() / count);
+        cdr1Freq = (int) count;
+
+    }
+
+    public CellSample getCellSample() {
+        return new CellSample(distinctCells, cdr1Freq);
     }
 
     public String getFilename() { return filename;}
 
-    public List<Integer[]> getCells(){
+    //Refactor everything that uses this to have access to a Cell Sample and get the cells there instead.
+    public List<Integer[]> getListOfDistinctCellsDEPRECATED(){
         return distinctCells;
     }
 
-    public Integer getCellCount() {
+    public Integer getCellCountDEPRECATED() {
+        //Refactor everything that uses this to have access to a Cell Sample and get the count there instead.
         return distinctCells.size();
     }
 }

src/main/java/CellSample.java

@@ -18,7 +18,7 @@ public class CellSample {
         return cdr1Freq;
     }
 
-    public Integer population(){
+    public Integer getCellCount(){
         return cells.size();
     }
 

src/main/java/CommandLineInterface.java

@@ -0,0 +1,328 @@
+import org.apache.commons.cli.*;
+
+/*
+ * Class for parsing options passed to program from command line
+ *
+ * Top-level flags:
+ * cells : to make a cell sample file
+ * plate : to make a sample plate file
+ * graph : to make a graph and data file
+ * match : to do a cdr3 matching (WITH OR WITHOUT MAKING A RESULTS FILE. May just want to print summary for piping.)
+ *
+ * Cell flags:
+ * count : number of cells to generate
+ * diversity factor : factor by which CDR3s are more diverse than CDR1s
+ * output : name of the output file
+ *
+ * Plate flags:
+ * cellfile : name of the cell sample file to use as input
+ * wells : the number of wells on the plate
+ * dist : the statistical distribution to use
+ *      (if exponential) lambda : the lambda value of the exponential distribution
+ *      (if gaussian) stddev : the standard deviation of the gaussian distribution
+ * rand : randomize well populations, take a minimum argument and a maximum argument
+ * populations : number of t cells per well per section (number of arguments determines number of sections)
+ * dropout : plate dropout rate, double from 0.0 to 1.0
+ * output : name of the output file
+ *
+ * Graph flags:
+ * 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
+ *
+ * Match flags:
+ * graphFile : name of graph and data file to use as input
+ * min : minimum number of overlap wells to attempt a matching
+ * max : the maximum number of overlap wells to attempt a matching
+ * maxdiff : (optional) the maximum difference in occupancy to attempt a matching
+ * minpercent : (optional) the minimum percent overlap to attempt a matching.
+ * writefile : (optional) the filename to write results to
+ * output : the values to print to System.out for piping
+ *
+ */
+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);
+
+
+
+        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);
+                }
+            }
+            else if(line.hasOption("cells")){
+                //line = parser.parse(mainOptions, args);
+                String filename = line.getOptionValue("o");
+                Integer numDistCells = Integer.valueOf(line.getOptionValue("nc"));
+                Integer freq = Integer.valueOf(line.getOptionValue("d"));
+                makeCells(filename, numDistCells, freq);
+            }
+            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]);
+                }
+                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("gaussian")){
+                    Double stdDev = Double.valueOf(line.getOptionValue("std-dev"));
+                    for(int i = 1; i <= numPlatesToMake; i++){
+                        makePlate(cellFile, filenamePrefix + i, stdDev, numWellsOnPlate,
+                                concentrationsToUse,dropOutRate);
+                    }
+
+                }
+                else if(line.hasOption("poisson")){
+                    for(int i = 1; i <= numPlatesToMake; i++){
+                        makePlatePoisson(cellFile, filenamePrefix + i, numWellsOnPlate,
+                                concentrationsToUse,dropOutRate);
+                    }
+                }
+            }
+        }
+        catch (ParseException exp) {
+            System.err.println("Parsing failed.  Reason: " + exp.getMessage());
+        }
+    }
+
+    //for calling from command line
+    public static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
+        CellSample sample = Simulator.generateCellSample(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/Equations.java

@@ -4,6 +4,9 @@ import java.math.MathContext;
 
 public abstract class Equations {
 
+    //pValue calculation as described in original pairSEQ paper.
+    //Included for comparison with original results.
+    //Not used by BiGpairSEQ for matching.
     public static double pValue(Integer w, Integer w_a, Integer w_b, double w_ab_d) {
         int w_ab = (int) w_ab_d;
         double pv = 0.0;
@@ -14,6 +17,9 @@ public abstract class Equations {
         return pv;
     }
 
+    //Implementation of the (corrected) probability equation from pairSEQ paper.
+    //Included for comparison with original results.
+    //Not used by BiGpairSEQ for matching.
     private static double probPairedByChance(Integer w, Integer w_a, Integer w_b, Integer w_ab){
         BigInteger numer1 = choose(w, w_ab);
         BigInteger numer2 = choose(w - w_ab, w_a - w_ab);
@@ -26,10 +32,9 @@ public abstract class Equations {
         return prob.doubleValue();
     }
 
-    /*
-     * This works because nC(k+1) = nCk * (n-k)/(k+1)
-     * Since nC0 = 1, can start there and generate all the rest.
-     */
+
+     //This works because nC(k+1) = nCk * (n-k)/(k+1)
+     //Since nC0 = 1, can start there and generate all the rest.
      public static BigInteger choose(final int N, final int K) {
          BigInteger nCk = BigInteger.ONE;
          for (int k = 0; k < K; k++) {

src/main/java/GraphDataObjectReader.java

@@ -0,0 +1,31 @@
+import java.io.*;
+
+public class GraphDataObjectReader {
+    private GraphWithMapData data;
+    private String filename;
+
+    public GraphDataObjectReader(String filename) throws IOException {
+        if(!filename.matches(".*\\.ser")){
+            filename = filename + ".ser";
+        }
+        this.filename = filename;
+        try(//don't need to close these because of try-with-resources
+            BufferedInputStream fileIn = new BufferedInputStream(new FileInputStream(filename));
+                ObjectInputStream in = new ObjectInputStream(fileIn))
+        {
+            System.out.println("Reading graph data from file. This may take some time");
+            System.out.println("File I/O time is not included in results");
+            data = (GraphWithMapData) in.readObject();
+        } catch (FileNotFoundException | ClassNotFoundException ex) {
+            ex.printStackTrace();
+        }
+    }
+
+    public GraphWithMapData getData() {
+        return data;
+    }
+
+    public String getFilename() {
+        return filename;
+    }
+}

src/main/java/GraphDataObjectWriter.java

@@ -0,0 +1,31 @@
+import java.io.BufferedOutputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectOutputStream;
+
+public class GraphDataObjectWriter {
+
+    private GraphWithMapData data;
+    private String filename;
+
+    public GraphDataObjectWriter(String filename, GraphWithMapData data) {
+        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.");
+            out.writeObject(data);
+        } catch (IOException ex) {
+            ex.printStackTrace();
+        }
+    }
+}

src/main/java/GraphMLFileReader.java

@@ -0,0 +1,35 @@
+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

@@ -0,0 +1,35 @@
+import org.jgrapht.graph.SimpleWeightedGraph;
+import org.jgrapht.nio.dot.DOTExporter;
+import org.jgrapht.nio.graphml.GraphMLExporter;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+
+public class GraphMLFileWriter {
+
+    String filename;
+    SimpleWeightedGraph graph;
+
+
+    public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) {
+        if(!filename.matches(".*\\.graphml")){
+            filename = filename + ".graphml";
+        }
+        this.filename = filename;
+        this.graph = graph;
+    }
+
+    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);
+        }
+    }
+}

src/main/java/GraphModificationFunctions.java

@@ -0,0 +1,90 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
+import org.jgrapht.graph.SimpleWeightedGraph;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public abstract class GraphModificationFunctions {
+
+    //remove over- and under-weight edges
+    public static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                            int low, int high) {
+        List<Integer[]> removedEdges = new ArrayList<>();
+        for(DefaultWeightedEdge e: graph.edgeSet()){
+            if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)){
+                Integer source = graph.getEdgeSource(e);
+                Integer target = graph.getEdgeTarget(e);
+                Integer weight = (int) graph.getEdgeWeight(e);
+                Integer[] edge = {source, target, weight};
+                removedEdges.add(edge);
+            }
+        }
+        for (Integer[] edge : removedEdges) {
+            graph.removeEdge(edge[0], edge[1]);
+        }
+        return removedEdges;
+    }
+
+    //Remove edges for pairs with large occupancy discrepancy
+    public static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                  Map<Integer, Integer> alphaWellCounts,
+                                                  Map<Integer, Integer> betaWellCounts,
+                                                  Map<Integer, Integer> plateVtoAMap,
+                                                  Map<Integer, Integer> plateVtoBMap,
+                                                  Integer maxOccupancyDifference) {
+        List<Integer[]> removedEdges = new ArrayList<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
+            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
+            if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
+                Integer source = graph.getEdgeSource(e);
+                Integer target = graph.getEdgeTarget(e);
+                Integer weight = (int) graph.getEdgeWeight(e);
+                Integer[] edge = {source, target, weight};
+                removedEdges.add(edge);
+            }
+        }
+        for (Integer[] edge : removedEdges) {
+            graph.removeEdge(edge[0], edge[1]);
+        }
+        return removedEdges;
+    }
+
+    //Remove edges for pairs where overlap size is significantly lower than the well occupancy
+    public static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                         Map<Integer, Integer> alphaWellCounts,
+                                                         Map<Integer, Integer> betaWellCounts,
+                                                         Map<Integer, Integer> plateVtoAMap,
+                                                         Map<Integer, Integer> plateVtoBMap,
+                                                         Integer minOverlapPercent) {
+        List<Integer[]> removedEdges = new ArrayList<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
+            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
+            double weight = graph.getEdgeWeight(e);
+            double min = minOverlapPercent / 100.0;
+            if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
+                Integer source = graph.getEdgeSource(e);
+                Integer target = graph.getEdgeTarget(e);
+                Integer intWeight = (int) graph.getEdgeWeight(e);
+                Integer[] edge = {source, target, intWeight};
+                removedEdges.add(edge);
+            }
+        }
+        for (Integer[] edge : removedEdges) {
+            graph.removeEdge(edge[0], edge[1]);
+        }
+        return removedEdges;
+    }
+
+    public static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                       List<Integer[]> removedEdges) {
+        for (Integer[] edge : removedEdges) {
+            DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);
+            graph.setEdgeWeight(e, (double) edge[2]);
+        }
+    }
+
+}

src/main/java/GraphWithMapData.java

@@ -0,0 +1,106 @@
+import org.jgrapht.graph.SimpleWeightedGraph;
+
+import java.time.Duration;
+import java.util.Map;
+
+//Can't just write the graph, because I need the occupancy data too.
+//Makes most sense to serialize object and write that to a file.
+//Which means there's no reason to split map data and graph data up.
+public class GraphWithMapData implements java.io.Serializable {
+
+    private String sourceFilename;
+    private final SimpleWeightedGraph graph;
+    private Integer numWells;
+    private Integer[] wellPopulations;
+    private Integer alphaCount;
+    private Integer betaCount;
+    private final Map<Integer, Integer> distCellsMapAlphaKey;
+    private final Map<Integer, Integer> plateVtoAMap;
+    private final Map<Integer, Integer> plateVtoBMap;
+    private final Map<Integer, Integer> plateAtoVMap;
+    private final Map<Integer, Integer> plateBtoVMap;
+    private final Map<Integer, Integer> alphaWellCounts;
+    private final Map<Integer, Integer> betaWellCounts;
+    private final Duration time;
+
+    public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
+                            Integer alphaCount, Integer betaCount,
+                            Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> plateVtoAMap,
+                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
+                            Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
+                            Map<Integer, Integer> betaWellCounts, Duration time) {
+        this.graph = graph;
+        this.numWells = numWells;
+        this.wellPopulations = wellConcentrations;
+        this.alphaCount = alphaCount;
+        this.betaCount = betaCount;
+        this.distCellsMapAlphaKey = distCellsMapAlphaKey;
+        this.plateVtoAMap = plateVtoAMap;
+        this.plateVtoBMap = plateVtoBMap;
+        this.plateAtoVMap = plateAtoVMap;
+        this.plateBtoVMap = plateBtoVMap;
+        this.alphaWellCounts = alphaWellCounts;
+        this.betaWellCounts = betaWellCounts;
+        this.time = time;
+    }
+
+    public SimpleWeightedGraph getGraph() {
+        return graph;
+    }
+
+    public Integer getNumWells() {
+        return numWells;
+    }
+
+    public Integer[] getWellPopulations() {
+        return wellPopulations;
+    }
+
+    public Integer getAlphaCount() {
+        return alphaCount;
+    }
+
+    public Integer getBetaCount() {
+        return betaCount;
+    }
+
+    public Map<Integer, Integer> getDistCellsMapAlphaKey() {
+        return distCellsMapAlphaKey;
+    }
+
+    public Map<Integer, Integer> getPlateVtoAMap() {
+        return plateVtoAMap;
+    }
+
+    public Map<Integer, Integer> getPlateVtoBMap() {
+        return plateVtoBMap;
+    }
+
+    public Map<Integer, Integer> getPlateAtoVMap() {
+        return plateAtoVMap;
+    }
+
+    public Map<Integer, Integer> getPlateBtoVMap() {
+        return plateBtoVMap;
+    }
+
+    public Map<Integer, Integer> getAlphaWellCounts() {
+        return alphaWellCounts;
+    }
+
+    public Map<Integer, Integer> getBetaWellCounts() {
+        return betaWellCounts;
+    }
+
+    public Duration getTime() {
+        return time;
+    }
+
+    public void setSourceFilename(String filename) {
+        this.sourceFilename = filename;
+    }
+
+    public String getSourceFilename() {
+        return sourceFilename;
+    }
+}

src/main/java/InteractiveInterface.java

@@ -0,0 +1,510 @@
+import java.io.IOException;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+//
+public class InteractiveInterface {
+
+    private static final Random rand = BiGpairSEQ.getRand();
+    private static final Scanner sc = new Scanner(System.in);
+    private static int input;
+    private static boolean quit = false;
+
+    public static void startInteractive() {
+
+            while (!quit) {
+                System.out.println();
+                System.out.println("--------BiGPairSEQ SIMULATOR--------");
+                System.out.println("ALPHA/BETA T CELL RECEPTOR MATCHING");
+                System.out.println("  USING WEIGHTED BIPARTITE GRAPHS  ");
+                System.out.println("------------------------------------");
+                System.out.println("Please select an option:");
+                System.out.println("1) Generate a population of distinct cells");
+                System.out.println("2) Generate a sample plate of T cells");
+                System.out.println("3) Generate CDR3 alpha/beta occupancy data and overlap graph");
+                System.out.println("4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ)");
+                //Need to re-do the CDR3/CDR1 matching to correspond to new pattern
+                //System.out.println("5) Generate CDR3/CDR1 occupancy graph");
+                //System.out.println("6) Simulate CDR3/CDR1 T cell matching");
+                System.out.println("9) About/Acknowledgments");
+                System.out.println("0) Exit");
+                try {
+                    input = sc.nextInt();
+                    switch (input) {
+                        case 1 -> makeCells();
+                        case 2 -> makePlate();
+                        case 3 -> makeCDR3Graph();
+                        case 4 -> matchCDR3s();
+                        //case 6 -> matchCellsCDR1();
+                        case 9 -> acknowledge();
+                        case 0 -> quit = true;
+                        default -> throw new InputMismatchException("Invalid input.");
+                    }
+                } catch (InputMismatchException | IOException ex) {
+                    System.out.println(ex);
+                    sc.next();
+                }
+            }
+            sc.close();
+    }
+
+    private static void makeCells() {
+        String filename = null;
+        Integer numCells = 0;
+        Integer cdr1Freq = 1;
+        try {
+            System.out.println("\nSimulated T-Cells consist of integer values representing:\n" +
+                    "* a pair of alpha and beta CDR3 peptides (unique within simulated population)\n" +
+                    "* a pair of alpha and beta CDR1 peptides (not necessarily unique).");
+            System.out.println("\nThe cells will be written to a CSV file.");
+            System.out.print("Please enter a file name: ");
+            filename = sc.next();
+            System.out.println("\nCDR3 sequences are more diverse than CDR1 sequences.");
+            System.out.println("Please enter the factor by which distinct CDR3s outnumber CDR1s: ");
+            cdr1Freq = sc.nextInt();
+            System.out.print("\nPlease enter the number of T-cells to generate: ");
+            numCells = sc.nextInt();
+            if(numCells <= 0){
+                throw new InputMismatchException("Number of cells must be a positive integer.");
+            }
+        } catch (InputMismatchException ex) {
+            System.out.println(ex);
+            sc.next();
+        }
+        CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
+        assert filename != null;
+        System.out.println("Writing cells to file");
+        CellFileWriter writer = new CellFileWriter(filename, sample);
+        writer.writeCellsToFile();
+        System.out.println("Cell sample written to: " + filename);
+        if(BiGpairSEQ.getCellSampleInMemory() != null) {
+            BiGpairSEQ.clearCellSampleInMemory();
+        }
+        BiGpairSEQ.setCellSampleInMemory(sample);
+        BiGpairSEQ.setCellFilename(filename);
+    }
+
+    //Output a CSV of sample plate
+    private static void makePlate() {
+        String cellFile = null;
+        String filename = null;
+        Double stdDev = 0.0;
+        Integer numWells = 0;
+        Integer numSections;
+        Integer[] populations = {1};
+        Double dropOutRate = 0.0;
+        boolean poisson = false;
+        boolean exponential = false;
+        double lambda = 1.5;
+        try {
+            System.out.println("\nSimulated sample plates consist of:");
+            System.out.println("* a number of wells");
+            System.out.println("  * separated into one or more sections");
+            System.out.println("    * each of which has a set quantity of cells per well");
+            System.out.println("    * selected from a statistical distribution of distinct cells");
+            System.out.println("    * with a set dropout rate for individual sequences within a cell");
+            System.out.println("\nMaking a sample plate requires a population of distinct cells");
+            System.out.print("Please enter name of an existing cell sample file: ");
+            cellFile = sc.next();
+            System.out.println("\nThe sample plate will be written to a CSV file");
+            System.out.print("Please enter a name for the output file: ");
+            filename = sc.next();
+            System.out.println("\nSelect T-cell frequency distribution function");
+            System.out.println("1) Poisson");
+            System.out.println("2) Gaussian");
+            System.out.println("3) Exponential");
+            System.out.println("(Note: approximate distribution in original paper is exponential, lambda = 0.6)");
+            System.out.println("(lambda value approximated from slope of log-log graph in figure 4c)");
+            System.out.println("(Note: wider distributions are more memory intensive to match)");
+            System.out.print("Enter selection value: ");
+            input = sc.nextInt();
+            switch (input) {
+                case 1 -> poisson = true;
+                case 2 -> {
+                    System.out.println("How many distinct T-cells within one standard deviation of peak frequency?");
+                    System.out.println("(Note: wider distributions are more memory intensive to match)");
+                    stdDev = sc.nextDouble();
+                    if (stdDev <= 0.0) {
+                        throw new InputMismatchException("Value must be positive.");
+                    }
+                }
+                case 3 -> {
+                    exponential = true;
+                    System.out.print("Please enter lambda value for exponential distribution: ");
+                    lambda = sc.nextDouble();
+                    if (lambda <= 0.0) {
+                        lambda = 0.6;
+                        System.out.println("Value must be positive. Defaulting to 0.6.");
+                    }
+                }
+                default -> {
+                    System.out.println("Invalid input. Defaulting to exponential.");
+                    exponential = true;
+                }
+            }
+            System.out.print("\nNumber of wells on plate: ");
+            numWells = sc.nextInt();
+            if(numWells < 1){
+                throw new InputMismatchException("No wells on plate");
+            }
+            //choose whether to make T cell population/well random
+            boolean randomWellPopulations;
+            System.out.println("Randomize number of T cells in each well? (y/n)");
+            String ans = sc.next();
+            Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
+            Matcher matcher = pattern.matcher(ans);
+            if(matcher.matches()){
+                randomWellPopulations = true;
+            }
+            else{
+                randomWellPopulations = false;
+            }
+            if(randomWellPopulations) { //if T cell population/well is random
+                numSections = numWells;
+                Integer minPop;
+                Integer maxPop;
+                System.out.print("Please enter minimum number of T cells in a well: ");
+                minPop = sc.nextInt();
+                if(minPop < 1) {
+                    throw new InputMismatchException("Minimum well population must be positive");
+                }
+                System.out.println("Please enter maximum number of T cells in a well: ");
+                maxPop = sc.nextInt();
+                if(maxPop < minPop) {
+                    throw new InputMismatchException("Max well population must be greater than min well population");
+                }
+                //maximum should be inclusive, so need to add one to max of randomly generated values
+                populations = rand.ints(minPop, maxPop + 1)
+                        .limit(numSections)
+                        .boxed()
+                        .toArray(Integer[]::new);
+                System.out.print("Populations: ");
+                System.out.println(Arrays.toString(populations));
+            }
+            else{ //if T cell population/well is not random
+                System.out.println("\nThe plate can be evenly sectioned to allow different numbers of T cells per well.");
+                System.out.println("How many sections would you like to make (minimum 1)?");
+                numSections = sc.nextInt();
+                if (numSections < 1) {
+                    throw new InputMismatchException("Too few sections.");
+                } else if (numSections > numWells) {
+                    throw new InputMismatchException("Cannot have more sections than wells.");
+                }
+                int i = 1;
+                populations = new Integer[numSections];
+                while (numSections > 0) {
+                    System.out.print("Enter number of T cells per well in section " + i + ": ");
+                    populations[i - 1] = sc.nextInt();
+                    i++;
+                    numSections--;
+                }
+            }
+            System.out.println("\nErrors in amplification can induce a well dropout rate for sequences");
+            System.out.print("Enter well dropout rate (0.0 to 1.0): ");
+            dropOutRate = sc.nextDouble();
+            if(dropOutRate < 0.0 || dropOutRate > 1.0) {
+                throw new InputMismatchException("The well dropout rate must be in the range [0.0, 1.0]");
+            }
+        }catch(InputMismatchException ex){
+            System.out.println(ex);
+            sc.next();
+        }
+        assert cellFile != null;
+        CellSample cells;
+        if (cellFile.equals(BiGpairSEQ.getCellFilename())){
+            cells = BiGpairSEQ.getCellSampleInMemory();
+        }
+        else {
+            System.out.println("Reading Cell Sample file: " + cellFile);
+            CellFileReader cellReader = new CellFileReader(cellFile);
+            cells = cellReader.getCellSample();
+            BiGpairSEQ.clearCellSampleInMemory();
+            BiGpairSEQ.setCellSampleInMemory(cells);
+            BiGpairSEQ.setCellFilename(cellFile);
+        }
+        assert filename != null;
+        Plate samplePlate;
+        PlateFileWriter writer;
+        if(exponential){
+            samplePlate = new Plate(numWells, dropOutRate, populations);
+            samplePlate.fillWellsExponential(cellFile, cells.getCells(), lambda);
+            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);
+            writer = new PlateFileWriter(filename, samplePlate);
+        }
+        System.out.println("Writing Sample Plate to file");
+        writer.writePlateFile();
+        System.out.println("Sample Plate written to file: " + filename);
+        BiGpairSEQ.setPlateInMemory(samplePlate);
+        BiGpairSEQ.setPlateFilename(filename);
+    }
+
+    //Output serialized binary of GraphAndMapData object
+    private static void makeCDR3Graph() {
+        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.");
+            System.out.println(str);
+            System.out.print("\nPlease enter name of an existing cell sample file: ");
+            cellFile = sc.next();
+            System.out.print("\nPlease enter name of an existing sample plate file: ");
+            plateFile = sc.next();
+            System.out.println("\nThe graph and occupancy data will be written to a serialized binary file.");
+            System.out.print("Please enter a name for the output file: ");
+            filename = sc.next();
+        } catch (InputMismatchException ex) {
+            System.out.println(ex);
+            sc.next();
+        }
+
+        assert cellFile != null;
+        CellSample cellSample;
+        //check if cells are already in memory
+        if(cellFile.equals(BiGpairSEQ.getCellFilename())) {
+            cellSample = BiGpairSEQ.getCellSampleInMemory();
+        }
+        else {
+            BiGpairSEQ.clearCellSampleInMemory();
+            System.out.println("Reading Cell Sample file: " + cellFile);
+            CellFileReader cellReader = new CellFileReader(cellFile);
+            cellSample = cellReader.getCellSample();
+            BiGpairSEQ.setCellSampleInMemory(cellSample);
+            BiGpairSEQ.setCellFilename(cellFile);
+        }
+
+        assert plateFile != null;
+        Plate plate;
+        //check if plate is already in memory
+        if(plateFile.equals(BiGpairSEQ.getPlateFilename())){
+            plate = BiGpairSEQ.getPlateInMemory();
+        }
+        else {
+            BiGpairSEQ.clearPlateInMemory();
+            System.out.println("Reading Sample Plate file: " + plateFile);
+            PlateFileReader plateReader = new PlateFileReader(plateFile);
+            plate = new Plate(plateReader.getFilename(), plateReader.getWells());
+            BiGpairSEQ.setPlateInMemory(plate);
+            BiGpairSEQ.setPlateFilename(plateFile);
+        }
+        if (cellSample.getCells().size() == 0){
+            System.out.println("No cell sample found.");
+            System.out.println("Returning to main menu.");
+        }
+        else if(plate.getWells().size() == 0 || plate.getPopulations().length == 0){
+            System.out.println("No sample plate found.");
+            System.out.println("Returning to main menu.");
+        }
+        else{
+            List<Integer[]> cells = cellSample.getCells();
+            GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
+            assert filename != null;
+            GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
+            dataWriter.writeDataToFile();
+            System.out.println("Graph and Data file written to: " + filename);
+            BiGpairSEQ.setGraphInMemory(data);
+            BiGpairSEQ.setGraphFilename(filename);
+            System.out.println("Graph and Data file " + filename + " cached.");
+        }
+    }
+
+    //Simulate matching and output CSV file of results
+    private static void matchCDR3s() throws IOException {
+        String filename = null;
+        String graphFilename = null;
+        Integer lowThreshold = 0;
+        Integer highThreshold = Integer.MAX_VALUE;
+        Integer maxOccupancyDiff = Integer.MAX_VALUE;
+        Integer minOverlapPercent = 0;
+        try {
+            System.out.println("\nBiGpairSEQ simulation requires an occupancy data and overlap graph file");
+            System.out.println("Please enter name of an existing graph and occupancy data file: ");
+            graphFilename = sc.next();
+            System.out.println("The matching results will be written to a file.");
+            System.out.print("Please enter a name for the output file: ");
+            filename = sc.next();
+            System.out.println("\nWhat is the minimum number of CDR3 alpha/beta overlap wells to attempt matching?");
+            lowThreshold = sc.nextInt();
+            if(lowThreshold < 1){
+                lowThreshold = 1;
+                System.out.println("Value for low occupancy overlap threshold must be positive");
+                System.out.println("Value for low occupancy overlap threshold set to 1");
+            }
+            System.out.println("\nWhat is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
+            highThreshold = sc.nextInt();
+            if(highThreshold < lowThreshold) {
+                highThreshold = lowThreshold;
+                System.out.println("Value for high occupancy overlap threshold must be >= low overlap threshold");
+                System.out.println("Value for high occupancy overlap threshold set to " + lowThreshold);
+            }
+            System.out.println("What is the minimum percentage of a sequence's wells in alpha/beta overlap to attempt matching? (0 - 100)");
+            minOverlapPercent = sc.nextInt();
+            if (minOverlapPercent < 0 || minOverlapPercent > 100) {
+                System.out.println("Value outside range. Minimum occupancy overlap percentage set to 0");
+            }
+            System.out.println("\nWhat is the maximum difference in alpha/beta occupancy to attempt matching?");
+            maxOccupancyDiff = sc.nextInt();
+            if (maxOccupancyDiff < 0) {
+                maxOccupancyDiff = 0;
+                System.out.println("Maximum allowable difference in alpha/beta occupancy must be nonnegative");
+                System.out.println("Maximum allowable difference in alpha/beta occupancy set to 0");
+            }
+        } catch (InputMismatchException ex) {
+            System.out.println(ex);
+            sc.next();
+        }
+        assert graphFilename != null;
+        //check if this is the same graph we already have in memory.
+        GraphWithMapData data;
+        if(!(graphFilename.equals(BiGpairSEQ.getGraphFilename())) || BiGpairSEQ.getGraphInMemory() == null) {
+            BiGpairSEQ.clearGraphInMemory();
+            //read object data from file
+            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
+            data = dataReader.getData();
+            //set new graph in memory and new filename
+            BiGpairSEQ.setGraphInMemory(data);
+            BiGpairSEQ.setGraphFilename(graphFilename);
+        }
+        else {
+            data = BiGpairSEQ.getGraphInMemory();
+        }
+        //simulate matching
+        MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
+                minOverlapPercent, true);
+        //write results to file
+        assert filename != null;
+        MatchingFileWriter writer = new MatchingFileWriter(filename, results);
+        System.out.println("Writing results to file");
+        writer.writeResultsToFile();
+        System.out.println("Results written to file: " + filename);
+    }
+
+    ///////
+    //Rewrite this to fit new matchCDR3 method with file I/O
+    ///////
+//    public static void matchCellsCDR1(){
+//    /*
+//    The idea here is that we'll get the CDR3 alpha/beta matches first. Then we'll try to match CDR3s to CDR1s by
+//    looking at the top two matches for each CDR3. If CDR3s in the same cell simply swap CDR1s, we assume a correct
+//    match
+//     */
+//        String filename = null;
+//        String preliminaryResultsFilename = null;
+//        String cellFile = null;
+//        String plateFile = null;
+//        Integer lowThresholdCDR3 = 0;
+//        Integer highThresholdCDR3 = Integer.MAX_VALUE;
+//        Integer maxOccupancyDiffCDR3 = 96; //no filtering if max difference is all wells by default
+//        Integer minOverlapPercentCDR3 = 0; //no filtering if min percentage is zero by default
+//        Integer lowThresholdCDR1 = 0;
+//        Integer highThresholdCDR1 = Integer.MAX_VALUE;
+//        boolean outputCDR3Matches = false;
+//        try {
+//            System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
+//            System.out.print("Please enter name of an existing cell sample file: ");
+//            cellFile = sc.next();
+//            System.out.print("Please enter name of an existing sample plate file: ");
+//            plateFile = sc.next();
+//            System.out.println("The matching results will be written to a file.");
+//            System.out.print("Please enter a name for the output file: ");
+//            filename = sc.next();
+//            System.out.println("What is the minimum number of CDR3 alpha/beta overlap wells to attempt matching?");
+//            lowThresholdCDR3 = sc.nextInt();
+//            if(lowThresholdCDR3 < 1){
+//                throw new InputMismatchException("Minimum value for low threshold is 1");
+//            }
+//            System.out.println("What is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
+//            highThresholdCDR3 = sc.nextInt();
+//            System.out.println("What is the maximum difference in CDR3 alpha/beta occupancy to attempt matching?");
+//            maxOccupancyDiffCDR3 = sc.nextInt();
+//            System.out.println("What is the minimum CDR3 overlap percentage to attempt matching? (0 - 100)");
+//            minOverlapPercentCDR3 = sc.nextInt();
+//            if (minOverlapPercentCDR3 < 0 || minOverlapPercentCDR3 > 100) {
+//                throw new InputMismatchException("Value outside range. Minimum percent set to 0");
+//            }
+//            System.out.println("What is the minimum number of CDR3/CDR1 overlap wells to attempt matching?");
+//            lowThresholdCDR1 = sc.nextInt();
+//            if(lowThresholdCDR1 < 1){
+//                throw new InputMismatchException("Minimum value for low threshold is 1");
+//            }
+//            System.out.println("What is the maximum number of CDR3/CDR1 overlap wells to attempt matching?");
+//            highThresholdCDR1 = sc.nextInt();
+//            System.out.println("Matching CDR3s to CDR1s requires first matching CDR3 alpha/betas.");
+//            System.out.println("Output a file for CDR3 alpha/beta match results as well?");
+//            System.out.print("Please enter y/n: ");
+//            String ans = sc.next();
+//            Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
+//            Matcher matcher = pattern.matcher(ans);
+//            if(matcher.matches()){
+//                outputCDR3Matches = true;
+//                System.out.println("Please enter filename for CDR3 alpha/beta match results");
+//                preliminaryResultsFilename = sc.next();
+//                System.out.println("CDR3 alpha/beta matches will be output to file");
+//            }
+//            else{
+//                System.out.println("CDR3 alpha/beta matches will not be output to file");
+//            }
+//        } catch (InputMismatchException ex) {
+//            System.out.println(ex);
+//            sc.next();
+//        }
+//        CellFileReader cellReader = new CellFileReader(cellFile);
+//        PlateFileReader plateReader = new PlateFileReader(plateFile);
+//        Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
+//        if (cellReader.getCells().size() == 0){
+//            System.out.println("No cell sample found.");
+//            System.out.println("Returning to main menu.");
+//        }
+//        else if(plate.getWells().size() == 0){
+//            System.out.println("No sample plate found.");
+//            System.out.println("Returning to main menu.");
+//
+//        }
+//        else{
+//            if(highThresholdCDR3 >= plate.getSize()){
+//                highThresholdCDR3 = plate.getSize() - 1;
+//            }
+//            if(highThresholdCDR1 >= plate.getSize()){
+//                highThresholdCDR1 = plate.getSize() - 1;
+//            }
+//            List<Integer[]> cells = cellReader.getCells();
+//            MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3,
+//                    maxOccupancyDiffCDR3, minOverlapPercentCDR3, true);
+//            MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
+//                    highThresholdCDR1, preliminaryResults);
+//            MatchingFileWriter writer = new MatchingFileWriter(filename + "_FirstPass", results[0]);
+//            writer.writeResultsToFile();
+//            writer = new MatchingFileWriter(filename + "_SecondPass", results[1]);
+//            writer.writeResultsToFile();
+//            if(outputCDR3Matches){
+//                writer = new MatchingFileWriter(preliminaryResultsFilename, preliminaryResults);
+//                writer.writeResultsToFile();
+//            }
+//        }
+//    }
+
+    private static void acknowledge(){
+        System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
+        System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
+        System.out.println();
+        System.out.println("For full documentation, view readme.md file distributed with this code");
+        System.out.println("or visit https://gitea.ejsf.synology.me/efischer/BiGpairSEQ.");
+        System.out.println();
+        System.out.println("pairSEQ citation:");
+        System.out.println("Howie, B., Sherwood, A. M., et. al.");
+        System.out.println("High-throughput pairing of T cell receptor alpha and beta sequences.");
+        System.out.println("Sci. Transl. Med. 7, 301ra131 (2015)");
+        System.out.println();
+        System.out.println("BiGpairSEQ_Sim by Eugene Fischer, 2021-2022");
+    }
+}

src/main/java/META-INF/MANIFEST.MF

@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Main-Class: BiGpairSEQ
+

src/main/java/MatchingFileWriter.java

@@ -7,13 +7,10 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.List;
-import java.util.regex.Pattern;
-
 
 public class MatchingFileWriter {
 
     private String filename;
-    private String sourceFileName;
     private List<String> comments;
     private List<String> headers;
     private List<List<String>> allResults;
@@ -23,7 +20,6 @@ public class MatchingFileWriter {
             filename = filename + ".csv";
         }
         this.filename = filename;
-        this.sourceFileName = result.getSourceFileName();
         this.comments = result.getComments();
         this.headers = result.getHeaders();
         this.allResults = result.getAllResults();

src/main/java/MatchingResult.java

@@ -1,18 +1,41 @@
 import java.time.Duration;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
 public class MatchingResult {
-    private String sourceFile;
-    private List<String> comments;
-    private List<String> headers;
-    private List<List<String>> allResults;
-    private Map<Integer, Integer> matchMap;
-    private Duration time;
 
-    public MatchingResult(String sourceFileName, List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
-        this.sourceFile = sourceFileName;
-        this.comments = comments;
+    private final Map<String, String> metadata;
+    private final List<String> comments;
+    private final List<String> headers;
+    private final List<List<String>> allResults;
+    private final Map<Integer, Integer> matchMap;
+    private final Duration time;
+
+    public MatchingResult(Map<String, String> metadata, List<String> headers,
+                          List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
+        /*
+         * POSSIBLE KEYS FOR METADATA MAP ARE:
+         * sample plate filename *
+         * graph filename *
+         * 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
+         */
+        this.metadata = metadata;
+        this.comments = new ArrayList<>();
+        for (String key : metadata.keySet()) {
+            comments.add(key +": " + metadata.get(key));
+        }
         this.headers = headers;
         this.allResults = allResults;
         this.matchMap = matchMap;
@@ -20,6 +43,8 @@ public class MatchingResult {
 
     }
 
+    public Map<String, String> getMetadata() {return metadata;}
+
     public List<String> getComments() {
         return comments;
     }
@@ -40,7 +65,32 @@ public class MatchingResult {
         return time;
     }
 
-    public String getSourceFileName() {
-        return sourceFile;
+    public String getPlateFilename() {
+        return metadata.get("sample plate filename");
     }
+
+    public String getGraphFilename() {
+        return metadata.get("graph filename");
+    }
+
+    public Integer[] getWellPopulations() {
+        List<Integer> wellPopulations = new ArrayList<>();
+        String popString = metadata.get("well populations");
+        for (String p : popString.split(", ")) {
+            wellPopulations.add(Integer.parseInt(p));
+        }
+        Integer[] popArray = new Integer[wellPopulations.size()];
+        return wellPopulations.toArray(popArray);
+    }
+
+    public Integer getAlphaCount() {
+        return Integer.parseInt(metadata.get("total alpha count"));
+    }
+
+    public Integer getBetaCount() {
+        return Integer.parseInt(metadata.get("total beta count"));
+    }
+
+    //put in the rest of these methods following the same pattern
+
 }

src/main/java/Plate.java

@@ -1,24 +1,28 @@
-import java.util.*;
+
 
 /*
+TODO: Implement exponential distribution using inversion method - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
+import java.util.*;
+
 public class Plate {
     private String sourceFile;
     private List<List<Integer[]>> wells;
-    private Random rand = new Random();
+    private final Random rand = BiGpairSEQ.getRand();
     private int size;
     private double error;
-    private Integer[] concentrations;
+    private Integer[] populations;
     private double stdDev;
+    private double lambda;
+    boolean exponential = false;
 
 
-    public Plate (int size, double error, Integer[] concentrations, double stdDev) {
+    public Plate(int size, double error, Integer[] populations) {
         this.size = size;
         this.error = error;
-        this.concentrations = concentrations;
-        this.stdDev = stdDev;
+        this.populations = populations;
         wells = new ArrayList<>();
     }
 
@@ -26,25 +30,39 @@ public class Plate {
         this.sourceFile = sourceFileName;
         this.wells = wells;
         this.size = wells.size();
+
+        List<Integer> concentrations = new ArrayList<>();
+        for (List<Integer[]> w: wells) {
+            if(!concentrations.contains(w.size())){
+                concentrations.add(w.size());
+            }
+        }
+        this.populations = new Integer[concentrations.size()];
+        for (int i = 0; i < this.populations.length; i++) {
+            this.populations[i] = concentrations.get(i);
+        }
     }
 
-    public void fillWells(String sourceFileName, List<Integer[]> cells) {
+    public void fillWellsExponential(String sourceFileName, List<Integer[]> cells, double lambda){
+        this.lambda = lambda;
+        exponential = true;
         sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.length;
         int section = 0;
         double m;
         int n;
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
                 List<Integer[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                     do {
-                        m = (rand.nextGaussian() * stdDev) + (cells.size() / 2);
+                        //inverse transform sampling: for random number u in [0,1), x = log(1-u) / (-lambda)
+                        m = (Math.log10((1 - rand.nextDouble()))/(-lambda)) * Math.sqrt(cells.size());
                     } while (m >= cells.size() || m < 0);
                     n = (int) Math.floor(m);
                     Integer[] cellToAdd = cells.get(n).clone();
                     for(int k = 0; k < cellToAdd.length; k++){
-                        if(Math.abs(rand.nextDouble()) < error){//error applied to each peptide
+                        if(Math.abs(rand.nextDouble()) < error){//error applied to each seqeunce
                             cellToAdd[k] = -1;
                         }
                     }
@@ -56,8 +74,37 @@ public class Plate {
         }
     }
 
-    public Integer[] getConcentrations(){
-        return concentrations;
+    public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
+        this.stdDev = stdDev;
+        sourceFile = sourceFileName;
+        int numSections = populations.length;
+        int section = 0;
+        double m;
+        int n;
+        while (section < numSections){
+            for (int i = 0; i < (size / numSections); i++) {
+                List<Integer[]> well = new ArrayList<>();
+                for (int j = 0; j < populations[section]; j++) {
+                    do {
+                        m = (rand.nextGaussian() * stdDev) + (cells.size() / 2);
+                    } while (m >= cells.size() || m < 0);
+                    n = (int) Math.floor(m);
+                    Integer[] cellToAdd = cells.get(n).clone();
+                    for(int k = 0; k < cellToAdd.length; k++){
+                        if(Math.abs(rand.nextDouble()) < error){//error applied to each sequence
+                            cellToAdd[k] = -1;
+                        }
+                    }
+                    well.add(cellToAdd);
+                }
+                wells.add(well);
+            }
+            section++;
+        }
+    }
+
+    public Integer[] getPopulations(){
+        return populations;
     }
 
     public int getSize(){
@@ -68,6 +115,10 @@ public class Plate {
         return stdDev;
     }
 
+    public boolean isExponential(){return exponential;}
+
+    public double getLambda(){return lambda;}
+
     public double getError() {
         return error;
     }
@@ -76,30 +127,30 @@ public class Plate {
         return wells;
     }
 
-    //returns a map of the counts of the peptide at cell index pIndex, in all wells
-    public Map<Integer, Integer> assayWellsPeptideP(int... pIndices){
-        return this.assayWellsPeptideP(0, size, pIndices);
+    //returns a map of the counts of the sequence at cell index sIndex, in all wells
+    public Map<Integer, Integer> assayWellsSequenceS(int... sIndices){
+        return this.assayWellsSequenceS(0, size, sIndices);
     }
 
-    //returns a map of the counts of the peptide at cell index pIndex, in a specific well
-    public Map<Integer, Integer> assayWellsPeptideP(int n, int... pIndices) { return this.assayWellsPeptideP(n, n+1, pIndices);}
+    //returns a map of the counts of the sequence at cell index sIndex, in a specific well
+    public Map<Integer, Integer> assayWellsSequenceS(int n, int... sIndices) { return this.assayWellsSequenceS(n, n+1, sIndices);}
 
-    //returns a map of the counts of the peptide at cell index pIndex, in a range of wells
-    public Map<Integer, Integer> assayWellsPeptideP(int start, int end, int... pIndices) {
+    //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
+    public Map<Integer, Integer> assayWellsSequenceS(int start, int end, int... sIndices) {
         Map<Integer,Integer> assay = new HashMap<>();
-        for(int pIndex: pIndices){
+        for(int pIndex: sIndices){
             for(int i = start; i < end; i++){
-                countPeptides(assay, wells.get(i), pIndex);
+                countSequences(assay, wells.get(i), pIndex);
             }
         }
         return assay;
     }
-    //For the peptides at cell indices pIndices, counts number of unique peptides in the given well into the given map
-    private void countPeptides(Map<Integer, Integer> wellMap, List<Integer[]> well, int... pIndices) {
+    //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
+    private void countSequences(Map<Integer, Integer> wellMap, List<Integer[]> well, int... sIndices) {
         for(Integer[] cell : well) {
-            for(int pIndex: pIndices){
-                if(cell[pIndex] != -1){
-                    wellMap.merge(cell[pIndex], 1, (oldValue, newValue) -> oldValue + newValue);
+            for(int sIndex: sIndices){
+                if(cell[sIndex] != -1){
+                    wellMap.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
                 }
             }
         }

src/main/java/PlateFileWriter.java

@@ -7,17 +7,17 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.*;
-import java.util.regex.Pattern;
 
 public class PlateFileWriter {
     private int size;
     private List<List<Integer[]>> wells;
     private double stdDev;
+    private double lambda;
     private Double error;
     private String filename;
     private String sourceFileName;
-    private String[] headers;
-    private List<Integer> concentrations;
+    private Integer[] populations;
+    private boolean isExponential = false;
 
     public PlateFileWriter(String filename, Plate plate) {
         if(!filename.matches(".*\\.csv")){
@@ -26,11 +26,17 @@ public class PlateFileWriter {
         this.filename = filename;
         this.sourceFileName = plate.getSourceFileName();
         this.size = plate.getSize();
+        this.isExponential = plate.isExponential();
+        if(isExponential) {
+            this.lambda = plate.getLambda();
+        }
+        else{
             this.stdDev = plate.getStdDev();
+        }
         this.error = plate.getError();
         this.wells = plate.getWells();
-        this.concentrations = Arrays.asList(plate.getConcentrations());
-        concentrations.sort(Comparator.reverseOrder());
+        this.populations = plate.getPopulations();
+        Arrays.sort(populations);
     }
 
     public void writePlateFile(){
@@ -51,28 +57,35 @@ public class PlateFileWriter {
             }
         }
 
-        //this took forever
-        List<List<String>> rows = new ArrayList<>();
-        List<String> tmp = new ArrayList<>();
-        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
-            tmp.add("well " + (i+1));
-        }
-        rows.add(tmp);
-        for(int row = 0; row < maxLength; row++){
-            tmp = new ArrayList<>();
-            for(List<String> c: wellsAsStrings){
-                tmp.add(c.get(row));
-            }
-            rows.add(tmp);
-        }
-        StringBuilder concen = new StringBuilder();
-        for(Integer i: concentrations){
-            concen.append(i.toString());
-            concen.append(" ");
-        }
-        String concenString = concen.toString();
+//        //this took forever and I don't use it
+//        //if I wanted to use it, I'd replace printer.printRecords(wellsAsStrings) with printer.printRecords(rows)
+//        List<List<String>> rows = new ArrayList<>();
+//        List<String> tmp = new ArrayList<>();
+//        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
+//            tmp.add("well " + (i+1));
+//        }
+//        rows.add(tmp);
+//        for(int row = 0; row < maxLength; row++){
+//            tmp = new ArrayList<>();
+//            for(List<String> c: wellsAsStrings){
+//                tmp.add(c.get(row));
+//            }
+//            rows.add(tmp);
+//        }
 
-        CSVFormat plateFileFormat = CSVFormat.Builder.create().setCommentMarker('#').build();
+        //make string out of populations array
+        StringBuilder populationsStringBuilder = new StringBuilder();
+        populationsStringBuilder.append(populations[0].toString());
+        for(int i = 1; i < populations.length; i++){
+            populationsStringBuilder.append(", ");
+            populationsStringBuilder.append(populations[i].toString());
+        }
+        String wellPopulationsString = populationsStringBuilder.toString();
+
+        //set CSV format
+        CSVFormat plateFileFormat = CSVFormat.Builder.create()
+                .setCommentMarker('#')
+                .build();
 
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
             CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
@@ -81,8 +94,13 @@ public class PlateFileWriter {
             printer.printComment("Each row represents one well on the plate.");
             printer.printComment("Plate size: " + size);
             printer.printComment("Error rate: " + error);
-            printer.printComment("Concentrations: " + concenString);
+            printer.printComment("Well populations: " + wellPopulationsString);
+            if(isExponential){
+                printer.printComment("Lambda: " + lambda);
+            }
+            else {
                 printer.printComment("Std. dev.: " + stdDev);
+            }
             printer.printRecords(wellsAsStrings);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);

src/main/java/UserInterface.java

@@ -1,395 +0,0 @@
-import org.apache.commons.cli.*;
-
-import java.util.List;
-import java.util.Scanner;
-import java.util.InputMismatchException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-//
-public class UserInterface {
-
-    final static Scanner sc = new Scanner(System.in);
-    static int input;
-    static boolean quit = false;
-
-    public static void main(String[] args) {
-
-        if(args.length != 0){
-            Options options = new Options();
-            Option matchCDR3 = Option.builder("m")
-                    .longOpt("match")
-                    .desc("Match CDR3s. Requires a cell sample file and any number of plate files.")
-                    .build();
-            options.addOption(matchCDR3);
-            Option inputCells = Option.builder("c")
-                    .longOpt("cellfile")
-                    .hasArg()
-                    .argName("file")
-                    .desc("The cell sample file used for matching")
-                    .required().build();
-            options.addOption(inputCells);
-            Option lowThresh = Option.builder("low")
-                    .hasArg()
-                    .argName("number")
-                    .desc("Sets the minimum occupancy overlap to attempt matching")
-                    .required().build();
-            options.addOption(lowThresh);
-            Option highThresh = Option.builder("high")
-                    .hasArg()
-                    .argName("number")
-                    .desc("Sets the maximum occupancy overlap to attempt matching")
-                    .required().build();
-            options.addOption(highThresh);
-            Option inputPlates = Option.builder("p")
-                    .longOpt("platefiles")
-                    .hasArgs()
-                    .desc("Plate files to match")
-                    .required().build();
-            options.addOption(inputPlates);
-
-            CommandLineParser parser = new DefaultParser();
-            try {
-                CommandLine line = parser.parse(options, args);
-                if(line.hasOption("m")){
-                    String cellFile = line.getOptionValue("c");
-                    Integer lowThreshold = Integer.valueOf(line.getOptionValue(lowThresh));
-                    Integer highThreshold = Integer.valueOf(line.getOptionValue(highThresh));
-                    for(String plate: line.getOptionValues("p")) {
-                        matchCDR3s(cellFile, plate, lowThreshold, highThreshold);
-                    }
-                }
-            }
-            catch (ParseException exp) {
-                System.err.println("Parsing failed.  Reason: " + exp.getMessage());
-            }
-        }
-        else {
-            while (!quit) {
-                System.out.println("\nALPHA/BETA T-CELL RECEPTOR MATCHING SIMULATOR");
-                System.out.println("Please select an option:");
-                System.out.println("1) Generate a population of distinct cells");
-                System.out.println("2) Generate a sample plate of T cells");
-                System.out.println("3) Simulate CDR3 alpha/beta T cell matching");
-                System.out.println("4) Simulate CDR3/CDR1 T cell matching");
-                System.out.println("5) Acknowledgements");
-                System.out.println("0) Exit");
-                try {
-                    input = sc.nextInt();
-                    switch (input) {
-                        case 1 -> makeCells();
-                        case 2 -> makePlate();
-                        case 3 -> matchCells();
-                        case 4 -> matchCellsCDR1();
-                        case 5 -> acknowledge();
-                        case 0 -> quit = true;
-                        default -> throw new InputMismatchException("Invalid input.");
-                    }
-                } catch (InputMismatchException ex) {
-                    System.out.println(ex);
-                    sc.next();
-                }
-            }
-            sc.close();
-        }
-    }
-
-    private static void makeCells() {
-        String filename = null;
-        Integer numCells = 0;
-        Integer cdr1Freq = 1;
-        try {
-            System.out.println("\nSimulated T-Cells consist of integer values representing:\n" +
-                    "* a pair of alpha and beta CDR3 peptides (unique within simulated population)\n" +
-                    "* a pair of alpha and beta CDR1 peptides (not necessarily unique).");
-            System.out.println("\nThe cells will be written to a file.");
-            System.out.print("Please enter a file name: ");
-            filename = sc.next();
-            System.out.println("CDR3 sequences are more diverse than CDR1 sequences.");
-            System.out.println("Please enter the factor by which distinct CDR3s outnumber CDR1s: ");
-            cdr1Freq = sc.nextInt();
-            System.out.print("Please enter the number of T-cells to generate: ");
-            numCells = sc.nextInt();
-            if(numCells <= 0){
-                throw new InputMismatchException("Number of cells must be a positive integer.");
-            }
-        } catch (InputMismatchException ex) {
-            System.out.println(ex);
-            sc.next();
-        }
-        CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
-        CellFileWriter writer = new CellFileWriter(filename, sample);
-        writer.writeCellsToFile();
-    }
-
-    private static void makeCells(String filename, Integer numCells, Integer cdr1Freq){
-        CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
-        CellFileWriter writer = new CellFileWriter(filename, sample);
-        writer.writeCellsToFile();
-    }
-
-    private static void makePlate(String cellFile, String filename, Double stdDev,
-                                  Integer numWells, Integer numSections,
-                                  Integer[] concentrations, Double dropOutRate){
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
-        samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells());
-        PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
-        writer.writePlateFile();
-    }
-
-    //method to output a CSV of
-    private static void makePlate() {
-        String cellFile = null;
-        String filename = null;
-        Double stdDev = 0.0;
-        Integer numWells = 0;
-        Integer numSections = 0;
-        Integer[] concentrations = {1};
-        Double dropOutRate = 0.0;
-        boolean poisson = false;
-        try {
-            System.out.println("\nMaking a sample plate requires a population of distinct cells");
-            System.out.println("Please enter name of an existing cell sample file: ");
-            cellFile = sc.next();
-            System.out.println("\nThe sample plate will be written to file");
-            System.out.print("Please enter a name for the output file: ");
-            filename = sc.next();
-            System.out.println("Select T-cell frequency distribution function");
-            System.out.println("1) Poisson");
-            System.out.println("2) Gaussian");
-            System.out.println("(Note: wider distributions are more memory intensive to match)");
-            System.out.print("Enter selection value: ");
-            input = sc.nextInt();
-            switch(input) {
-                case 1:
-                    poisson = true;
-                    break;
-                case 2:
-                    System.out.println("How many distinct T-cells within one standard deviation of peak frequency?");
-                    System.out.println("(Note: wider distributions are more memory intensive to match)");
-                    stdDev = sc.nextDouble();
-                    if(stdDev <= 0.0){
-                        throw new InputMismatchException("Value must be positive.");
-                    }
-                    break;
-                default:
-                    System.out.println("Invalid input. Defaulting to Poisson.");
-                    poisson = true;
-            }
-            System.out.print("Number of wells on plate: ");
-            numWells = sc.nextInt();
-            if(numWells < 1){
-                throw new InputMismatchException("No wells on plate");
-            }
-            System.out.println("The plate can be evenly sectioned to allow multiple concentrations of T-cells/well");
-            System.out.println("How many sections would you like to make (minimum 1)?");
-            numSections = sc.nextInt();
-            if(numSections < 1) {
-                throw new InputMismatchException("Too few sections.");
-            }
-            else if (numSections > numWells) {
-                throw new InputMismatchException("Cannot have more sections than wells.");
-            }
-            int i = 1;
-            concentrations = new Integer[numSections];
-            while(numSections > 0) {
-                System.out.print("Enter number of T-cells per well in section " + i +": ");
-                concentrations[i - 1] = sc.nextInt();
-                i++;
-                numSections--;
-            }
-            System.out.println("Errors in amplification can induce a well dropout rate for peptides");
-            System.out.print("Enter well dropout rate (0.0 to 1.0): ");
-            dropOutRate = sc.nextDouble();
-            if(dropOutRate < 0.0 || dropOutRate > 1.0) {
-                throw new InputMismatchException("The well dropout rate must be in the range [0.0, 1.0]");
-            }
-        }catch(InputMismatchException ex){
-            System.out.println(ex);
-            sc.next();
-        }
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        if(poisson) {
-            stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
-        }
-        Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
-        samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells());
-        PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
-        writer.writePlateFile();
-    }
-
-    private static void matchCDR3s(String cellFile, String plateFile, Integer lowThreshold, Integer highThreshold){
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        PlateFileReader plateReader = new PlateFileReader(plateFile);
-        Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
-        if (cellReader.getCells().size() == 0){
-            System.exit(0);
-        }
-        else if(plate.getWells().size() == 0){
-            System.exit(0);
-
-        }
-        else{
-            if(highThreshold >= plate.getSize()){
-                highThreshold = plate.getSize() - 1;
-            }
-            List<Integer[]> cells = cellReader.getCells();
-            MatchingResult results = Simulator.matchCDR3s(cells, plate, lowThreshold, highThreshold, false);
-            //result writer
-            MatchingFileWriter writer = new MatchingFileWriter("", results);
-            writer.writeErrorRateToTerminal();
-        }
-    }
-
-
-    private static void matchCells() {
-        String filename = null;
-        String cellFile = null;
-        String plateFile = null;
-        Integer lowThreshold = 0;
-        Integer highThreshold = Integer.MAX_VALUE;
-        try {
-            System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
-            System.out.print("Please enter name of an existing cell sample file: ");
-            cellFile = sc.next();
-            System.out.print("Please enter name of an existing sample plate file: ");
-            plateFile = sc.next();
-            System.out.println("The matching results will be written to a file.");
-            System.out.print("Please enter a name for the output file: ");
-            filename = sc.next();
-            System.out.println("What is the minimum number of alpha/beta overlap wells to attempt matching?");
-            lowThreshold = sc.nextInt();
-            if(lowThreshold < 1){
-                throw new InputMismatchException("Minimum value for low threshold is 1");
-            }
-            System.out.println("What is the maximum number of alpha/beta overlap wells to attempt matching?");
-            highThreshold = sc.nextInt();
-        } catch (InputMismatchException ex) {
-            System.out.println(ex);
-            sc.next();
-        }
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        PlateFileReader plateReader = new PlateFileReader(plateFile);
-        Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
-        if (cellReader.getCells().size() == 0){
-            System.out.println("No cell sample found.");
-            System.out.println("Returning to main menu.");
-        }
-        else if(plate.getWells().size() == 0){
-            System.out.println("No sample plate found.");
-            System.out.println("Returning to main menu.");
-
-        }
-        else{
-            if(highThreshold >= plate.getSize()){
-                highThreshold = plate.getSize() - 1;
-            }
-            List<Integer[]> cells = cellReader.getCells();
-            MatchingResult results = Simulator.matchCDR3s(cells, plate, lowThreshold, highThreshold, true);
-            //result writer
-            MatchingFileWriter writer = new MatchingFileWriter(filename, results);
-            writer.writeResultsToFile();
-        }
-    }
-
-    public static void matchCellsCDR1(){
-    /*
-    The idea here is that we'll get the CDR3 alpha/beta matches first. Then we'll try to match CDR3s to CDR1s by
-    looking at the top two matches for each CDR3. If CDR3s in the same cell simply swap CDR1s, we assume a correct
-    match
-     */
-        String filename = null;
-        String preliminaryResultsFilename = null;
-        String cellFile = null;
-        String plateFile = null;
-        Integer lowThresholdCDR3 = 0;
-        Integer highThresholdCDR3 = Integer.MAX_VALUE;
-        Integer lowThresholdCDR1 = 0;
-        Integer highThresholdCDR1 = Integer.MAX_VALUE;
-        boolean outputCDR3Matches = false;
-        try {
-            System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
-            System.out.print("Please enter name of an existing cell sample file: ");
-            cellFile = sc.next();
-            System.out.print("Please enter name of an existing sample plate file: ");
-            plateFile = sc.next();
-            System.out.println("The matching results will be written to a file.");
-            System.out.print("Please enter a name for the output file: ");
-            filename = sc.next();
-            System.out.println("What is the minimum number of CDR3 alpha/beta overlap wells to attempt matching?");
-            lowThresholdCDR3 = sc.nextInt();
-            if(lowThresholdCDR3 < 1){
-                throw new InputMismatchException("Minimum value for low threshold is 1");
-            }
-            System.out.println("What is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
-            highThresholdCDR3 = sc.nextInt();
-            System.out.println("What is the minimum number of CDR3/CDR1 overlap wells to attempt matching?");
-            lowThresholdCDR1 = sc.nextInt();
-            if(lowThresholdCDR1 < 1){
-                throw new InputMismatchException("Minimum value for low threshold is 1");
-            }
-            System.out.println("What is the maximum number of CDR3/CDR1 overlap wells to attempt matching?");
-            highThresholdCDR1 = sc.nextInt();
-            System.out.println("Matching CDR3s to CDR1s requires first matching CDR3 alpha/betas.");
-            System.out.println("Output a file for CDR3 alpha/beta match results as well?");
-            System.out.print("Please enter y/n: ");
-            String ans = sc.next();
-            Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
-            Matcher matcher = pattern.matcher(ans);
-            if(matcher.matches()){
-                outputCDR3Matches = true;
-                System.out.println("Please enter filename for CDR3 alpha/beta match results");
-                preliminaryResultsFilename = sc.next();
-                System.out.println("CDR3 alpha/beta matches will be output to file");
-            }
-            else{
-                System.out.println("CDR3 alpha/beta matches will not be output to file");
-            }
-        } catch (InputMismatchException ex) {
-            System.out.println(ex);
-            sc.next();
-        }
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        PlateFileReader plateReader = new PlateFileReader(plateFile);
-        Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
-        if (cellReader.getCells().size() == 0){
-            System.out.println("No cell sample found.");
-            System.out.println("Returning to main menu.");
-        }
-        else if(plate.getWells().size() == 0){
-            System.out.println("No sample plate found.");
-            System.out.println("Returning to main menu.");
-
-        }
-        else{
-            if(highThresholdCDR3 >= plate.getSize()){
-                highThresholdCDR3 = plate.getSize() - 1;
-            }
-            if(highThresholdCDR1 >= plate.getSize()){
-                highThresholdCDR1 = plate.getSize() - 1;
-            }
-            List<Integer[]> cells = cellReader.getCells();
-            MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3, true);
-            MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
-                    highThresholdCDR1, preliminaryResults);
-            MatchingFileWriter writer = new MatchingFileWriter(filename + "_FirstPass", results[0]);
-            writer.writeResultsToFile();
-            writer = new MatchingFileWriter(filename + "_SecondPass", results[1]);
-            writer.writeResultsToFile();
-            if(outputCDR3Matches){
-                writer = new MatchingFileWriter(preliminaryResultsFilename, preliminaryResults);
-                writer.writeResultsToFile();
-            }
-        }
-    }
-
-    private static void acknowledge(){
-        System.out.println("Simulation based on:");
-        System.out.println("Howie, B., Sherwood, A. M., et. al.");
-        System.out.println("High-throughput pairing of T cell receptor alpha and beta sequences.");
-        System.out.println("Sci. Transl. Med. 7, 301ra131 (2015)");
-        System.out.println("");
-        System.out.println("Simulation by Eugene Fischer, 2021");
-    }
-}

src/main/java/Vertex.java

@@ -0,0 +1,17 @@
+public class Vertex {
+    private final Integer peptide;
+    private final Integer occupancy;
+
+    public Vertex(Integer peptide, Integer occupancy) {
+        this.peptide = peptide;
+        this.occupancy = occupancy;
+    }
+
+    public Integer getPeptide() {
+        return peptide;
+    }
+
+    public Integer getOccupancy() {
+        return occupancy;
+    }
+}