update readme

This reverts commit adebe1542e.

.gitignore

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

readme.md

@@ -4,7 +4,7 @@
 ## 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.
+of the pairSEQ algorithm (Howie, et al. 2015) for pairing T cell receptor sequences.
 
 ## THEORY
 
@@ -12,33 +12,30 @@ Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and c
 against a null distribution, BiGpairSEQ does not do any statistical calculations
 directly.
 
-BiGpairSEQ creates a [simple bipartite weighted graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
+BiGpairSEQ creates a [weighted bipartite graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
 The distinct TCRA and TCRB sequences form the two sets of vertices. Every TCRA/TCRB pair that share a well
 are connected by an edge, with the edge weight set to the number of wells in which both sequences appear.
-(Sequences in all wells are filtered out prior to creating the graph, as there is no signal in their occupancy pattern.)
+(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 best currently-known algorithm for bipartite graphs with integer weights--which is what BiGpairSEQ uses--
+The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral
-is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 
+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. This is the best known efficiency for finding a maximum weight
+their algorithm runs in **O(m sqrt(n) log(N))** time. As the graph representation of a pairSEQ experiment is 
-matching on a bipartite graph, and the integer edge weight requirement makes it ideal for BiGpairSEQ.
+bipartite with integer weights, this algorithm is ideal for BiGpairSEQ.
 
-Unfortunately, it's a fairly new algorithm, and the integer edge weight requirement makes it less generically useful.
+Unfortunately, it's a fairly new algorithm, and not yet implemented by the graph theory library used in this simulator.
-It is not implemented by the graph theory library used in this simulator. So this program
+So this program instead uses the Fibonacci heap-based algorithm of Fredman and Tarjan (1987), which has a worst-case
-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
 
-BiGpairSEQ_Sim is an executable .jar file. Requires Java 11 or higher. [OpenJDK 17](https://jdk.java.net/17/)
+[Download the current version of BiGpairSEQ_Sim.](https://gitea.ejsf.synology.me/efischer/BiGpairSEQ/releases)
+
+BiGpairSEQ_Sim is an executable .jar file. Requires Java 14 or higher. [OpenJDK 17](https://jdk.java.net/17/)
 recommended.
 
 Run with the command:
@@ -46,17 +43,22 @@ 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.
+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
+There are a number of command line options, to allow the program to be used in shell scripts. For a full list,
-main menu looks like this:
+use the `-help` flag:
+
+`java -jar BiGpairSEQ_Sim.jar -help`
+
+If no command line arguments are given, BiGpairSEQ_Sim will launch with an interactive, menu-driven CLI for 
+generating files and simulating TCR pairing. The main menu looks like this:
 
 ```
 --------BiGPairSEQ SIMULATOR--------
-ALPHA/BETA T-CELL RECEPTOR MATCHING
+ALPHA/BETA T CELL RECEPTOR MATCHING
   USING WEIGHTED BIPARTITE GRAPHS  
 ------------------------------------
 Please select an option:
@@ -64,26 +66,57 @@ Please select an option:
 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)
+8) Options
 9) About/Acknowledgments
 0) Exit
 ```
 
-### OUTPUT
+By default, the Options menu looks like this:
+```
+--------------OPTIONS---------------
+1) Turn on cell sample file caching
+2) Turn on plate file caching
+3) Turn on graph/data file caching
+4) Turn off serialized binary graph output
+5) Turn on GraphML graph output
+6) Maximum weight matching algorithm options
+0) Return to main menu
+```
+
+
+### INPUT/OUTPUT
 
 To run the simulation, the program reads and writes 4 kinds of files:
 * Cell Sample files in CSV format
 * Sample Plate files in CSV format
-* Graph and Data files in binary object serialization format
+* Graph/Data files in binary object serialization format
 * Matching Results files in CSV format
 
-When entering filenames, it is not necessary to include the file extension (.csv or .ser). When reading or
+These files are often generated in sequence. When entering filenames, it is not necessary to include the file extension
-writing files, the program will automatically add the correct extension to any filename without one.
+(.csv or .ser). When reading or writing files, the program will automatically add the correct extension to any filename 
+without one.
 
+To save file I/O time when using the interactive interface, the most recent instance of each of these four
+files either generated or read from disk can be cached in program memory. When caching is active, subsequent uses of the 
+same data file won't need to be read in again until another file of that type is used or generated,
+or caching is turned off for that file type. The program checks whether it needs to update its cached data by comparing
+filenames as entered by the user. On encountering a new filename, the program flushes its cache and reads in the new file.
+
+(Note that cached Graph/Data files must be transformed back into their original state after a matching experiment, which
+may take some time. Whether file I/O or graph transformation takes longer for graph/data files is likely to be
+device-specific.)
+
+The program's caching behavior can be controlled in the Options menu. By default, all caching is OFF.
+
+The program can optionally output Graph/Data files in GraphML format (.graphml) for data portability. This can be 
+turned on in the Options menu. By default, GraphML output is OFF.
+
+---
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
-four sequences: Alpha CDR3, Beta CDR, Alpha CDR1, Beta CDR1. The sequences are represented by
+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. CDR1 Alpha and Beta sequences
+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 a Cell Sample file.
+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.)
 
@@ -94,9 +127,8 @@ Options when making a Cell Sample file:
 Files are in CSV format. Rows are distinct T cells, columns are sequences within the cells.
 Comments are preceded by `#`
 
-Structure example:
+Structure:
 
----
     # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
 | Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
 |---|---|---|---|
@@ -108,9 +140,9 @@ Structure example:
 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
+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 (approximately) evenly-sized
+prior to sequencing. Plates can also be partitioned into any number of sections, each of which can have a 
-sections, each of which can have a different number of T cells per well.
+different concentration of T cells per well.
 
 Options when making a Sample Plate file:
 * Cell Sample file to use
@@ -120,59 +152,78 @@ Options when making a Sample Plate file:
     * Standard deviation size 
   * Exponential
     * Lambda value
-      * Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was exponential with a lambda of approximately 0.6. (Howie et al. 2015)
+      * *(Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was approximately exponential with a lambda ~0.6. (Howie, et al. 2015))*
 * Total number of wells on the plate
+* Well populations random or fixed
+  * If random, minimum and maximum population sizes
+  * If fixed
     * Number of sections on plate
     * Number of T cells per well
       * per section, if more than one section
-* Dropout rate
+* Sequence dropout rate
 
 Files are in CSV format. There are no header labels. Every row represents a well. 
-Every column represents an individual cell, containing four sequences, represented by an array string:
+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 Alpha CDR1 is missing in the cell above, due to sequence dropout.
+Notice that the CDR1 Alpha is missing in the cell above--sequence dropout from simulated amplification error.
-Dropouts are represented by replacing sequences with the value `-1`. Comments are preceded by `#`
+Dropout sequences are replaced with the value `-1`. Comments are preceded by `#`
 
-Structure Example:
+Structure:
 
----
 ```
-# Cell source file name: 4MilCells.csv
+# Cell source file name:
-# Plate size: 96
+# Each row represents one well on the plate
-# Error rate: 0.1
+# Plate size:
-# Concentrations: 10000 5000 500
+# Concentrations:
-# Lambda: 0.6
+# Lambda -or- StdDev: 
 ```
-| well 1 | well 2 | well 3| ... |
+| Well 1, cell 1 | Well 1, cell 2 | Well 1, cell 3| ... |
 |---|---|---|---|
-| [105383, 786528, 959247, 925928] | [525902, 791533, -1, 866282] | [409236, 132303, 804465, 942261]| ... |
+| **Well 2, cell 1** | **Well 2, cell 2** | **Well 2, cell 3**| **...** |
-| [249930, 301502, 970003, 881099] | [523787, 552952, 997194, 970507]| [425363, 417411, 845399, -1]| ... |
+| **Well 3, cell 1** | **Well 3, cell 2** | **Well 3, cell 3**| **...** |
-| ... | ... | ... | ... |
+| **...** | **...** | **...** | **...** |
 
 ---
 
-#### Graph and Data Files
+#### Graph/Data Files
-Graph and Data files are serialized binaries of a Java object containing the graph representation of a
+Graph/Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
-Sample Plate and necessary metadata for matching and results output. Making them requires a Cell Sample file (to construct a list of correct sequence pairs for checking
+Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file 
-the accuracy of BiGpairSEQ simulations) and a Sample Plate file (to construct the associated
+(to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a 
-occupancy graph). These files can be several gigabytes in size. Writing them to a file lets us generate a graph and 
+Sample Plate file (to construct the associated occupancy graph).
-its metadata once, then use it for multiple different BiGpairSEQ simulations.
 
-Options for creating a Graph and Data file:
+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 (generated from the given Cell Sample file) to use.
+* The Sample Plate file to use. (This must have been generated from the selected Cell Sample file.)
+* Whether to simulate sequence read depth. If simulated:
+  * The read depth (number of times each sequence is read)
+  * The read error rate (probability a sequence is misread)
+  * The error collision rate (probability two misreads produce the same spurious sequence)
+  * The real sequence collision rate (probability that a misread will produce a different, real sequence from the sample plate. Only applies to new misreads; once an error of this type has occurred, it's likelihood of ocurring again is dominated by the error collision probability.)
 
-These files do not have a human-readable structure, and are not portable to other programs. (Export of graphs in a 
+These files do not have a human-readable structure, and are not portable to other programs.
-portable data format may be implemented in the future. The tricky part is encoding the necessary metadata.)
+
+*Optional GraphML output*
+
+For portability of graph data to other software, turn on [GraphML](http://graphml.graphdrawing.org/index.html) output 
+in the Options menu in interactive mode, or use the `-graphml`command line argument. This will produce a .graphml file 
+for the weighted graph, with vertex attributes for sequence, type, total occupancy, total read count, and the read count for every individual occupied well.
+This graph contains all the data necessary for the BiGpairSEQ matching algorithm. It does not include the data to measure pairing accuracy; for that, 
+compare the matching results to the original Cell Sample .csv file.
 
 ---
 
 #### Matching Results Files 
-Matching results files consist of the results of a BiGpairSEQ matching simulation.
+Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a serialized
-Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
+binary Graph/Data file (.ser). (Because .graphML files are larger than .ser files, BiGpairSEQ_Sim supports .graphML
+output only. Graph/data input must use a serialized binary.)
+
+Matching results files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
 Metadata about the matching simulation is included as comments. Comments are preceded by `#`.
 
 Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
@@ -181,14 +232,12 @@ Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
 * 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
-  * (To skip using this filter, enter a value >= the number of wells on the plate)
+  * (Optional. To skip using this filter, enter a value >= the number of wells on the plate)
-* The minimum percentage of a sequence's occupied wells shared by another sequence to attempt to match
+* 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.
-  * given value from 0 to 100
+  * (Optional. To skip using this filter, enter 0)
-  * (To skip using this filter, enter 0)
 
 Example output:
 
----
 ```
 # Source Sample Plate file: 4MilCellsPlate.csv
 # Source Graph and Data file: 4MilCellsPlateGraph.ser
@@ -217,44 +266,138 @@ Example output:
 ---
 
 **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, 
+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 (old results; need updating to reflect current, improved simulator performance)
+
+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 (lambda 0.6).
+
+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 total 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.
+
+As mentioned in the theory section, performance could be improved by implementing a more efficient algorithm for finding
+the maximum weight matching.
+
+## BEHAVIOR WITH RANDOMIZED WELL POPULATIONS
+
+A series of BiGpairSEQ simulations were conducted using a cell sample file of 3.5 million unique T cells. From these cells,
+10 sample plate files were created. All of these sample plates had 96 wells, used an exponential distribution with a lambda of 0.6, and
+had a sequence dropout rate of 10%.
+
+The well populations of the plates were:
+* One sample plate with 1000 T cells/well
+* One sample plate with 2000 T cells/well
+* One sample plate with 3000 T cells/well
+* One sample plate with 4000 T cells/well
+* One sample plate with 5000 T cells/well
+* Five sample plates with each individual well's population randomized, from 1000 to 5000 T cells. (Average population ~3000 T cells/well.)
+
+All BiGpairSEQ simulations were run with a low overlap threshold of 3 and a high overlap threshold of 94.
+No optional filters were used, so pairing was attempted for all sequences with overlaps within the threshold values.
+
+Constant well population plate results:
+
+| |1000 Cell/Well Plate|2000 Cell/Well Plate|3000 Cell/Well Plate|4000 Cell/Well Plate|5000 Cell/Well Plate
+|---|---|---|---|---|---|
+|Total Alphas Found|6407|7330|7936|8278|8553|
+|Total Betas Found|6405|7333|7968|8269|8582|
+|Pairing Attempt Rate|0.661|0.653|0.600|0.579|0.559|
+|Correct Pairing Count|4231|4749|4723|4761|4750|
+|Incorrect Pairing Count|3|34|40|26|29|
+|Pairing Error Rate|0.000709|0.00711|0.00840|0.00543|0.00607|
+|Simulation Time (Seconds)|500|643|700|589|598|
+
+Randomized well population plate results:
+
+| |Random Plate 1 | Random Plate 2|Random Plate 3|Random Plate 4|Random Plate 5|Average|
+|---|---|---|---|---|---|---|
+Total Alphas Found|7853|7904|7964|7898|7917|7907|
+Total Betas Found|7851|7891|7920|7910|7894|7893|
+Pairing Attempt Rate|0.607|0.610|0.601|0.605|0.603|0.605|
+Correct Pairing Count|4718|4782|4721|4755|4731|4741|
+Incorrect Pairing Count|51|35|42|27|29|37|
+Pairing Error Rate|0.0107|0.00727|0.00882|0.00565|0.00609|0.00771|
+Simulation Time (Seconds)|590|677|730|618|615|646|
+
+The average results for the randomized plates are closest to the constant plate with 3000 T cells/well.
+This and several other tests indicate that BiGpairSEQ treats a sample plate with a highly variable number of T cells/well
+roughly as though it had a constant well population equal to the plate's average well population.
+
 ## 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?~~
+* ~~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.
+  * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~
-* ~~See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows~~ DONE
+  * 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.
-* Enable GraphML output in addition to serialized object binaries, for data portability
+  * It is possible, though the modifications to the graph incur their own performance penalties. Need testing to see which option is best. It may be computer-specific.
-  * Custom vertex type with attribute for sequence occupancy?
+* ~~Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm~~ DONE
-* Re-implement CDR1 matching method
+  * ~~in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage~~
-* Re-implement command line arguments, to enable scripting and statistical simulation studies
+  * ~~Add controllable heap-type parameter?~~
-* Implement Duan and Su's maximum weight matching algorithms
+    * Parameter implemented. Fibonacci heap the current default.
-  * Add controllable algorithm-type parameter?
+* ~~Implement sample plates with random numbers of T cells per well.~~ DONE
-* Test whether pairing heap (currently used) or Fibonacci heap is more efficient for current matching algorithm
+  * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not due to nature of probability calculations.
-  * in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage
-  * Add controllable heap-type parameter?
-* Implement sample plates with random numbers of T cells per well
-  * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well populations; pairSEQ is not.
     * preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
+* ~~See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows.~~
+  * ~~Problem is variable number of cells in a well~~
+  * ~~Apache Commons CSV library writes entries a row at a time~~ 
+    * Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing.
+* ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
+  * ~~Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.~~
+* ~~Re-implement command line arguments, to enable scripting and statistical simulation studies~~ DONE
+* ~~Implement custom Vertex class to simplify code and make it easier to implement different MWM algorithms~~ DONE
+  * Advantage: would eliminate the need to use maps to associate vertices with sequences, which would make the code easier to understand.
+  * This also seems to be faster when using the same algorithm than the version with lots of maps, which is a nice bonus!
+* ~~Implement simulation of read depth, and of read errors. Pre-filter graph for difference in read count to eliminate spurious sequences.~~ DONE
+  * Pre-filtering based on comparing (read depth) * (occupancy) to (read count) for each sequence works extremely well
+* ~~Add read depth simulation options to CLI~~ DONE
+* ~~Update graphml output to reflect current Vertex class attributes~~ DONE
+  * Individual well data from the SequenceRecords could be included, if there's ever a reason for it
+* ~~Implement simulation of sequences being misread as other real sequence~~ DONE
+* Update matching metadata output options in CLI
+* Update performance data in this readme
+* Add section to ReadMe describing data filtering methods.
+* Re-implement CDR1 matching method
+* Refactor simulator code to collect all needed data in a single scan of the plate
+  * Currently it scans once for the vertices and then again for the edge weights. This made simulating read depth awkward, and incompatible with caching of plate files.
+  * This would be a fairly major rewrite of the simulator code, but could make things faster, and would definitely make them cleaner.
+* Implement Duan and Su's maximum weight matching algorithm
+    * Add controllable algorithm-type parameter?
+    * This would be fun and valuable, but probably take more time than I have for a hobby project.
+* Implement an auction algorithm for maximum weight matching
+* Implement an algorithm for approximating a maximum weight matching
+  * Some of these run in linear or near-linear time
+  * given that the underlying biological samples have many, many sources of error, this would probably be the most useful option in practice. It seems less mathematically elegant, though, and so less fun for me.
+* Implement Vose's alias method for arbitrary statistical distributions of cells
+  * Should probably refactor to use apache commons rng for this
+* Use commons JCS for caching
+* Parameterize pre-filtering. Currently, sequences present in all wells are filtered out before constructing the graph, which massively reduces graph size. But, ideally, no pre-filtering would be necessary.
   
   
 ## 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)
-* K. Melhorn, St. Näher. [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)
+* 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)
-* M. Fredman, R. Tarjan. ["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))
+* 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**.)
+* [Apache Commons CLI](https://commons.apache.org/proper/commons-cli/) -- To enable command line arguments for scripting.
 
 ## 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
-Eugene Fischer, 2021. UI improvements and documentation, 2022.
+BiGpairSEQ algorithm and simulation by Eugene Fischer, 2021. UI improvements and documentation, 2022.

src/main/java/BiGpairSEQ.java

@@ -0,0 +1,177 @@
+import java.util.Random;
+
+//main class. For choosing interface type and holding settings
+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;
+    private static boolean cacheCells = false;
+    private static boolean cachePlate = false;
+    private static boolean cacheGraph = false;
+    private static HeapType priorityQueueHeapType = HeapType.FIBONACCI;
+    private static boolean outputBinary = true;
+    private static boolean outputGraphML = false;
+    private static final String version = "version 3.0";
+
+    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 cellSample, String filename) {
+        if(cellSampleInMemory != null) {
+            clearCellSampleInMemory();
+        }
+        cellSampleInMemory = cellSample;
+        cellFilename = filename;
+        System.out.println("Cell sample file " + filename + " cached.");
+    }
+
+    public static void clearCellSampleInMemory() {
+        cellSampleInMemory = null;
+        cellFilename = null;
+        System.gc();
+        System.out.println("Cell sample file cache cleared.");
+
+    }
+
+    public static String getCellFilename() {
+        return cellFilename;
+    }
+
+    public static Plate getPlateInMemory() {
+        return plateInMemory;
+    }
+
+    public static void setPlateInMemory(Plate plate, String filename) {
+        if(plateInMemory != null) {
+            clearPlateInMemory();
+        }
+        plateInMemory = plate;
+        plateFilename = filename;
+        System.out.println("Sample plate file " + filename + " cached.");
+    }
+
+    public static void clearPlateInMemory() {
+        plateInMemory = null;
+        plateFilename = null;
+        System.gc();
+        System.out.println("Sample plate file cache cleared.");
+
+    }
+
+    public static String getPlateFilename() {
+        return plateFilename;
+    }
+
+
+    public static GraphWithMapData getGraphInMemory() {return graphInMemory;
+    }
+
+    public static void setGraphInMemory(GraphWithMapData g, String filename) {
+        if (graphInMemory != null) {
+            clearGraphInMemory();
+        }
+        graphInMemory = g;
+        graphFilename = filename;
+        System.out.println("Graph and data file " + filename + " cached.");
+    }
+
+    public static void clearGraphInMemory() {
+        graphInMemory = null;
+        graphFilename = null;
+        System.gc();
+        System.out.println("Graph and data file cache cleared.");
+    }
+
+    public static String getGraphFilename() {
+        return graphFilename;
+    }
+
+
+    public static boolean cacheCells() {
+        return cacheCells;
+    }
+
+    public static void setCacheCells(boolean cacheCells) {
+        //if not caching, clear the memory
+        if(!cacheCells){
+            BiGpairSEQ.clearCellSampleInMemory();
+            System.out.println("Cell sample file caching: OFF.");
+        }
+        else {
+            System.out.println("Cell sample file caching: ON.");
+        }
+        BiGpairSEQ.cacheCells = cacheCells;
+    }
+
+    public static boolean cachePlate() {
+        return cachePlate;
+    }
+
+    public static void setCachePlate(boolean cachePlate) {
+        //if not caching, clear the memory
+        if(!cachePlate) {
+            BiGpairSEQ.clearPlateInMemory();
+            System.out.println("Sample plate file caching: OFF.");
+        }
+        else {
+            System.out.println("Sample plate file caching: ON.");
+        }
+        BiGpairSEQ.cachePlate = cachePlate;
+    }
+
+    public static boolean cacheGraph() {
+        return cacheGraph;
+    }
+
+    public static void setCacheGraph(boolean cacheGraph) {
+        //if not caching, clear the memory
+        if(!cacheGraph) {
+            BiGpairSEQ.clearGraphInMemory();
+            System.out.println("Graph/data file caching: OFF.");
+        }
+        else {
+            System.out.println("Graph/data file caching: ON.");
+        }
+        BiGpairSEQ.cacheGraph = cacheGraph;
+    }
+
+    public static String getPriorityQueueHeapType() {
+        return priorityQueueHeapType.name();
+    }
+
+    public static void setPairingHeap() {
+        priorityQueueHeapType = HeapType.PAIRING;
+    }
+
+    public static void setFibonacciHeap() {
+        priorityQueueHeapType = HeapType.FIBONACCI;
+    }
+
+    public static boolean outputBinary() {return outputBinary;}
+    public static void setOutputBinary(boolean b) {outputBinary = b;}
+
+    public static boolean outputGraphML() {return outputGraphML;}
+    public static void setOutputGraphML(boolean b) {outputGraphML = b;}
+    public static String getVersion() { return version; }
+}

src/main/java/CellFileReader.java

@@ -12,7 +12,8 @@ import java.util.List;
 public class CellFileReader {
 
     private String filename;
-    private List<Integer[]> distinctCells = new ArrayList<>();
+    private List<String[]> distinctCells = new ArrayList<>();
+    private Integer cdr1Freq;
 
     public CellFileReader(String filename) {
         if(!filename.matches(".*\\.csv")){
@@ -31,26 +32,34 @@ public class CellFileReader {
             CSVParser parser = new CSVParser(reader, cellFileFormat);
         ){
             for(CSVRecord record: parser.getRecords()) {
-                Integer[] cell = new Integer[4];
+                String[] cell = new String[4];
-                cell[0] = Integer.valueOf(record.get("Alpha CDR3"));
+                cell[0] = record.get("Alpha CDR3");
-                cell[1] = Integer.valueOf(record.get("Beta CDR3"));
+                cell[1] = record.get("Beta CDR3");
-                cell[2] = Integer.valueOf(record.get("Alpha CDR1"));
+                cell[2] = record.get("Alpha CDR1");
-                cell[3] = Integer.valueOf(record.get("Beta CDR1"));
+                cell[3] = 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<String> cdr1Alphas = new ArrayList<>();
+        for (String[] 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(){
-        return distinctCells;
-    }
-
-    public Integer getCellCount() {
-        return distinctCells.size();
-    }
 }

src/main/java/CellFileWriter.java

@@ -11,7 +11,7 @@ import java.util.List;
 public class CellFileWriter {
 
     private String[] headers = {"Alpha CDR3", "Beta CDR3", "Alpha CDR1", "Beta CDR1"};
-    List<Integer[]> cells;
+    List<String[]> cells;
     String filename;
     Integer cdr1Freq;
 

src/main/java/CellSample.java

@@ -1,16 +1,51 @@
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.stream.IntStream;
 
 public class CellSample {
 
-    private List<Integer[]> cells;
+    private List<String[]> cells;
     private Integer cdr1Freq;
 
-    public CellSample(List<Integer[]> cells, Integer cdr1Freq){
+    public CellSample(Integer numDistinctCells, Integer cdr1Freq){
+        this.cdr1Freq = cdr1Freq;
+        List<Integer> numbersCDR3 = new ArrayList<>();
+        List<Integer> numbersCDR1 = new ArrayList<>();
+        Integer numDistCDR3s = 2 * numDistinctCells + 1;
+        //Assign consecutive integers for each CDR3. This ensures they are all unique.
+        IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
+        //After all CDR3s are assigned, start assigning consecutive integers to CDR1s
+        //There will usually be fewer integers in the CDR1 list, which will allow repeats below
+        IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
+        //randomize the order of the numbers in the lists
+        Collections.shuffle(numbersCDR3);
+        Collections.shuffle(numbersCDR1);
+
+        //Each cell represented by 4 values
+        //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
+        List<String[]> distinctCells = new ArrayList<>();
+        for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
+            //Go through entire CDR3 list once, make pairs of alphas and betas
+            String tmpCDR3a = numbersCDR3.get(i).toString();
+            String tmpCDR3b = numbersCDR3.get(i+1).toString();
+            //Go through the (likely shorter) CDR1 list as many times as necessary, make pairs of alphas and betas
+            String tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size()).toString();
+            String tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size()).toString();
+            //Make the array representing the cell
+            String[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
+            //Add the cell to the list of distinct cells
+            distinctCells.add(tmp);
+        }
+        this.cells = distinctCells;
+    }
+
+    public CellSample(List<String[]> cells, Integer cdr1Freq){
         this.cells = cells;
         this.cdr1Freq = cdr1Freq;
     }
 
-    public List<Integer[]> getCells(){
+    public List<String[]> getCells(){
         return cells;
     }
 
@@ -18,7 +53,7 @@ public class CellSample {
         return cdr1Freq;
     }
 
-    public Integer population(){
+    public Integer getCellCount(){
         return cells.size();
     }
 

src/main/java/CommandLineInterface.java

@@ -0,0 +1,551 @@
+import org.apache.commons.cli.*;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.stream.Stream;
+
+/*
+ * Class for parsing options passed to program from command line
+ *
+ * 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
+ * graphml : output a graphml file
+ * binary : output a serialized binary object file
+ * IF SIMULATING READ DEPTH, ALL THESE ARE REQUIRED. Absence indicates not simulating read depth
+ * readdepth: number of reads per sequence
+ * readerrorprob: probability of reading a sequence incorrectly
+ * errcollisionprob: probability of two read errors being identical
+ *
+ * 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) {
+        //Options sets for the different modes
+        Options mainOptions = buildMainOptions();
+        Options cellOptions = buildCellOptions();
+        Options plateOptions = buildPlateOptions();
+        Options graphOptions = buildGraphOptions();
+        Options matchOptions = buildMatchCDR3options();
+
+        CommandLineParser parser = new DefaultParser();
+        try{
+            CommandLine line = parser.parse(mainOptions, Arrays.copyOfRange(args, 0, 1));
+
+            if (line.hasOption("help")) {
+                HelpFormatter formatter = new HelpFormatter();
+                formatter.printHelp("BiGpairSEQ_Sim.jar", mainOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim.jar -cells", cellOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim.jar -plate", plateOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim.jar -graph", graphOptions);
+                System.out.println();
+                formatter.printHelp("BiGpairSEQ_Sim.jar -match", matchOptions);
+            }
+            else if (line.hasOption("version")) {
+                System.out.println("BiGpairSEQ_Sim " + BiGpairSEQ.getVersion());
+            }
+            else if (line.hasOption("cells")) {
+                line = parser.parse(cellOptions, Arrays.copyOfRange(args, 1, args.length));
+                Integer number = Integer.valueOf(line.getOptionValue("n"));
+                Integer diversity = Integer.valueOf(line.getOptionValue("d"));
+                String filename = line.getOptionValue("o");
+                makeCells(filename, number, diversity);
+            }
+
+            else if (line.hasOption("plate")) {
+                line = parser.parse(plateOptions, Arrays.copyOfRange(args, 1, args.length));
+                //get the cells
+                String cellFilename = line.getOptionValue("c");
+                CellSample cells = getCells(cellFilename);
+                //get the rest of the parameters
+                Integer[] populations;
+                String outputFilename = line.getOptionValue("o");
+                Integer numWells = Integer.parseInt(line.getOptionValue("w"));
+                Double dropoutRate = Double.parseDouble(line.getOptionValue("err"));
+                if (line.hasOption("random")) {
+                    //Array holding values of minimum and maximum populations
+                   Integer[] min_max = Stream.of(line.getOptionValues("random"))
+                           .mapToInt(Integer::parseInt)
+                           .boxed()
+                           .toArray(Integer[]::new);
+                   populations = BiGpairSEQ.getRand().ints(min_max[0], min_max[1] + 1)
+                            .limit(numWells)
+                            .boxed()
+                            .toArray(Integer[]::new);
+                }
+                else if (line.hasOption("pop")) {
+                    populations = Stream.of(line.getOptionValues("pop"))
+                            .mapToInt(Integer::parseInt)
+                            .boxed()
+                            .toArray(Integer[]::new);
+                }
+                else{
+                    populations = new Integer[1];
+                    populations[0] = 1;
+                }
+                //make the plate
+                Plate plate;
+                if (line.hasOption("poisson")) {
+                    Double stdDev = Math.sqrt(numWells);
+                    plate = new Plate(cells, cellFilename, numWells, populations, dropoutRate, stdDev, false);
+                }
+                else if (line.hasOption("gaussian")) {
+                    Double stdDev = Double.parseDouble(line.getOptionValue("stddev"));
+                    plate = new Plate(cells, cellFilename, numWells, populations, dropoutRate, stdDev, false);
+                }
+                else {
+                    assert line.hasOption("exponential");
+                    Double lambda = Double.parseDouble(line.getOptionValue("lambda"));
+                    plate = new Plate(cells, cellFilename, numWells, populations, dropoutRate, lambda, true);
+                }
+                PlateFileWriter writer = new PlateFileWriter(outputFilename, plate);
+                writer.writePlateFile();
+            }
+
+            else if (line.hasOption("graph")) { //Making a graph
+                line = parser.parse(graphOptions, Arrays.copyOfRange(args, 1, args.length));
+                String cellFilename = line.getOptionValue("c");
+                String plateFilename = line.getOptionValue("p");
+                String outputFilename = line.getOptionValue("o");
+                //get cells
+                CellSample cells = getCells(cellFilename);
+                //get plate
+                Plate plate = getPlate(plateFilename);
+                GraphWithMapData graph;
+                Integer readDepth = 1;
+                Double readErrorRate = 0.0;
+                Double errorCollisionRate = 0.0;
+                Double realSequenceCollisionRate = 0.0;
+                if (line.hasOption("rd")) {
+                    readDepth = Integer.parseInt(line.getOptionValue("rd"));
+                }
+                if (line.hasOption("err")) {
+                    readErrorRate = Double.parseDouble(line.getOptionValue("err"));
+                }
+                if (line.hasOption("errcoll")) {
+                    errorCollisionRate = Double.parseDouble(line.getOptionValue("errcoll"));
+                }
+                if (line.hasOption("realcoll")) {
+                    realSequenceCollisionRate = Double.parseDouble(line.getOptionValue("realcoll"));
+                }
+                graph = Simulator.makeCDR3Graph(cells, plate, readDepth, readErrorRate, errorCollisionRate,
+                        realSequenceCollisionRate, false);
+                if (!line.hasOption("no-binary")) { //output binary file unless told not to
+                    GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
+                    writer.writeDataToFile();
+                }
+                if (line.hasOption("graphml")) { //if told to, output graphml file
+                    GraphMLFileWriter gmlwriter = new GraphMLFileWriter(outputFilename, graph);
+                    gmlwriter.writeGraphToFile();
+                }
+            }
+
+            else if (line.hasOption("match")) { //can add a flag for which match type in future, spit this in two
+                line = parser.parse(matchOptions, Arrays.copyOfRange(args, 1, args.length));
+                String graphFilename = line.getOptionValue("g");
+
+                String outputFilename;
+                if(line.hasOption("o")) {
+                    outputFilename = line.getOptionValue("o");
+                }
+                else {
+                    outputFilename = null;
+                }
+                Integer minThreshold = Integer.parseInt(line.getOptionValue("min"));
+                Integer maxThreshold = Integer.parseInt(line.getOptionValue("max"));
+                int minOverlapPct;
+                if (line.hasOption("minpct")) { //see if this filter is being used
+                    minOverlapPct = Integer.parseInt(line.getOptionValue("minpct"));
+                }
+                else {
+                    minOverlapPct = 0;
+                }
+                int maxOccupancyDiff;
+                if (line.hasOption("maxdiff")) { //see if this filter is being used
+                    maxOccupancyDiff = Integer.parseInt(line.getOptionValue("maxdiff"));
+                }
+                else {
+                    maxOccupancyDiff = Integer.MAX_VALUE;
+                }
+                GraphWithMapData graph = getGraph(graphFilename);
+                MatchingResult result = Simulator.matchCDR3s(graph, graphFilename, minThreshold, maxThreshold,
+                        maxOccupancyDiff, minOverlapPct, false);
+                if(outputFilename != null){
+                    MatchingFileWriter writer = new MatchingFileWriter(outputFilename, result);
+                    writer.writeResultsToFile();
+                }
+                //can put a bunch of ifs for outputting various things from the MatchingResult to System.out here
+                //after I put those flags in the matchOptions
+                if(line.hasOption("print-metadata")) {
+                    for (String k : result.getMetadata().keySet()) {
+                        System.out.println(k + ": " + result.getMetadata().get(k));
+                    }
+                }
+                if(line.hasOption("print-error")) {
+                    System.out.println("pairing error rate: " + result.getPairingErrorRate());
+                }
+                if(line.hasOption("print-attempt")) {
+                    System.out.println("pairing attempt rate: " +result.getPairingAttemptRate());
+                }
+                if(line.hasOption("print-correct")) {
+                    System.out.println("correct pairings: " + result.getCorrectPairingCount());
+                }
+                if(line.hasOption("print-incorrect")) {
+                    System.out.println("incorrect pairings: " + result.getIncorrectPairingCount());
+                }
+                if(line.hasOption("print-alphas")) {
+                    System.out.println("total alphas found: " + result.getAlphaCount());
+                }
+                if(line.hasOption("print-betas")) {
+                    System.out.println("total betas found: " + result.getBetaCount());
+                }
+                if(line.hasOption("print-time")) {
+                    System.out.println("simulation time (seconds): " + result.getSimulationTime());
+                }
+            }
+        }
+        catch (ParseException exp) {
+            System.err.println("Parsing failed.  Reason: " + exp.getMessage());
+        }
+    }
+
+    private static Option outputFileOption() {
+        Option outputFile = Option.builder("o")
+                .longOpt("output-file")
+                .hasArg()
+                .argName("filename")
+                .desc("Name of output file")
+                .required()
+                .build();
+        return outputFile;
+    }
+
+    private static Options buildMainOptions() {
+        Options mainOptions = new Options();
+        Option help = Option.builder("help")
+                .desc("Displays this help menu")
+                .build();
+        Option makeCells = Option.builder("cells")
+                .longOpt("make-cells")
+                .desc("Makes a cell sample file of distinct T cells")
+                .build();
+        Option makePlate = Option.builder("plate")
+                .longOpt("make-plate")
+                .desc("Makes a sample plate file. Requires a cell sample file.")
+                .build();
+        Option makeGraph = Option.builder("graph")
+                .longOpt("make-graph")
+                .desc("Makes a graph/data file. Requires a cell sample file and a sample plate file")
+                .build();
+        Option matchCDR3 = Option.builder("match")
+                .longOpt("match-cdr3")
+                .desc("Matches CDR3s. Requires a graph/data file.")
+                .build();
+        Option printVersion = Option.builder("version")
+                .desc("Prints the program version number to stdout").build();
+        OptionGroup mainGroup = new OptionGroup();
+        mainGroup.addOption(help);
+        mainGroup.addOption(printVersion);
+        mainGroup.addOption(makeCells);
+        mainGroup.addOption(makePlate);
+        mainGroup.addOption(makeGraph);
+        mainGroup.addOption(matchCDR3);
+        mainGroup.setRequired(true);
+        mainOptions.addOptionGroup(mainGroup);
+        return mainOptions;
+    }
+
+    private static Options buildCellOptions() {
+        Options cellOptions = new Options();
+        Option numCells = Option.builder("n")
+                .longOpt("num-cells")
+                .desc("The number of distinct cells to generate")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option cdr3Diversity = Option.builder("d")
+                .longOpt("diversity-factor")
+                .desc("The factor by which unique CDR3s outnumber unique CDR1s")
+                .hasArg()
+                .argName("factor")
+                .required().build();
+        cellOptions.addOption(numCells);
+        cellOptions.addOption(cdr3Diversity);
+        cellOptions.addOption(outputFileOption());
+        return cellOptions;
+    }
+
+    private static Options buildPlateOptions() {
+        Options plateOptions = new Options();
+        Option cellFile = Option.builder("c") // add this to plate options
+                .longOpt("cell-file")
+                .desc("The cell sample file to use")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option numWells = Option.builder("w")// add this to plate options
+                .longOpt("wells")
+                .desc("The number of wells on the sample plate")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        //options group for choosing with distribution to use
+        OptionGroup distributions = new OptionGroup();// add this to plate options
+        distributions.setRequired(true);
+        Option poisson = Option.builder("poisson")
+                .desc("Use a Poisson distribution for cell sample")
+                .build();
+        Option gaussian = Option.builder("gaussian")
+                .desc("Use a Gaussian distribution for cell sample")
+                .build();
+        Option exponential = Option.builder("exponential")
+                .desc("Use an exponential distribution for cell sample")
+                .build();
+        distributions.addOption(poisson);
+        distributions.addOption(gaussian);
+        distributions.addOption(exponential);
+        //options group for statistical distribution parameters
+        OptionGroup statParams = new OptionGroup();// add this to plate options
+        Option stdDev = Option.builder("stddev")
+                .desc("If using -gaussian flag, standard deviation for distrbution")
+                .hasArg()
+                .argName("value")
+                .build();
+        Option lambda = Option.builder("lambda")
+                .desc("If using -exponential flag, lambda value for distribution")
+                .hasArg()
+                .argName("value")
+                .build();
+        statParams.addOption(stdDev);
+        statParams.addOption(lambda);
+        //Option group for random plate or set populations
+        OptionGroup wellPopOptions = new OptionGroup(); // add this to plate options
+        wellPopOptions.setRequired(true);
+        Option randomWellPopulations = Option.builder("random")
+                .desc("Randomize well populations on sample plate. Takes two arguments: the minimum possible population and the maximum possible population.")
+                .hasArgs()
+                .numberOfArgs(2)
+                .argName("min> <max")
+                .build();
+        Option specificWellPopulations = Option.builder("pop")
+                .desc("The well populations for each section of the sample plate. There will be as many sections as there are populations given.")
+                .hasArgs()
+                .argName("number [number]...")
+                .build();
+        Option dropoutRate = Option.builder("err") //add this to plate options
+                .hasArg()
+                .desc("The sequence dropout rate due to amplification error. (0.0 - 1.0)")
+                .argName("rate")
+                .required()
+                .build();
+        wellPopOptions.addOption(randomWellPopulations);
+        wellPopOptions.addOption(specificWellPopulations);
+        plateOptions.addOption(cellFile);
+        plateOptions.addOption(numWells);
+        plateOptions.addOptionGroup(distributions);
+        plateOptions.addOptionGroup(statParams);
+        plateOptions.addOptionGroup(wellPopOptions);
+        plateOptions.addOption(dropoutRate);
+        plateOptions.addOption(outputFileOption());
+        return plateOptions;
+    }
+
+    private static Options buildGraphOptions() {
+        Options graphOptions = new Options();
+        Option cellFilename = Option.builder("c")
+                .longOpt("cell-file")
+                .desc("Cell sample file to use for checking pairing accuracy")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option plateFilename = Option.builder("p")
+                .longOpt("plate-filename")
+                .desc("Sample plate file from which to construct graph")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option outputGraphML = Option.builder("graphml")
+                .desc("(Optional) Output GraphML file")
+                .build();
+        Option outputSerializedBinary = Option.builder("nb")
+                .longOpt("no-binary")
+                .desc("(Optional) Don't output serialized binary file")
+                .build();
+        Option readDepth = Option.builder("rd")
+                .longOpt("read-depth")
+                .desc("(Optional) The number of times to read each sequence.")
+                .hasArg()
+                .argName("depth")
+                .build();
+        Option readErrorProb = Option.builder("err")
+                .longOpt("read-error-prob")
+                .desc("(Optional) The probability that a sequence will be misread. (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
+                .build();
+        Option errorCollisionProb = Option.builder("errcoll")
+                .longOpt("error-collision-prob")
+                .desc("(Optional) The probability that two misreads will produce the same spurious sequence. (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
+                .build();
+        Option realSequenceCollisionProb = Option.builder("realcoll")
+                .longOpt("real-collision-prob")
+                .desc("(Optional) The probability that a sequence will be misread " +
+                        "as another real sequence. (Only applies to unique misreads; after this has happened once, " +
+                        "future error collisions could produce the real sequence again) (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
+                .build();
+        graphOptions.addOption(cellFilename);
+        graphOptions.addOption(plateFilename);
+        graphOptions.addOption(outputFileOption());
+        graphOptions.addOption(outputGraphML);
+        graphOptions.addOption(outputSerializedBinary);
+        graphOptions.addOption(readDepth);
+        graphOptions.addOption(readErrorProb);
+        graphOptions.addOption(errorCollisionProb);
+        graphOptions.addOption(realSequenceCollisionProb);
+        return graphOptions;
+    }
+
+    private static Options buildMatchCDR3options() {
+        Options matchCDR3options = new Options();
+        Option graphFilename = Option.builder("g")
+                .longOpt("graph-file")
+                .desc("The graph/data file to use")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option minOccupancyOverlap = Option.builder("min")
+                .desc("The minimum number of shared wells to attempt to match a sequence pair")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option maxOccupancyOverlap = Option.builder("max")
+                .desc("The maximum number of shared wells to attempt to match a sequence pair")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option minOverlapPercent = Option.builder("minpct")
+                .desc("(Optional) The minimum percentage of a sequence's total occupancy shared by another sequence to attempt matching. (0 - 100) ")
+                .hasArg()
+                .argName("percent")
+                .build();
+        Option maxOccupancyDifference = Option.builder("maxdiff")
+                .desc("(Optional) The maximum difference in total occupancy between two sequences to attempt matching.")
+                .hasArg()
+                .argName("number")
+                .build();
+        Option outputFile = Option.builder("o") //can't call the method this time, because this one's optional
+                .longOpt("output-file")
+                .hasArg()
+                .argName("filename")
+                .desc("(Optional) Name of output the output file. If not present, no file will be written.")
+                .build();
+        matchCDR3options.addOption(graphFilename)
+                .addOption(minOccupancyOverlap)
+                .addOption(maxOccupancyOverlap)
+                .addOption(minOverlapPercent)
+                .addOption(maxOccupancyDifference)
+                .addOption(outputFile);
+
+        //options for output to System.out
+        Option printAlphaCount = Option.builder().longOpt("print-alphas")
+                .desc("(Optional) Print the number of distinct alpha sequences to stdout.").build();
+        Option printBetaCount = Option.builder().longOpt("print-betas")
+                .desc("(Optional) Print the number of distinct beta sequences to stdout.").build();
+        Option printTime = Option.builder().longOpt("print-time")
+                .desc("(Optional) Print the total simulation time to stdout.").build();
+        Option printErrorRate = Option.builder().longOpt("print-error")
+               .desc("(Optional) Print the pairing error rate to stdout").build();
+        Option printAttempt = Option.builder().longOpt("print-attempt")
+               .desc("(Optional) Print the pairing attempt rate to stdout").build();
+        Option printCorrect = Option.builder().longOpt("print-correct")
+               .desc("(Optional) Print the number of correct pairs to stdout").build();
+        Option printIncorrect = Option.builder().longOpt("print-incorrect")
+               .desc("(Optional) Print the number of incorrect pairs to stdout").build();
+        Option printMetadata = Option.builder().longOpt("print-metadata")
+                       .desc("(Optional) Print a full summary of the matching results to stdout.").build();
+
+       matchCDR3options
+               .addOption(printErrorRate)
+               .addOption(printAttempt)
+               .addOption(printCorrect)
+               .addOption(printIncorrect)
+               .addOption(printMetadata)
+               .addOption(printAlphaCount)
+               .addOption(printBetaCount)
+               .addOption(printTime);
+        return matchCDR3options;
+    }
+
+
+
+    private static CellSample getCells(String cellFilename) {
+        assert cellFilename != null;
+        CellFileReader reader = new CellFileReader(cellFilename);
+        return reader.getCellSample();
+    }
+
+    private static Plate getPlate(String plateFilename) {
+        assert plateFilename != null;
+        PlateFileReader reader = new PlateFileReader(plateFilename);
+        return reader.getSamplePlate();
+    }
+
+    private static GraphWithMapData getGraph(String graphFilename) {
+        assert graphFilename != null;
+        try{
+            GraphDataObjectReader reader = new GraphDataObjectReader(graphFilename, false);
+            return reader.getData();
+
+        }
+        catch (IOException ex) {
+            ex.printStackTrace();
+            return null;
+        }
+    }
+
+    //for calling from command line
+    public static void makeCells(String filename, Integer numCells, Integer cdr1Freq) {
+        CellSample sample = new CellSample(numCells, cdr1Freq);
+        CellFileWriter writer = new CellFileWriter(filename, sample);
+        writer.writeCellsToFile();
+    }
+}

src/main/java/Equations.java

@@ -4,10 +4,9 @@ import java.math.MathContext;
 
 public abstract class Equations {
 
-    public static int getRandomNumber(int min, int max) {
+    //pValue calculation as described in original pairSEQ paper.
-        return (int) ((Math.random() * (max - min)) + min);
+    //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;
@@ -18,6 +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);
@@ -30,10 +32,9 @@ public abstract class Equations {
         return prob.doubleValue();
     }
 
-    /*
+
-     * This works because nC(k+1) = nCk * (n-k)/(k+1)
+     //This works because nC(k+1) = nCk * (n-k)/(k+1)
-     * Since nC0 = 1, can start there and generate all the rest.
+     //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

@@ -1,10 +1,12 @@
 import java.io.*;
 
 public class GraphDataObjectReader {
+
     private GraphWithMapData data;
     private String filename;
 
-    public GraphDataObjectReader(String filename) throws IOException {
+
+    public GraphDataObjectReader(String filename, boolean verbose) throws IOException {
         if(!filename.matches(".*\\.ser")){
             filename = filename + ".ser";
         }
@@ -13,8 +15,13 @@ public class GraphDataObjectReader {
             BufferedInputStream fileIn = new BufferedInputStream(new FileInputStream(filename));
                 ObjectInputStream in = new ObjectInputStream(fileIn))
         {
+            if (verbose) {
+                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) {
+            System.out.println("Graph/data file " + filename + " not found.");
             ex.printStackTrace();
         }
     }

src/main/java/GraphDataObjectWriter.java

@@ -1,3 +1,5 @@
+import org.jgrapht.Graph;
+
 import java.io.BufferedOutputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -7,6 +9,7 @@ public class GraphDataObjectWriter {
 
     private GraphWithMapData data;
     private String filename;
+    private boolean verbose = true;
 
     public GraphDataObjectWriter(String filename, GraphWithMapData data) {
         if(!filename.matches(".*\\.ser")){
@@ -16,10 +19,24 @@ public class GraphDataObjectWriter {
         this.data = data;
     }
 
+    public GraphDataObjectWriter(String filename, GraphWithMapData data, boolean verbose) {
+        this.verbose = verbose;
+        if(!filename.matches(".*\\.ser")){
+            filename = filename + ".ser";
+        }
+        this.filename = filename;
+        this.data = data;
+    }
+
     public void writeDataToFile() {
         try (BufferedOutputStream bufferedOut = new BufferedOutputStream(new FileOutputStream(filename));
+
              ObjectOutputStream out = new ObjectOutputStream(bufferedOut);
         ){
+            if(verbose) {
+                System.out.println("Writing graph and occupancy data to file. This may take some time.");
+                System.out.println("File I/O time is not included in results.");
+            }
             out.writeObject(data);
         } catch (IOException ex) {
             ex.printStackTrace();

src/main/java/GraphMLFileReader.java

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

src/main/java/GraphMLFileWriter.java

@@ -1,20 +1,38 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
-import org.jgrapht.nio.dot.DOTExporter;
+import org.jgrapht.nio.Attribute;
+import org.jgrapht.nio.AttributeType;
+import org.jgrapht.nio.DefaultAttribute;
 import org.jgrapht.nio.graphml.GraphMLExporter;
+import org.jgrapht.nio.graphml.GraphMLExporter.AttributeCategory;
 
 import java.io.BufferedWriter;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
 
 public class GraphMLFileWriter {
 
     String filename;
     SimpleWeightedGraph graph;
+    GraphWithMapData data;
+    Map<String, Attribute> graphAttributes;
 
+    public GraphMLFileWriter(String filename, GraphWithMapData data) {
+        if(!filename.matches(".*\\.graphml")){
+            filename = filename + ".graphml";
+        }
+        this.filename = filename;
+        this.data = data;
+        this.graph = data.getGraph();
+        graphAttributes = createGraphAttributes();
+    }
 
-    public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) {
+    public GraphMLFileWriter(String filename, SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph) {
         if(!filename.matches(".*\\.graphml")){
             filename = filename + ".graphml";
         }
@@ -22,10 +40,75 @@ public class GraphMLFileWriter {
         this.graph = graph;
     }
 
+    private Map<String, Attribute> createGraphAttributes(){
+        Map<String, Attribute> attributes = new HashMap<>();
+        //Sample plate filename
+        attributes.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
+        // Number of wells
+        attributes.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
+        //Well populations
+        Integer[] wellPopulations = data.getWellPopulations();
+        StringBuilder populationsStringBuilder = new StringBuilder();
+        populationsStringBuilder.append(wellPopulations[0].toString());
+        for(int i = 1; i < wellPopulations.length; i++){
+            populationsStringBuilder.append(", ");
+            populationsStringBuilder.append(wellPopulations[i].toString());
+        }
+        String wellPopulationsString = populationsStringBuilder.toString();
+        attributes.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
+        attributes.put("read depth", DefaultAttribute.createAttribute(data.getReadDepth().toString()));
+        attributes.put("read error rate", DefaultAttribute.createAttribute(data.getReadErrorRate().toString()));
+        attributes.put("error collision rate", DefaultAttribute.createAttribute(data.getErrorCollisionRate().toString()));
+        attributes.put("real sequence collision rate", DefaultAttribute.createAttribute(data.getRealSequenceCollisionRate()));
+        return attributes;
+    }
+
+    private Map<String, Attribute> createVertexAttributes(Vertex v){
+        Map<String, Attribute> attributes = new HashMap<>();
+        //sequence type
+        attributes.put("type", DefaultAttribute.createAttribute(v.getType().name()));
+        //sequence
+        attributes.put("sequence", DefaultAttribute.createAttribute(v.getSequence()));
+        //number of wells the sequence appears in
+        attributes.put("occupancy", DefaultAttribute.createAttribute(v.getOccupancy()));
+        //total number of times the sequence was read
+        attributes.put("total read count", DefaultAttribute.createAttribute(v.getReadCount()));
+        StringBuilder wellsAndReadCountsBuilder = new StringBuilder();
+        Iterator<Map.Entry<Integer, Integer>> wellOccupancies = v.getWellOccupancies().entrySet().iterator();
+        while (wellOccupancies.hasNext()) {
+            Map.Entry<Integer, Integer> entry = wellOccupancies.next();
+            wellsAndReadCountsBuilder.append(entry.getKey() + ":" + entry.getValue());
+            if (wellOccupancies.hasNext()) {
+                wellsAndReadCountsBuilder.append(", ");
+            }
+        }
+        String wellsAndReadCounts = wellsAndReadCountsBuilder.toString();
+        //the wells the sequence appears in and the read counts in those wells
+        attributes.put("wells:read counts", DefaultAttribute.createAttribute(wellsAndReadCounts));
+        return attributes;
+    }
+
     public void writeGraphToFile() {
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
         ){
-            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+            //create exporter. Let the vertex labels be the unique ids for the vertices
+            GraphMLExporter<Vertex, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(v -> v.getVertexLabel().toString());
+            //set to export weights
+            exporter.setExportEdgeWeights(true);
+            //Set graph attributes
+            exporter.setGraphAttributeProvider( () -> graphAttributes);
+            //set type, sequence, and occupancy attributes for each vertex
+            exporter.setVertexAttributeProvider(this::createVertexAttributes);
+            //register the attributes
+            for(String s : graphAttributes.keySet()) {
+                exporter.registerAttribute(s, AttributeCategory.GRAPH, AttributeType.STRING);
+            }
+            exporter.registerAttribute("type", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("sequence", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("occupancy", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("total read count", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("wells:read counts", AttributeCategory.NODE, AttributeType.STRING);
+            //export the graph
             exporter.exportGraph(graph, writer);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);

src/main/java/GraphModificationFunctions.java

@@ -0,0 +1,138 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
+import org.jgrapht.graph.SimpleWeightedGraph;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public interface GraphModificationFunctions {
+
+    //remove over- and under-weight edges, return removed edges
+    static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+                                                            int low, int high, boolean saveEdges) {
+        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
+                if(saveEdges) {
+                    Vertex source = graph.getEdgeSource(e);
+                    Vertex target = graph.getEdgeTarget(e);
+                    Integer weight = (int) graph.getEdgeWeight(e);
+                    Vertex[] edge = {source, target};
+                    removedEdges.put(edge, weight);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Vertex[] edge : removedEdges.keySet()) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    //Remove edges for pairs with large occupancy discrepancy, return removed edges
+    static Map<Vertex[], Integer> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+                                                  Integer maxOccupancyDifference, boolean saveEdges) {
+        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
+            Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
+            if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
+                if (saveEdges) {
+                    Vertex source = graph.getEdgeSource(e);
+                    Vertex target = graph.getEdgeTarget(e);
+                    Integer weight = (int) graph.getEdgeWeight(e);
+                    Vertex[] edge = {source, target};
+                    removedEdges.put(edge, weight);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Vertex[] edge : removedEdges.keySet()) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    //Remove edges for pairs where overlap size is significantly lower than the well occupancy, return removed edges
+    static Map<Vertex[], Integer> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+                                                         Integer minOverlapPercent,
+                                                         boolean saveEdges) {
+        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
+            Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
+            double weight = graph.getEdgeWeight(e);
+            double min = minOverlapPercent / 100.0;
+            if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
+                if (saveEdges) {
+                    Vertex source = graph.getEdgeSource(e);
+                    Vertex target = graph.getEdgeTarget(e);
+                    Integer intWeight = (int) graph.getEdgeWeight(e);
+                    Vertex[] edge = {source, target};
+                    removedEdges.put(edge, intWeight);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Vertex[] edge : removedEdges.keySet()) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    static Map<Vertex[], Integer> filterByRelativeReadCount (SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph, Integer threshold, boolean saveEdges) {
+        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        Boolean passes;
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaReadCount = graph.getEdgeSource(e).getReadCount();
+            Integer betaReadCount = graph.getEdgeTarget(e).getReadCount();
+            passes = RelativeReadCountFilterFunction(threshold, alphaReadCount, betaReadCount);
+            if (!passes) {
+                if (saveEdges) {
+                    Vertex source = graph.getEdgeSource(e);
+                    Vertex target = graph.getEdgeTarget(e);
+                    Integer intWeight = (int) graph.getEdgeWeight(e);
+                    Vertex[] edge = {source, target};
+                    removedEdges.put(edge, intWeight);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Vertex[] edge : removedEdges.keySet()) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    static Boolean RelativeReadCountFilterFunction(Integer threshold, Integer alphaReadCount, Integer betaReadCount) {
+        return Math.abs(alphaReadCount - betaReadCount) < threshold;
+    }
+
+    static void addRemovedEdges(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+                                Map<Vertex[], Integer> removedEdges) {
+        for (Vertex[] edge : removedEdges.keySet()) {
+            DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);
+            graph.setEdgeWeight(e, removedEdges.get(edge));
+        }
+    }
+
+
+
+}

src/main/java/GraphWithMapData.java

@@ -6,41 +6,53 @@ 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.
+//Custom vertex class means a lot of the map data can now be encoded in the graph itself
 public class GraphWithMapData implements java.io.Serializable {
 
     private String sourceFilename;
     private final SimpleWeightedGraph graph;
-    private Integer numWells;
+    private final int numWells;
-    private Integer[] wellConcentrations;
+    private final Integer[] wellPopulations;
-    private Integer alphaCount;
+    private final int alphaCount;
-    private Integer betaCount;
+    private final int betaCount;
-    private final Map<Integer, Integer> distCellsMapAlphaKey;
+    private final int readDepth;
-    private final Map<Integer, Integer> plateVtoAMap;
+    private final double readErrorRate;
-    private final Map<Integer, Integer> plateVtoBMap;
+    private final double errorCollisionRate;
-    private final Map<Integer, Integer> plateAtoVMap;
+    private final double realSequenceCollisionRate;
-    private final Map<Integer, Integer> plateBtoVMap;
+    private final Map<String, String> distCellsMapAlphaKey;
-    private final Map<Integer, Integer> alphaWellCounts;
+//    private final Map<Integer, Integer> plateVtoAMap;
-    private final Map<Integer, Integer> betaWellCounts;
+//    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<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount,
-                            Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> plateVtoAMap,
+                            Integer readDepth, Double readErrorRate, Double errorCollisionRate,
-                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
+                            Double realSequenceCollisionRate, Duration time){
-                            Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
+
-                            Map<Integer, Integer> betaWellCounts, Duration time) {
+//                            Map<Integer, Integer> plateVtoAMap,
+//                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
+//                            Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
+//                            Map<Integer, Integer> betaWellCounts,) {
         this.graph = graph;
         this.numWells = numWells;
-        this.wellConcentrations = wellConcentrations;
+        this.wellPopulations = wellConcentrations;
         this.alphaCount = alphaCount;
         this.betaCount = betaCount;
         this.distCellsMapAlphaKey = distCellsMapAlphaKey;
-        this.plateVtoAMap = plateVtoAMap;
+//        this.plateVtoAMap = plateVtoAMap;
-        this.plateVtoBMap = plateVtoBMap;
+//        this.plateVtoBMap = plateVtoBMap;
-        this.plateAtoVMap = plateAtoVMap;
+//        this.plateAtoVMap = plateAtoVMap;
-        this.plateBtoVMap = plateBtoVMap;
+//        this.plateBtoVMap = plateBtoVMap;
-        this.alphaWellCounts = alphaWellCounts;
+//        this.alphaWellCounts = alphaWellCounts;
-        this.betaWellCounts = betaWellCounts;
+//        this.betaWellCounts = betaWellCounts;
+        this.readDepth = readDepth;
+        this.readErrorRate = readErrorRate;
+        this.errorCollisionRate = errorCollisionRate;
+        this.realSequenceCollisionRate = realSequenceCollisionRate;
         this.time = time;
     }
 
@@ -52,8 +64,8 @@ public class GraphWithMapData implements java.io.Serializable {
         return numWells;
     }
 
-    public Integer[] getWellConcentrations() {
+    public Integer[] getWellPopulations() {
-        return wellConcentrations;
+        return wellPopulations;
     }
 
     public Integer getAlphaCount() {
@@ -64,33 +76,35 @@ public class GraphWithMapData implements java.io.Serializable {
         return betaCount;
     }
 
-    public Map<Integer, Integer> getDistCellsMapAlphaKey() {
+    public Map<String, String> getDistCellsMapAlphaKey() {
         return distCellsMapAlphaKey;
     }
 
-    public Map<Integer, Integer> getPlateVtoAMap() {
+//    public Map<Integer, Integer> getPlateVtoAMap() {
-        return plateVtoAMap;
+//        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 Map<Integer, Integer> getPlateVtoBMap() {
+    public Integer getReadDepth() { return readDepth; }
-        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;
@@ -103,4 +117,14 @@ public class GraphWithMapData implements java.io.Serializable {
     public String getSourceFilename() {
         return sourceFilename;
     }
+
+    public Double getReadErrorRate() {
+        return readErrorRate;
+    }
+
+    public Double getErrorCollisionRate() {
+        return errorCollisionRate;
+    }
+
+    public Double getRealSequenceCollisionRate() { return realSequenceCollisionRate; }
 }

src/main/java/HeapType.java

@@ -0,0 +1,4 @@
+public enum HeapType {
+    FIBONACCI,
+    PAIRING
+}

src/main/java/InteractiveInterface.java

@@ -0,0 +1,627 @@
+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("8) Options");
+                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 8 -> mainOptions();
+                        case 9 -> acknowledge();
+                        case 0 -> quit = true;
+                        default -> System.out.println("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 = new CellSample(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.cacheCells()) {
+            BiGpairSEQ.setCellSampleInMemory(sample, 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();
+            if(BiGpairSEQ.cacheCells()) {
+                BiGpairSEQ.setCellSampleInMemory(cells, cellFile);
+            }
+        }
+        assert filename != null;
+        Plate samplePlate;
+        PlateFileWriter writer;
+        if(exponential){
+            samplePlate = new Plate(cells, cellFile, numWells, populations, dropOutRate, lambda, true);
+            writer = new PlateFileWriter(filename, samplePlate);
+        }
+        else {
+            if (poisson) {
+                stdDev = Math.sqrt(cells.getCellCount()); //gaussian with square root of elements approximates poisson
+            }
+            samplePlate = new Plate(cells, cellFile, numWells, populations, dropOutRate, stdDev, false);
+            writer = new PlateFileWriter(filename, samplePlate);
+        }
+        System.out.println("Writing Sample Plate to file");
+        writer.writePlateFile();
+        System.out.println("Sample Plate written to file: " + filename);
+        if(BiGpairSEQ.cachePlate()) {
+            BiGpairSEQ.setPlateInMemory(samplePlate, filename);
+        }
+    }
+
+    //Output serialized binary of GraphAndMapData object
+    private static void makeCDR3Graph() {
+        String filename = null;
+        String cellFile = null;
+        String plateFile = null;
+        Boolean simulateReadDepth = false;
+        //number of times to read each sequence in a well
+        int readDepth = 1;
+        double readErrorRate = 0.0;
+        double errorCollisionRate = 0.0;
+        double realSequenceCollisionRate = 0.0;
+        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("\nEnable simulation of sequence read depth and sequence read errors? (y/n)");
+            String ans = sc.next();
+            Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
+            Matcher matcher = pattern.matcher(ans);
+            if(matcher.matches()){
+                simulateReadDepth = true;
+            }
+            if (simulateReadDepth) {
+                System.out.print("\nPlease enter the read depth (the integer number of times a sequence is read): ");
+                readDepth = sc.nextInt();
+                if(readDepth < 1) {
+                    throw new InputMismatchException("The read depth must be an integer >= 1");
+                }
+                System.out.println("\nPlease enter the read error probability (0.0 to 1.0)");
+                System.out.print("(The probability that a sequence will be misread): ");
+                readErrorRate = sc.nextDouble();
+                if(readErrorRate < 0.0 || readErrorRate > 1.0) {
+                    throw new InputMismatchException("The read error probability must be in the range [0.0, 1.0]");
+                }
+                System.out.println("\nPlease enter the error collision probability (0.0 to 1.0)");
+                System.out.print("(The probability of a sequence being misread in a way it has been misread before): ");
+                errorCollisionRate = sc.nextDouble();
+                if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) {
+                    throw new InputMismatchException("The error collision probability must be an in the range [0.0, 1.0]");
+                }
+                System.out.println("\nPlease enter the real sequence collision probability (0.0 to 1.0)");
+                System.out.print("(The probability that a (non-collision) misread produces a different, real sequence): ");
+                realSequenceCollisionRate = sc.nextDouble();
+                if(realSequenceCollisionRate < 0.0 || realSequenceCollisionRate > 1.0) {
+                    throw new InputMismatchException("The real sequence collision probability must be an in the range [0.0, 1.0]");
+                }
+            }
+            System.out.println("\nThe graph and occupancy data will be written to a 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()) && BiGpairSEQ.getCellSampleInMemory() != null) {
+            cellSample = BiGpairSEQ.getCellSampleInMemory();
+        }
+        else {
+            System.out.println("Reading Cell Sample file: " + cellFile);
+            CellFileReader cellReader = new CellFileReader(cellFile);
+            cellSample = cellReader.getCellSample();
+            if(BiGpairSEQ.cacheCells()) {
+                BiGpairSEQ.setCellSampleInMemory(cellSample, cellFile);
+            }
+        }
+
+        assert plateFile != null;
+        Plate plate;
+        //check if plate is already in memory
+        if(plateFile.equals(BiGpairSEQ.getPlateFilename())){
+            plate = BiGpairSEQ.getPlateInMemory();
+        }
+        else {
+            System.out.println("Reading Sample Plate file: " + plateFile);
+            PlateFileReader plateReader = new PlateFileReader(plateFile);
+            plate = plateReader.getSamplePlate();
+            if(BiGpairSEQ.cachePlate()) {
+                BiGpairSEQ.setPlateInMemory(plate, 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{
+            GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate,
+                    errorCollisionRate, realSequenceCollisionRate, true);
+            assert filename != null;
+            if(BiGpairSEQ.outputBinary()) {
+                GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
+                dataWriter.writeDataToFile();
+                System.out.println("Serialized binary graph/data file written to: " + filename);
+            }
+            if(BiGpairSEQ.outputGraphML()) {
+                GraphMLFileWriter graphMLWriter = new GraphMLFileWriter(filename, data);
+                graphMLWriter.writeGraphToFile();
+                System.out.println("GraphML file written to: " + filename);
+            }
+            if(BiGpairSEQ.cacheGraph()) {
+                BiGpairSEQ.setGraphInMemory(data, filename);
+
+            }
+        }
+    }
+
+    //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())) {
+            data = BiGpairSEQ.getGraphInMemory();
+        }
+        else {
+            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename, true);
+            data = dataReader.getData();
+            if(BiGpairSEQ.cacheGraph()) {
+                BiGpairSEQ.setGraphInMemory(data, graphFilename);
+            }
+        }
+        //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 mainOptions(){
+        boolean backToMain = false;
+        while(!backToMain) {
+            System.out.println("\n--------------OPTIONS---------------");
+            System.out.println("1) Turn " + getOnOff(!BiGpairSEQ.cacheCells()) + " cell sample file caching");
+            System.out.println("2) Turn " + getOnOff(!BiGpairSEQ.cachePlate()) + " plate file caching");
+            System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
+            System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
+            System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
+            System.out.println("6) Maximum weight matching algorithm options");
+            System.out.println("0) Return to main menu");
+            try {
+                input = sc.nextInt();
+                switch (input) {
+                    case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
+                    case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
+                    case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
+                    case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
+                    case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
+                    case 6 -> algorithmOptions();
+                    case 0 -> backToMain = true;
+                    default -> System.out.println("Invalid input");
+                }
+            } catch (InputMismatchException ex) {
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+    }
+
+    /**
+     * Helper function for printing menu items in mainOptions(). Returns a string based on the value of parameter.
+     *
+     * @param b - a boolean value
+     * @return String "on" if b is true, "off" if b is false
+     */
+    private static String getOnOff(boolean b) {
+        if (b) { return "on";}
+        else { return "off"; }
+    }
+
+    private static void algorithmOptions(){
+        boolean backToOptions = false;
+        while(!backToOptions) {
+            System.out.println("\n---------ALGORITHM OPTIONS----------");
+            System.out.println("1) Use scaling algorithm by Duan and Su.");
+            System.out.println("2) Use LEDA book algorithm with Fibonacci heap priority queue");
+            System.out.println("3) Use LEDA book algorithm with pairing heap priority queue");
+            System.out.println("0) Return to Options menu");
+            try {
+                input = sc.nextInt();
+                switch (input) {
+                    case 1 -> System.out.println("This option is not yet implemented. Choose another.");
+                    case 2 -> {
+                        BiGpairSEQ.setFibonacciHeap();
+                        System.out.println("MWM algorithm set to LEDA with Fibonacci heap");
+                        backToOptions = true;
+                    }
+                    case 3 -> {
+                        BiGpairSEQ.setPairingHeap();
+                        System.out.println("MWM algorithm set to LEDA with pairing heap");
+                        backToOptions = true;
+                    }
+                    case 0 -> backToOptions = true;
+                    default -> System.out.println("Invalid input");
+                }
+            } catch (InputMismatchException ex) {
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+    }
+
+    private static void acknowledge(){
+        System.out.println("BiGpairSEQ_Sim " + BiGpairSEQ.getVersion());
+        System.out.println();
+        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

@@ -1,25 +1,55 @@
 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){
+    private final Map<String, String> metadata;
-        this.sourceFile = sourceFileName;
+    private final List<String> comments;
-        this.comments = comments;
+    private final List<String> headers;
+    private final List<List<String>> allResults;
+    private final Map<String, String> matchMap;
+
+    public MatchingResult(Map<String, String> metadata, List<String> headers,
+                          List<List<String>> allResults, Map<String, String>matchMap){
+        /*
+         * POSSIBLE KEYS FOR METADATA MAP ARE:
+         * sample plate filename *
+         * graph filename *
+         * matching weight *
+         * well populations *
+         * sequence read depth *
+         * sequence read error rate *
+         * read error collision rate *
+         * total alphas read from plate *
+         * total betas read from plate *
+         * alphas in graph (after pre-filtering) *
+         * betas in graph (after pre-filtering) *
+         * high overlap threshold for pairing *
+         * low overlap threshold for pairing *
+         * maximum occupancy difference for pairing *
+         * minimum overlap percent for pairing *
+         * pairing attempt rate *
+         * correct pairing count *
+         * incorrect pairing count *
+         * pairing error rate *
+         * time to generate graph (seconds) *
+         * time to pair sequences (seconds) *
+         * total simulation time (seconds) *
+         */
+        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;
-        this.time = time;
-
     }
 
+    public Map<String, String> getMetadata() {return metadata;}
+
     public List<String> getComments() {
         return comments;
     }
@@ -32,15 +62,56 @@ public class MatchingResult {
         return headers;
     }
 
-    public Map<Integer, Integer> getMatchMap() {
+    public Map<String, String> getMatchMap() {
         return matchMap;
     }
 
-    public Duration getTime() {
+//    public Duration getTime() {
-        return time;
+//        return time;
+//    }
+
+    public String getPlateFilename() {
+        return metadata.get("sample plate filename");
     }
 
-    public String getSourceFileName() {
+    public String getGraphFilename() {
-        return sourceFile;
+        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 alphas read from plate"));
+    }
+
+    public Integer getBetaCount() {
+        return Integer.parseInt(metadata.get("total betas read from plate"));
+    }
+
+    public Integer getHighOverlapThreshold() { return Integer.parseInt(metadata.get("high overlap threshold for pairing"));}
+
+    public Integer getLowOverlapThreshold() { return Integer.parseInt(metadata.get("low overlap threshold for pairing"));}
+
+    public Integer getMaxOccupancyDifference() { return Integer.parseInt(metadata.get("maximum occupancy difference for pairing"));}
+
+    public Integer getMinOverlapPercent() { return Integer.parseInt(metadata.get("minimum overlap percent for pairing"));}
+
+    public Double getPairingAttemptRate() { return Double.parseDouble(metadata.get("pairing attempt rate"));}
+
+    public Integer getCorrectPairingCount() { return Integer.parseInt(metadata.get("correct pairing count"));}
+
+    public Integer getIncorrectPairingCount() { return Integer.parseInt(metadata.get("incorrect pairing count"));}
+
+    public Double getPairingErrorRate() { return Double.parseDouble(metadata.get("pairing error rate"));}
+
+    public String getSimulationTime() { return metadata.get("total simulation time (seconds)"); }
+
 }

src/main/java/Plate.java

@@ -1,75 +1,98 @@
-import java.util.*;
+
 
 /*
 TODO: Implement exponential distribution using inversion method - DONE
+TODO: Implement collisions with real sequences by having the counting function keep a map of all sequences it's read,
+with values of all misreads. Can then have a spurious/real collision rate, which will have count randomly select a sequence
+it's already read at least once, and put that into the list of spurious sequences for the given real sequence. Will let me get rid
+of the distinctMisreadCount map, and use this new map instead. Doing it this way, once a sequence has been misread as another
+sequence once, it is more likely to be misread that way again, as future read error collisions can also be real sequence collisions
+Prob A: a read error occurs. Prob B: it's a new error (otherwise it's a repeated error). Prob C: if new error, prob that it's
+a real sequence collision (otherwise it's a new spurious sequence) - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
+
+import java.util.*;
+
 public class Plate {
+    private CellSample cells;
     private String sourceFile;
-    private List<List<Integer[]>> wells;
+    private String filename;
-    private Random rand = new Random();
+    private List<List<String[]>> wells;
+    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(CellSample cells, String cellFilename, int numWells, Integer[] populations,
+                 double dropoutRate, double stdDev_or_lambda, boolean exponential){
+        this.cells = cells;
+        this.sourceFile = cellFilename;
+        this.size = numWells;
+        this.wells = new ArrayList<>();
+        this.error = dropoutRate;
+        this.populations = populations;
+        this.exponential = exponential;
+        if (this.exponential) {
+            this.lambda = stdDev_or_lambda;
+            fillWellsExponential(cells.getCells(), this.lambda);
+        }
+        else {
+            this.stdDev = stdDev_or_lambda;
+            fillWells(cells.getCells(), this.stdDev);
+        }
+    }
 
-    public Plate(int size, double error, Integer[] concentrations) {
+
+    public Plate(int size, double error, Integer[] populations) {
         this.size = size;
         this.error = error;
-        this.concentrations = concentrations;
+        this.populations = populations;
         wells = new ArrayList<>();
     }
 
-    public Plate(String sourceFileName, List<List<Integer[]>> wells) {
+    //constructor for returning a Plate from a PlateFileReader
-        this.sourceFile = sourceFileName;
+    public Plate(String filename, List<List<String[]>> wells) {
+        this.filename = filename;
         this.wells = wells;
         this.size = wells.size();
 
         List<Integer> concentrations = new ArrayList<>();
-        for (List<Integer[]> w: wells) {
+        for (List<String[]> w: wells) {
             if(!concentrations.contains(w.size())){
                 concentrations.add(w.size());
             }
         }
-        this.concentrations = new Integer[concentrations.size()];
+        this.populations = new Integer[concentrations.size()];
-        for (int i = 0; i < this.concentrations.length; i++) {
+        for (int i = 0; i < this.populations.length; i++) {
-            this.concentrations[i] = concentrations.get(i);
+            this.populations[i] = concentrations.get(i);
         }
     }
 
-    public void fillWellsExponential(String sourceFileName, List<Integer[]> cells, double lambda){
+    private void fillWellsExponential(List<String[]> cells, double lambda){
         this.lambda = lambda;
         exponential = true;
-        sourceFile = sourceFileName;
+        int numSections = populations.length;
-        int numSections = concentrations.length;
         int section = 0;
         double m;
         int n;
-        int test=0;
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
-                List<Integer[]> well = new ArrayList<>();
+                List<String[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                     do {
                         //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);
-                    //n = Equations.getRandomNumber(0, cells.size());
+                    String[] cellToAdd = cells.get(n).clone();
-                    // was testing generating the cell sample file with exponential dist, then sampling flat here
-                    //that would be more realistic
-                    //But would mess up other things in the simulation with how I've coded it.
-                    if(n > test){
-                        test = n;
-                    }
-                    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 sequence
-                            cellToAdd[k] = -1;
+                            cellToAdd[k] = "-1";
                         }
                     }
                     well.add(cellToAdd);
@@ -78,28 +101,26 @@ public class Plate {
             }
             section++;
         }
-        System.out.println("Highest index: " +test);
     }
 
-    public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
+    private void fillWells( List<String[]> cells, double stdDev) {
         this.stdDev = stdDev;
-        sourceFile = sourceFileName;
+        int numSections = populations.length;
-        int numSections = concentrations.length;
         int section = 0;
         double m;
         int n;
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
-                List<Integer[]> well = new ArrayList<>();
+                List<String[]> 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);
                     } while (m >= cells.size() || m < 0);
                     n = (int) Math.floor(m);
-                    Integer[] cellToAdd = cells.get(n).clone();
+                    String[] 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 sequence
-                            cellToAdd[k] = -1;
+                            cellToAdd[k] = "-1";
                         }
                     }
                     well.add(cellToAdd);
@@ -110,8 +131,8 @@ public class Plate {
         }
     }
 
-    public Integer[] getConcentrations(){
+    public Integer[] getPopulations(){
-        return concentrations;
+        return populations;
     }
 
     public int getSize(){
@@ -130,40 +151,112 @@ public class Plate {
         return error;
     }
 
-    public List<List<Integer[]>> getWells() {
+    public List<List<String[]>> getWells() {
         return wells;
     }
 
-    //returns a map of the counts of the peptide at cell index pIndex, in all wells
+    //For the sequences at cell indices sIndices, counts number of unique sequences in all wells.
-    public Map<Integer, Integer> assayWellsPeptideP(int... pIndices){
+    //Also simulates sequence read errors with given probabilities.
-        return this.assayWellsPeptideP(0, size, pIndices);
+    //Returns a map of SequenceRecords containing plate data for all sequences read.
+    //TODO actually implement usage of misreadSequences - DONE
+    public Map<String, SequenceRecord> countSequences(Integer readDepth, Double readErrorRate,
+                                                       Double errorCollisionRate, Double realSequenceCollisionRate, int... sIndices) {
+        SequenceType[] sequenceTypes = EnumSet.allOf(SequenceType.class).toArray(new SequenceType[0]);
+        //Map of all real sequences read. Keys are sequences, values are ways sequence has been misread.
+        Map<String, List<String>> sequencesAndMisreads = new HashMap<>();
+        //Map of all sequences read. Keys are sequences, values are associated SequenceRecords
+        Map<String, SequenceRecord> sequenceMap = new LinkedHashMap<>();
+        //get list of all distinct, real sequences
+        String[] realSequences = assayWells(sIndices).toArray(new String[0]);
+        for (int well = 0; well < size; well++) {
+            for (String[] cell: wells.get(well)) {
+                for (int sIndex: sIndices) {
+                    //the sequence being read
+                    String currentSequence = cell[sIndex];
+                    //skip dropout sequences, which have value -1
+                    if (!"-1".equals(currentSequence)) {
+                        //keep rereading the sequence until the read depth is reached
+                        for (int j = 0; j < readDepth; j++) {
+                            //The sequence is misread
+                            if (rand.nextDouble() < readErrorRate) {
+                                //The sequence hasn't been read or misread before
+                                if (!sequencesAndMisreads.containsKey(currentSequence)) {
+                                    sequencesAndMisreads.put(currentSequence, new ArrayList<>());
+                                }
+                                //The specific misread hasn't happened before
+                                if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).size() == 0) {
+                                    //The misread doesn't collide with a real sequence already on the plate and some sequences have already been read
+                                    if(rand.nextDouble() >= realSequenceCollisionRate || !sequenceMap.isEmpty()){
+                                        StringBuilder spurious = new StringBuilder(currentSequence);
+                                        for (int k = 0; k <= sequencesAndMisreads.get(currentSequence).size(); k++) {
+                                            spurious.append("*");
+                                        }
+                                        //New sequence record for the spurious sequence
+                                        SequenceRecord tmp = new SequenceRecord(spurious.toString(), sequenceTypes[sIndex]);
+                                        tmp.addRead(well);
+                                        sequenceMap.put(spurious.toString(), tmp);
+                                        //add spurious sequence to list of misreads for the real sequence
+                                        sequencesAndMisreads.get(currentSequence).add(spurious.toString());
+                                    }
+                                    //The misread collides with a real sequence already read from plate
+                                    else {
+                                        String wrongSequence;
+                                        do{
+                                            //get a random real sequence that's been read from the plate before
+                                            int index = rand.nextInt(realSequences.length);
+                                            wrongSequence = realSequences[index];
+                                            //make sure it's not accidentally the *right* sequence
+                                            //Also that it's not a wrong sequence already in the misread list
+                                        } while(currentSequence.equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence));
+                                        //update the SequenceRecord for wrongSequence
+                                        sequenceMap.get(wrongSequence).addRead(well);
+                                        //add wrongSequence to the misreads for currentSequence
+                                        sequencesAndMisreads.get(currentSequence).add(wrongSequence);
+                                    }
+                                }
+                            }
+                            //The sequence is read correctly
+                            else {
+                                //the sequence hasn't been read before
+                                if (!sequenceMap.containsKey(currentSequence)) {
+                                    //create new record for the sequence
+                                    SequenceRecord tmp = new SequenceRecord(currentSequence, sequenceTypes[sIndex]);
+                                    //add this read to the sequence record
+                                    tmp.addRead(well);
+                                    //add the sequence and its record to the sequence map
+                                    sequenceMap.put(currentSequence, tmp);
+                                    //add the sequence to the sequences and misreads map
+                                    sequencesAndMisreads.put(currentSequence, new ArrayList<>());
+                                }
+                                //the sequence has been read before
+                                else {
+                                    //get the sequence's record and add this read to it
+                                    sequenceMap.get(currentSequence).addRead(well);
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        return sequenceMap;
     }
 
-    //returns a map of the counts of the peptide at cell index pIndex, in a specific well
+    private HashSet<String> assayWells(int[] indices) {
-    public Map<Integer, Integer> assayWellsPeptideP(int n, int... pIndices) { return this.assayWellsPeptideP(n, n+1, pIndices);}
+        HashSet<String> allSequences = new HashSet<>();
-
+        for (List<String[]> well: wells) {
-    //returns a map of the counts of the peptide at cell index pIndex, in a range of wells
+            for (String[] cell: well) {
-    public Map<Integer, Integer> assayWellsPeptideP(int start, int end, int... pIndices) {
+                for(int index: indices) {
-        Map<Integer,Integer> assay = new HashMap<>();
+                    allSequences.add(cell[index]);
-        for(int pIndex: pIndices){
-            for(int i = start; i < end; i++){
-                countPeptides(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(Integer[] cell : well) {
-            for(int pIndex: pIndices){
-                if(cell[pIndex] != -1){
-                    wellMap.merge(cell[pIndex], 1, (oldValue, newValue) -> oldValue + newValue);
                 }
             }
         }
+        return allSequences;
     }
 
     public String getSourceFileName() {
         return sourceFile;
     }
+
+    public String getFilename() { return filename; }
 }

src/main/java/PlateFileReader.java

@@ -13,7 +13,7 @@ import java.util.regex.Pattern;
 
 public class PlateFileReader {
 
-    private List<List<Integer[]>> wells = new ArrayList<>();
+    private List<List<String[]>> wells = new ArrayList<>();
     private String filename;
 
     public PlateFileReader(String filename){
@@ -31,54 +31,23 @@ public class PlateFileReader {
             BufferedReader reader = Files.newBufferedReader(Path.of(filename));
             CSVParser parser = new CSVParser(reader, plateFileFormat);
         ){
-            //old code for wells as rows
-//            for(CSVRecord record: parser.getRecords()) {
-//                List<Integer[]> well = new ArrayList<>();
-//                for(String s: record) {
-//                    if(!"".equals(s)) {
-//                        String[] intString = s.replaceAll("\\[", "")
-//                                .replaceAll("]", "")
-//                                .replaceAll(" ", "")
-//                                .split(",");
-//                        //System.out.println(intString);
-//                        Integer[] arr = new Integer[intString.length];
-//                        for (int i = 0; i < intString.length; i++) {
-//                            arr[i] = Integer.valueOf(intString[i]);
-//                        }
-//                        well.add(arr);
-//                    }
-//                }
-//                wells.add(well);
             for(CSVRecord record: parser.getRecords()) {
-                if (wells.size() == 0) {
+                List<String[]> well = new ArrayList<>();
-                    int num = 0;
                 for(String s: record) {
-                        num++;
+                    if(!"".equals(s)) {
-                    }
+                        String[] sequences = s.replaceAll("\\[", "")
-                    for (int i = 0; i < num; i++) {
-                        wells.add(new ArrayList<>());
-                    }
-                } else {
-                    int i = 0;
-                    for (String s : record) {
-                        if (!"".equals(s)) { //if value isn't the empty string
-                            //get rid of brackets, split at commas into a string array
-                            String[] intsAsStrings = s.replaceAll("\\[", "")
                                 .replaceAll("]", "")
                                 .replaceAll(" ", "")
                                 .split(",");
-                            //Make Integer array with the same values
+                        //System.out.println(sequences);
-                            Integer[] arr = new Integer[intsAsStrings.length];
+                        String[] arr = new String[sequences.length];
-                            for (int j = 0; j < intsAsStrings.length; j++) {
+                        for (int i = 0; i < sequences.length; i++) {
-                                arr[j] = Integer.valueOf(intsAsStrings[j]);
+                            arr[i] = sequences[i];
                         }
-                            //Add Integer array to the correct well
+                        well.add(arr);
-                            wells.get(i).add(arr);
-                            i++;
                     }
                 }
-
+                wells.add(well);
-                }
             }
         } catch(IOException ex){
             System.out.println("plate file " + filename + " not found.");
@@ -87,11 +56,8 @@ public class PlateFileReader {
 
     }
 
-    public List<List<Integer[]>> getWells() {
+    public Plate getSamplePlate() {
-        return wells;
+        return new Plate(filename, wells);
     }
 
-    public String getFilename() {
-        return filename;
-    }
 }

src/main/java/PlateFileWriter.java

@@ -7,18 +7,16 @@ 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 List<List<String[]>> wells;
     private double stdDev;
     private double lambda;
     private Double error;
     private String filename;
     private String sourceFileName;
-    private String[] headers;
+    private Integer[] populations;
-    private List<Integer> concentrations;
     private boolean isExponential = false;
 
     public PlateFileWriter(String filename, Plate plate) {
@@ -37,18 +35,18 @@ public class PlateFileWriter {
         }
         this.error = plate.getError();
         this.wells = plate.getWells();
-        this.concentrations = Arrays.asList(plate.getConcentrations());
+        this.populations = plate.getPopulations();
-        concentrations.sort(Comparator.reverseOrder());
+        Arrays.sort(populations);
     }
 
     public void writePlateFile(){
-        Comparator<List<Integer[]>> listLengthDescending = Comparator.comparingInt(List::size);
+        Comparator<List<String[]>> listLengthDescending = Comparator.comparingInt(List::size);
         wells.sort(listLengthDescending.reversed());
         int maxLength = wells.get(0).size();
         List<List<String>> wellsAsStrings = new ArrayList<>();
-        for (List<Integer[]> w: wells){
+        for (List<String[]> w: wells){
             List<String> tmp = new ArrayList<>();
-            for(Integer[] c: w) {
+            for(String[] c: w) {
                 tmp.add(Arrays.toString(c));
             }
             wellsAsStrings.add(tmp);
@@ -59,28 +57,32 @@ public class PlateFileWriter {
             }
         }
 
-        //this took forever, and I don't use it, because it makes reading data in a huge pain
+//        //this took forever and I don't use it
-        List<List<String>> rows = new ArrayList<>();
+//        //if I wanted to use it, I'd replace printer.printRecords(wellsAsStrings) with printer.printRecords(rows)
-        List<String> tmp = new ArrayList<>();
+//        List<List<String>> rows = new ArrayList<>();
-        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
+//        List<String> tmp = new ArrayList<>();
-            tmp.add("well " + (i+1));
+//        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++){
+//        rows.add(tmp);
-            tmp = new ArrayList<>();
+//        for(int row = 0; row < maxLength; row++){
-            for(List<String> c: wellsAsStrings){
+//            tmp = new ArrayList<>();
-                tmp.add(c.get(row));
+//            for(List<String> c: wellsAsStrings){
-            }
+//                tmp.add(c.get(row));
-            rows.add(tmp);
+//            }
-        }
+//            rows.add(tmp);
-        //build string of well concentrations
+//        }
-        StringBuilder concen = new StringBuilder();
-        for(Integer i: concentrations){
-            concen.append(i.toString());
-            concen.append(" ");
-        }
-        String concenString = concen.toString();
 
+        //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();
@@ -89,16 +91,17 @@ public class PlateFileWriter {
             CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
         ){
             printer.printComment("Cell source file name: " + sourceFileName);
+            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(rows);
+            printer.printRecords(wellsAsStrings);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);
             System.err.println(ex);

src/main/java/SequenceRecord.java

@@ -0,0 +1,65 @@
+/*
+Class to represent individual sequences, holding their well occupancy and read count information.
+Will make a map of these keyed to the sequences themselves.
+Ideally, I'll be able to construct both the Vertices and the weights matrix from this map.
+
+ */
+
+import java.io.Serializable;
+import java.util.*;
+
+public class SequenceRecord implements Serializable {
+    private final String sequence;
+    private final SequenceType type;
+    //keys are well numbers, values are read count in that well
+    private final Map<Integer, Integer> wells;
+
+    public SequenceRecord (String sequence, SequenceType type) {
+        this.sequence = sequence;
+        this.type = type;
+        this.wells = new LinkedHashMap<>();
+    }
+
+    //this shouldn't be necessary, since the sequence will be the map key, but
+    public String getSequence() {
+        return sequence;
+    }
+
+    public SequenceType getSequenceType(){
+        return type;
+    }
+
+    //use this to update the record for each new read
+    public void addRead(Integer wellNumber) {
+        wells.merge(wellNumber,1, Integer::sum);
+    }
+
+    //don't know if I'll ever need this
+    public void addWellData(Integer wellNumber, Integer readCount) {
+        wells.put(wellNumber, readCount);
+    }
+
+    public Set<Integer> getWells() {
+        return wells.keySet();
+    }
+
+    public Map<Integer, Integer> getWellOccupancies() { return wells;}
+
+    public boolean isInWell(Integer wellNumber) {
+        return wells.containsKey(wellNumber);
+    }
+
+    public Integer getOccupancy() {
+        return wells.size();
+    }
+
+    //read count for whole plate
+    public Integer getReadCount(){
+        return wells.values().stream().mapToInt(Integer::valueOf).sum();
+    }
+
+    //read count in a specific well
+    public Integer getReadCount(Integer wellNumber) {
+        return wells.get(wellNumber);
+    }
+ }

src/main/java/SequenceType.java

@@ -0,0 +1,8 @@
+//enum for tagging types of sequences
+//Listed in order that they appear in a cell array, so ordinal() method will return correct index
+public enum SequenceType {
+    CDR3_ALPHA,
+    CDR3_BETA,
+    CDR1_ALPHA,
+    CDR1_BETA
+}

src/main/java/UserInterface.java

@@ -1,704 +0,0 @@
-import org.apache.commons.cli.*;
-
-import java.io.IOException;
-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) {
-        //for now, commenting out all the command line argument stuff.
-        // Refactoring to output files of graphs, so it would all need to change anyway.
-
-//        if(args.length != 0){
-//            //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?
-//
-//            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 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(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");
-//                    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(cellFile, plate, 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());
-//            }
-//        }
-//        else {
-            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;
-        CellFileWriter writer = new CellFileWriter(filename, sample);
-        writer.writeCellsToFile();
-        System.gc();
-    }
-
-//    //for calling from command line
-//    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 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.getCells(), 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.getCellCount());
-//        Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
-//        samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), 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.getCells(), stdDev);
-//        PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
-//        writer.writePlateFile();
-//    }
-
-    //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[] concentrations = {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.println("Please enter lambda value for exponential distribution.");
-                    lambda = sc.nextDouble();
-                    if (lambda <= 0.0) {
-                        throw new InputMismatchException("Value must be positive.");
-                    }
-                }
-                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");
-            }
-            System.out.println("\nThe 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("\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();
-        }
-        System.out.println("Reading Cell Sample file: " + cellFile);
-        assert cellFile != null;
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        if(exponential){
-            Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
-            samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
-            PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
-            writer.writePlateFile();
-        }
-        else {
-            if (poisson) {
-                stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
-            }
-            Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
-            samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
-            assert filename != null;
-            PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
-            System.out.println("Writing Sample Plate to file");
-            writer.writePlateFile();
-            System.out.println("Sample Plate written to file: " + filename);
-            System.gc();
-        }
-    }
-
-    //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();
-        }
-        System.out.println("Reading Cell Sample file: " + cellFile);
-        assert cellFile != null;
-        CellFileReader cellReader = new CellFileReader(cellFile);
-        System.out.println("Reading Sample Plate file: " + plateFile);
-        assert plateFile != null;
-        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 || plate.getConcentrations().length == 0){
-            System.out.println("No sample plate found.");
-            System.out.println("Returning to main menu.");
-        }
-        else{
-            List<Integer[]> cells = cellReader.getCells();
-            GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
-            assert filename != null;
-            GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
-            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.");
-            dataWriter.writeDataToFile();
-            System.out.println("Graph and Data file written to: " + filename);
-            System.gc();
-        }
-    }
-
-    //Simulate matching and output CSV file of results
-    private static void matchCDR3s() throws IOException {
-        String filename = null;
-        String dataFilename = 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: ");
-            dataFilename = 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){
-                throw new InputMismatchException("Minimum value for low threshold set to 1");
-            }
-            System.out.println("\nWhat is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
-            highThreshold = sc.nextInt();
-            System.out.println("\nWhat is the maximum difference in alpha/beta occupancy to attempt matching?");
-            maxOccupancyDiff = sc.nextInt();
-            System.out.println("\nWell overlap percentage = pair overlap / sequence occupancy");
-            System.out.println("What is the minimum well overlap percentage to attempt matching? (0 to 100)");
-            minOverlapPercent = sc.nextInt();
-            if (minOverlapPercent < 0 || minOverlapPercent > 100) {
-                throw new InputMismatchException("Value outside range. Minimum percent set to 0");
-            }
-        } catch (InputMismatchException ex) {
-            System.out.println(ex);
-            sc.next();
-        }
-        //read object data from file
-        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");
-        assert dataFilename != null;
-        GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFilename);
-        GraphWithMapData data = dataReader.getData();
-        //set source file name
-        data.setSourceFilename(dataFilename);
-        //simulate matching
-        MatchingResult results = Simulator.matchCDR3s(data, dataFilename, 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);
-        System.gc();
-    }
-
-    ///////
-    //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("Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and compares");
-        System.out.println("against a null distribution, BiGpairSEQ does not do any statistical calculations");
-        System.out.println("directly. Instead, BiGpairSEQ creates a simple bipartite weighted graph representing");
-        System.out.println("the sample plate. The distinct TCRA and TCRB sequences form the two sets of vertices.");
-        System.out.println("Every TCRA/TCRB pair that share a well are connected by an edge, with the edge weight");
-        System.out.println("set to the number of wells in which both sequences appear. (Sequences in all wells are");
-        System.out.println("filtered out prior to creating the graph, as there is no signal in their occupancy");
-        System.out.println("pattern.) The problem of pairing TCRA/TCRB sequences thus reduces to the \"assignment");
-        System.out.println("problem\" of finding a maximum weight matching on a bipartite graph--the subset of");
-        System.out.println("vertex-disjoint edges whose weights sum to the maximum possible value.");
-        System.out.println();
-        System.out.println("For full documentation, see: 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/Vertex.java

@@ -1,17 +1,77 @@
-public class Vertex {
+import org.jheaps.AddressableHeap;
-    private final Integer peptide;
-    private final Integer occupancy;
 
-    public Vertex(Integer peptide, Integer occupancy) {
+import java.io.Serializable;
-        this.peptide = peptide;
+import java.util.Map;
-        this.occupancy = occupancy;
+
+public class Vertex implements Serializable, Comparable<Vertex> {
+    private SequenceRecord record;
+    private Integer vertexLabel;
+    private Double potential;
+    private AddressableHeap queue;
+
+    public Vertex(SequenceRecord record, Integer vertexLabel) {
+        this.record = record;
+        this.vertexLabel = vertexLabel;
     }
 
-    public Integer getPeptide() {
+    public SequenceRecord getRecord() { return record; }
-        return peptide;
+
+    public SequenceType getType() { return record.getSequenceType(); }
+
+    public Integer getVertexLabel() {
+        return vertexLabel;
+    }
+
+    public String getSequence() {
+        return record.getSequence();
     }
 
     public Integer getOccupancy() {
-        return occupancy;
+        return record.getOccupancy();
+    }
+
+    public Integer getReadCount() { return record.getReadCount(); }
+
+    public Integer getReadCount(Integer well) { return record.getReadCount(well); }
+
+    public Map<Integer, Integer> getWellOccupancies() { return record.getWellOccupancies(); }
+
+    @Override //adapted from JGraphT example code
+    public int hashCode()
+    {
+        return (this.getSequence() == null) ? 0 : this.getSequence().hashCode();
+    }
+
+    @Override //adapted from JGraphT example code
+    public boolean equals(Object obj)
+    {
+        if (this == obj)
+            return true;
+        if (obj == null)
+            return false;
+        if (getClass() != obj.getClass())
+            return false;
+        Vertex other = (Vertex) obj;
+        if (this.getSequence() == null) {
+            return other.getSequence() == null;
+        } else {
+            return this.getSequence().equals(other.getSequence());
+        }
+    }
+
+    @Override //adapted from JGraphT example code
+    public String toString()
+    {
+        StringBuilder sb = new StringBuilder();
+        sb.append("(").append(vertexLabel)
+                .append(", Type: ").append(this.getType().name())
+                .append(", Sequence: ").append(this.getSequence())
+                .append(", Occupancy: ").append(this.getOccupancy()).append(")");
+        return sb.toString();
+    }
+
+    @Override
+    public int compareTo(Vertex other) {
+        return this.vertexLabel - other.getVertexLabel();
     }
 }