Remove singleton sequences from wells in initial filtering

Remove obsolete comments
Add data on randomized well population behavior
2022-03-04 16:14:17 -06:00 · 2022-03-02 23:35:24 -06:00 · 2022-03-02 23:21:56 -06:00 · 2022-03-02 22:54:17 -06:00 · 2022-03-02 18:55:19 -06:00 · 2022-03-02 12:39:40 -06:00
22 changed files with 2239 additions and 1313 deletions
--- a/readme.md
+++ b/readme.md
@@ -12,7 +12,7 @@ Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and c
 against a null distribution, BiGpairSEQ does not do any statistical calculations
 directly.

-BiGpairSEQ creates a [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 present in *all* wells are filtered out prior to creating the graph, as there is no signal in their occupancy pattern.)
@@ -20,8 +20,8 @@ The problem of pairing TCRA/TCRB sequences thus reduces to the "assignment probl
 matching on a bipartite graph--the subset of vertex-disjoint edges whose weights sum to the maximum possible value.

 This is a well-studied combinatorial optimization problem, with many known solutions.
-The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral weights
-is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 
+The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral
+weights is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 
 their algorithm runs in **O(m sqrt(n) log(N))** time. As the graph representation of a pairSEQ experiment is 
 bipartite with integer weights, this algorithm is ideal for BiGpairSEQ.

@@ -29,15 +29,13 @@ Unfortunately, it's a fairly new algorithm, and not yet implemented by the graph
 So this program instead uses the Fibonacci heap-based algorithm of Fredman and Tarjan (1987), which has a worst-case
 runtime of **O(n (n log(n) + m))**. The algorithm is implemented as described in Melhorn and Näher (1999).

-The current version of the program uses a pairing heap instead of a Fibonacci heap for its priority queue,
-which has lower theoretical efficiency but also lower complexity overhead, and is often equivalently performant
-in practice.
-
 ## USAGE

 ### RUNNING THE PROGRAM

-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:
@@ -45,39 +43,75 @@ 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
-main menu looks like this:
+There are a number of command line options, to allow the program to be used in shell scripts. For a full list,
+use the `-help` flag:
+
+`java -jar BiGpairSEQ_Sim.jar -help`
+
+If no command line arguments are given, BiGpairSEQ_Sim will launch with an interactive, menu-driven CLI for 
+generating files and simulating TCR pairing. The main menu looks like this:

 ```
 --------BiGPairSEQ SIMULATOR--------
 ALPHA/BETA T CELL RECEPTOR MATCHING
-  USING WEIGHTED BIPARTITE GRAPHS
+  USING WEIGHTED BIPARTITE GRAPHS  
 ------------------------------------
 Please select an option:
 1) Generate a population of distinct cells
 2) Generate a sample plate of T cells
 3) Generate CDR3 alpha/beta occupancy data and overlap graph
 4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ)
+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
-writing files, the program will automatically add the correct extension to any filename without one.
+These files are often generated in sequence. When entering filenames, it is not necessary to include the file extension
+(.csv or .ser). When reading or writing files, the program will automatically add the correct extension to any filename 
+without one.

+To save file I/O time, the most recent instance of each of these four
+files either generated or read from disk can be cached in program memory. When caching is active, subsequent uses of the 
+same data file won't need to be read in again until another file of that type is used or generated,
+or caching is turned off for that file type. The program checks whether it needs to update its cached data by comparing
+filenames as entered by the user. On encountering a new filename, the program flushes its cache and reads in the new file.
+
+(Note that cached Graph/Data files must be transformed back into their original state after a matching experiment, which
+may take some time. Whether file I/O or graph transformation takes longer for graph/data files is likely to be
+device-specific.)
+
+The program's caching behavior can be controlled in the Options menu. By default, all caching is OFF.
+
+The program can optionally output Graph/Data files in GraphML format (.graphml) for data portability. This can be 
+turned on in the Options menu. By default, GraphML output is OFF.
+
+---
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
 four sequences: Alpha CDR3, Beta CDR3, Alpha CDR1, Beta CDR1. The sequences are represented by
@@ -95,7 +129,6 @@ Comments are preceded by `#`

 Structure:

---
    # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
 | Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
 |---|---|---|---|
@@ -119,15 +152,18 @@ Options when making a Sample Plate file:
    * Standard deviation size 
  * Exponential
    * Lambda value
-      * (Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was exponential with a lambda of approximately 0.6. (Howie, et al. 2015))
+      * *(Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was approximately exponential with a lambda ~0.6. (Howie, et al. 2015))*
 * Total number of wells on the plate
-* Number of sections on plate
-* Number of T cells per well
-  * per section, if more than one section
+* Well populations random or fixed
+  * If random, minimum and maximum population sizes
+  * If fixed
+    * Number of sections on plate
+    * Number of T cells per well
+      * per section, if more than one section
 * Dropout rate

 Files are in CSV format. There are no header labels. Every row represents a well. 
-Every column represents an individual cell, containing four sequences, depicted as 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]`
@@ -137,7 +173,6 @@ Dropout sequences are replaced with the value `-1`. Comments are preceded by `#`

 Structure:

---
 ```
 # Cell source file name:
 # Each row represents one well on the plate
@@ -153,25 +188,37 @@ Structure:

 ---

-#### Graph and Data Files
-Graph and Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
+#### Graph/Data Files
+Graph/Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
 Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file 
 (to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a 
-Sample Plate file (to construct the associated occupancy graph). These files can be several gigabytes in size.
-Writing them to a file lets us generate a graph and its metadata once, then use it for multiple different BiGpairSEQ simulations.
+Sample Plate file (to construct the associated occupancy graph).

-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 to use. (This must have been generated from the selected Cell Sample file.)

-These files do not have a human-readable structure, and are not portable to other programs. (Export of graphs in a 
-portable data format may be implemented in the future. The tricky part is encoding the necessary metadata.)
+These files do not have a human-readable structure, and are not portable to other programs.
+
+*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, and occupancy data. 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.
-Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
+Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a serialized
+binary Graph/Data file (.ser). (Because .graphML files are larger than .ser files, BiGpairSEQ_Sim supports .graphML
+output only. Graph/data input must use a serialized binary.)
+
+Matching results files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
 Metadata about the matching simulation is included as comments. Comments are preceded by `#`.

 Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
@@ -186,7 +233,6 @@ Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:

 Example output:

---
 ```
 # Source Sample Plate file: 4MilCellsPlate.csv
 # Source Graph and Data file: 4MilCellsPlateGraph.ser
@@ -218,45 +264,99 @@ Example output:
 P-values are calculated *after* BiGpairSEQ matching is completed, for purposes of comparison only, 
 using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et al. 2015)

-### PERFORMANCE
-Performance details of the example excerpted above:
+
+## 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.
+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 simulation time was 14'22". If intermediate results were held in memory, this would be equivalent to the total elapsed time.
+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 weighted 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?~~ ABANDONED
-  * *No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*
+* ~~Hold graph data in memory until another graph is read-in? ABANDONED UNABANDONED~~ DONE
+  * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~
+  * Might have figured out a way to do it, by taking edges out and then putting them back into the graph. This may actually be possible.
+  * It is possible, though the modifications to the graph incur their own performance penalties. Need testing to see which option is best. It may be computer-specific.
+* ~~Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm~~ DONE
+  * ~~in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage~~
+  * ~~Add controllable heap-type parameter?~~
+    * Parameter implemented. Fibonacci heap the current default.
+* ~~Implement sample plates with random numbers of T cells per well.~~ DONE
+  * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not.
+    * preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
 * See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows. 
  * ~~Problem is variable number of cells in a well~~
  * ~~Apache Commons CSV library writes entries a row at a time~~ 
-    * _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing._
-* Re-implement command line arguments, to enable scripting and statistical simulation studies
-* Implement sample plates with random numbers of T cells per well.
-  * Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not.
-    * preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
-* Enable GraphML output in addition to serialized object binaries, for data portability
-  * Custom vertex type with attribute for sequence occupancy?
+    * _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing.
+* ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
+  * ~~Custom vertex type with attribute for sequence occupancy?~~ ABANDONED
+    * Advantage: would eliminate the need to use maps to associate vertices with sequences, which would make the code easier to understand.
+    * Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.
+* ~~Re-implement command line arguments, to enable scripting and statistical simulation studies~~ DONE
 * Re-implement CDR1 matching method
 * Implement Duan and Su's maximum weight matching algorithm
-  * Add controllable algorithm-type parameter?
-* Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm
-  * in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage
-  * Add controllable heap-type parameter?
-
-
+    * Add controllable algorithm-type parameter?
+    * This would be fun and valuable, but probably take more time than I have for a hobby project.
+* Implement Vose's alias method for arbitrary statistical distributions of cells
+  
  
 ## CITATIONS
 * Howie, B., Sherwood, A. M., et al. ["High-throughput pairing of T cell receptor alpha and beta sequences."](https://pubmed.ncbi.nlm.nih.gov/26290413/) Sci. Transl. Med. 7, 301ra131 (2015)
@@ -268,7 +368,7 @@ slightly less time than the simulation itself. Real elapsed time from start to f
 * [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 
--- a/src/main/java/BiGpairSEQ.java
+++ b/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 String priorityQueueHeapType = "FIBONACCI";
+    private static boolean outputBinary = true;
+    private static boolean outputGraphML = false;
+    private static final String version = "version 2.0";
+
+    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;
+    }
+
+    public static void setPairingHeap() {
+        priorityQueueHeapType = "PAIRING";
+    }
+
+    public static void setFibonacciHeap() {
+        priorityQueueHeapType = "FIBONACCI";
+    }
+
+    public static boolean outputBinary() {return outputBinary;}
+    public static void setOutputBinary(boolean b) {outputBinary = b;}
+
+    public static boolean outputGraphML() {return outputGraphML;}
+    public static void setOutputGraphML(boolean b) {outputGraphML = b;}
+    public static String getVersion() { return version; }
+}
--- a/src/main/java/CellFileReader.java
+++ b/src/main/java/CellFileReader.java
@@ -13,6 +13,7 @@ public class CellFileReader {

    private String filename;
    private List<Integer[]> distinctCells = new ArrayList<>();
+    private Integer cdr1Freq;

    public CellFileReader(String filename) {
        if(!filename.matches(".*\\.csv")){
@@ -38,19 +39,37 @@ public class CellFileReader {
                cell[3] = Integer.valueOf(record.get("Beta CDR1"));
                distinctCells.add(cell);
            }
+
+
        } catch(IOException ex){
            System.out.println("cell file " + filename + " not found.");
            System.err.println(ex);
        }
+
+        //get CDR1 frequency
+        ArrayList<Integer> cdr1Alphas = new ArrayList<>();
+        for (Integer[] cell : distinctCells) {
+            cdr1Alphas.add(cell[3]);
+        }
+        double count = cdr1Alphas.stream().distinct().count();
+        count = Math.ceil(distinctCells.size() / count);
+        cdr1Freq = (int) count;
+
+    }
+
+    public CellSample getCellSample() {
+        return new CellSample(distinctCells, cdr1Freq);
    }

    public String getFilename() { return filename;}

-    public List<Integer[]> getCells(){
+    //Refactor everything that uses this to have access to a Cell Sample and get the cells there instead.
+    public List<Integer[]> getListOfDistinctCellsDEPRECATED(){
        return distinctCells;
    }

-    public Integer getCellCount() {
+    public Integer getCellCountDEPRECATED() {
+        //Refactor everything that uses this to have access to a Cell Sample and get the count there instead.
        return distinctCells.size();
    }
 }
--- a/src/main/java/CellSample.java
+++ b/src/main/java/CellSample.java
@@ -1,10 +1,37 @@
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.stream.IntStream;

 public class CellSample {

    private List<Integer[]> cells;
    private Integer cdr1Freq;

+    public CellSample(Integer numDistinctCells, Integer cdr1Freq){
+        this.cdr1Freq = cdr1Freq;
+        List<Integer> numbersCDR3 = new ArrayList<>();
+        List<Integer> numbersCDR1 = new ArrayList<>();
+        Integer numDistCDR3s = 2 * numDistinctCells + 1;
+        IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
+        IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
+        Collections.shuffle(numbersCDR3);
+        Collections.shuffle(numbersCDR1);
+
+        //Each cell represented by 4 values
+        //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
+        List<Integer[]> distinctCells = new ArrayList<>();
+        for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
+            Integer tmpCDR3a = numbersCDR3.get(i);
+            Integer tmpCDR3b = numbersCDR3.get(i+1);
+            Integer tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size());
+            Integer tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size());
+            Integer[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
+            distinctCells.add(tmp);
+        }
+        this.cells = distinctCells;
+    }
+
    public CellSample(List<Integer[]> cells, Integer cdr1Freq){
        this.cells = cells;
        this.cdr1Freq = cdr1Freq;
@@ -18,7 +45,7 @@ public class CellSample {
        return cdr1Freq;
    }

-    public Integer population(){
+    public Integer getCellCount(){
        return cells.size();
    }

--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -0,0 +1,499 @@
+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
+ *
+ * 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 = Simulator.makeGraph(cells, plate, false);
+                if (!line.hasOption("no-binary")) { //output binary file unless told not to
+                    GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
+                    writer.writeDataToFile();
+                }
+                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();
+        graphOptions.addOption(cellFilename);
+        graphOptions.addOption(plateFilename);
+        graphOptions.addOption(outputFileOption());
+        graphOptions.addOption(outputGraphML);
+        graphOptions.addOption(outputSerializedBinary);
+        return graphOptions;
+    }
+
+    private static Options buildMatchCDR3options() {
+        Options matchCDR3options = new Options();
+        Option graphFilename = Option.builder("g")
+                .longOpt("graph-file")
+                .desc("The graph/data file to use")
+                .hasArg()
+                .argName("filename")
+                .required().build();
+        Option minOccupancyOverlap = Option.builder("min")
+                .desc("The minimum number of shared wells to attempt to match a sequence pair")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option maxOccupancyOverlap = Option.builder("max")
+                .desc("The maximum number of shared wells to attempt to match a sequence pair")
+                .hasArg()
+                .argName("number")
+                .required().build();
+        Option minOverlapPercent = Option.builder("minpct")
+                .desc("(Optional) The minimum percentage of a sequence's total occupancy shared by another sequence to attempt matching. (0 - 100) ")
+                .hasArg()
+                .argName("percent")
+                .build();
+        Option maxOccupancyDifference = Option.builder("maxdiff")
+                .desc("(Optional) The maximum difference in total occupancy between two sequences to attempt matching.")
+                .hasArg()
+                .argName("number")
+                .build();
+        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();
+    }
+}
--- a/src/main/java/Equations.java
+++ b/src/main/java/Equations.java
@@ -4,10 +4,6 @@ import java.math.MathContext;

 public abstract class Equations {

-    public static int getRandomNumber(int min, int max) {
-        return (int) ((Math.random() * (max - min)) + min);
-    }
-
    //pValue calculation as described in original pairSEQ paper.
    //Included for comparison with original results.
    //Not used by BiGpairSEQ for matching.
--- a/src/main/java/GraphDataObjectReader.java
+++ b/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();
        }
    }
--- a/src/main/java/GraphDataObjectWriter.java
+++ b/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();
--- a/src/main/java/GraphMLFileReader.java
+++ b/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; }
-
-}
--- a/src/main/java/GraphMLFileWriter.java
+++ b/src/main/java/GraphMLFileWriter.java
@@ -1,4 +1,8 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
+import org.jgrapht.nio.Attribute;
+import org.jgrapht.nio.AttributeType;
+import org.jgrapht.nio.DefaultAttribute;
 import org.jgrapht.nio.dot.DOTExporter;
 import org.jgrapht.nio.graphml.GraphMLExporter;

@@ -7,25 +11,69 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;

 public class GraphMLFileWriter {

    String filename;
-    SimpleWeightedGraph graph;
+    GraphWithMapData data;


-    public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) {
+    public GraphMLFileWriter(String filename, GraphWithMapData data) {
        if(!filename.matches(".*\\.graphml")){
            filename = filename + ".graphml";
        }
        this.filename = filename;
-        this.graph = graph;
+        this.data = data;
    }

+//    public void writeGraphToFile() {
+//        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+//        ){
+//            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+//            exporter.exportGraph(graph, writer);
+//        } catch(IOException ex){
+//            System.out.println("Could not make new file named "+filename);
+//            System.err.println(ex);
+//        }
+//    }
+
    public void writeGraphToFile() {
+        SimpleWeightedGraph graph = data.getGraph();
+        Map<Integer, Integer> vertexToAlphaMap = data.getPlateVtoAMap();
+        Map<Integer, Integer> vertexToBetaMap = data.getPlateVtoBMap();
+        Map<Integer, Integer> alphaOccs = data.getAlphaWellCounts();
+        Map<Integer, Integer> betaOccs = data.getBetaWellCounts();
        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
        ){
-            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+            //create exporter. Let the vertex labels be the unique ids for the vertices
+            GraphMLExporter<Integer, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(v -> v.toString());
+            //set to export weights
+            exporter.setExportEdgeWeights(true);
+            //set type, sequence, and occupancy attributes for each vertex
+            exporter.setVertexAttributeProvider( v -> {
+                Map<String, Attribute> attributes = new HashMap<>();
+                if(vertexToAlphaMap.containsKey(v)) {
+                    attributes.put("type", DefaultAttribute.createAttribute("CDR3 Alpha"));
+                    attributes.put("sequence", DefaultAttribute.createAttribute(vertexToAlphaMap.get(v)));
+                    attributes.put("occupancy", DefaultAttribute.createAttribute(
+                            alphaOccs.get(vertexToAlphaMap.get(v))));
+                }
+                else if(vertexToBetaMap.containsKey(v)) {
+                    attributes.put("type", DefaultAttribute.createAttribute("CDR3 Beta"));
+                    attributes.put("sequence", DefaultAttribute.createAttribute(vertexToBetaMap.get(v)));
+                    attributes.put("occupancy", DefaultAttribute.createAttribute(
+                            betaOccs.get(vertexToBetaMap.get(v))));
+                }
+                return attributes;
+            });
+            //register the attributes
+            exporter.registerAttribute("type", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("sequence", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("occupancy", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            //export the graph
            exporter.exportGraph(graph, writer);
        } catch(IOException ex){
            System.out.println("Could not make new file named "+filename);
@@ -33,3 +81,4 @@ public class GraphMLFileWriter {
        }
    }
 }
+
--- a/src/main/java/GraphModificationFunctions.java
+++ b/src/main/java/GraphModificationFunctions.java
@@ -0,0 +1,111 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
+import org.jgrapht.graph.SimpleWeightedGraph;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+public interface GraphModificationFunctions {
+
+    //remove over- and under-weight edges
+    static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                            int low, int high, boolean saveEdges) {
+        List<Integer[]> removedEdges = new ArrayList<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
+                if(saveEdges) {
+                    Integer source = graph.getEdgeSource(e);
+                    Integer target = graph.getEdgeTarget(e);
+                    Integer weight = (int) graph.getEdgeWeight(e);
+                    Integer[] edge = {source, target, weight};
+                    removedEdges.add(edge);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Integer[] edge : removedEdges) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    //Remove edges for pairs with large occupancy discrepancy
+    static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                  Map<Integer, Integer> alphaWellCounts,
+                                                  Map<Integer, Integer> betaWellCounts,
+                                                  Map<Integer, Integer> plateVtoAMap,
+                                                  Map<Integer, Integer> plateVtoBMap,
+                                                  Integer maxOccupancyDifference, boolean saveEdges) {
+        List<Integer[]> removedEdges = new ArrayList<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
+            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
+            if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
+                if (saveEdges) {
+                    Integer source = graph.getEdgeSource(e);
+                    Integer target = graph.getEdgeTarget(e);
+                    Integer weight = (int) graph.getEdgeWeight(e);
+                    Integer[] edge = {source, target, weight};
+                    removedEdges.add(edge);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Integer[] edge : removedEdges) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    //Remove edges for pairs where overlap size is significantly lower than the well occupancy
+    static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                         Map<Integer, Integer> alphaWellCounts,
+                                                         Map<Integer, Integer> betaWellCounts,
+                                                         Map<Integer, Integer> plateVtoAMap,
+                                                         Map<Integer, Integer> plateVtoBMap,
+                                                         Integer minOverlapPercent,
+                                                         boolean saveEdges) {
+        List<Integer[]> removedEdges = new ArrayList<>();
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
+            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
+            double weight = graph.getEdgeWeight(e);
+            double min = minOverlapPercent / 100.0;
+            if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
+                if(saveEdges) {
+                    Integer source = graph.getEdgeSource(e);
+                    Integer target = graph.getEdgeTarget(e);
+                    Integer intWeight = (int) graph.getEdgeWeight(e);
+                    Integer[] edge = {source, target, intWeight};
+                    removedEdges.add(edge);
+                }
+                else {
+                    graph.setEdgeWeight(e, 0.0);
+                }
+            }
+        }
+        if(saveEdges) {
+            for (Integer[] edge : removedEdges) {
+                graph.removeEdge(edge[0], edge[1]);
+            }
+        }
+        return removedEdges;
+    }
+
+    static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                       List<Integer[]> removedEdges) {
+        for (Integer[] edge : removedEdges) {
+            DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);
+            graph.setEdgeWeight(e, (double) edge[2]);
+        }
+    }
+
+}
--- a/src/main/java/GraphWithMapData.java
+++ b/src/main/java/GraphWithMapData.java
@@ -11,7 +11,7 @@ public class GraphWithMapData implements java.io.Serializable {
    private String sourceFilename;
    private final SimpleWeightedGraph graph;
    private Integer numWells;
-    private Integer[] wellConcentrations;
+    private Integer[] wellPopulations;
    private Integer alphaCount;
    private Integer betaCount;
    private final Map<Integer, Integer> distCellsMapAlphaKey;
@@ -31,7 +31,7 @@ public class GraphWithMapData implements java.io.Serializable {
                            Map<Integer, Integer> betaWellCounts, Duration time) {
        this.graph = graph;
        this.numWells = numWells;
-        this.wellConcentrations = wellConcentrations;
+        this.wellPopulations = wellConcentrations;
        this.alphaCount = alphaCount;
        this.betaCount = betaCount;
        this.distCellsMapAlphaKey = distCellsMapAlphaKey;
@@ -52,8 +52,8 @@ public class GraphWithMapData implements java.io.Serializable {
        return numWells;
    }

-    public Integer[] getWellConcentrations() {
-        return wellConcentrations;
+    public Integer[] getWellPopulations() {
+        return wellPopulations;
    }

    public Integer getAlphaCount() {
--- a/src/main/java/InteractiveInterface.java
+++ b/src/main/java/InteractiveInterface.java
@@ -0,0 +1,588 @@
+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;
+        try {
+            String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
+            str = str.concat("\nrequires a cell sample file and a sample plate file.");
+            System.out.println(str);
+            System.out.print("\nPlease enter name of an existing cell sample file: ");
+            cellFile = sc.next();
+            System.out.print("\nPlease enter name of an existing sample plate file: ");
+            plateFile = sc.next();
+            System.out.println("\nThe graph and occupancy data will be written to a serialized binary file.");
+            System.out.print("Please enter a name for the output file: ");
+            filename = sc.next();
+        } catch (InputMismatchException ex) {
+            System.out.println(ex);
+            sc.next();
+        }
+
+        assert cellFile != null;
+        CellSample cellSample;
+        //check if cells are already in memory
+        if(cellFile.equals(BiGpairSEQ.getCellFilename()) && 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.makeGraph(cellSample, plate, 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");
+            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");
+    }
+}
--- a/src/main/java/META-INF/MANIFEST.MF
+++ b/src/main/java/META-INF/MANIFEST.MF
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Main-Class: BiGpairSEQ
+
--- a/src/main/java/MatchingFileWriter.java
+++ b/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();
--- a/src/main/java/MatchingResult.java
+++ b/src/main/java/MatchingResult.java
@@ -1,18 +1,41 @@
 import java.time.Duration;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;

 public class MatchingResult {
-    private String sourceFile;
-    private List<String> comments;
-    private List<String> headers;
-    private List<List<String>> allResults;
-    private Map<Integer, Integer> matchMap;
-    private Duration time;

-    public MatchingResult(String sourceFileName, List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
-        this.sourceFile = sourceFileName;
-        this.comments = comments;
+    private final Map<String, String> metadata;
+    private final List<String> comments;
+    private final List<String> headers;
+    private final List<List<String>> allResults;
+    private final Map<Integer, Integer> matchMap;
+    private final Duration time;
+
+    public MatchingResult(Map<String, String> metadata, List<String> headers,
+                          List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
+        /*
+         * POSSIBLE KEYS FOR METADATA MAP ARE:
+         * sample plate filename *
+         * graph filename *
+         * well populations *
+         * total alphas found *
+         * total betas found *
+         * high overlap threshold *
+         * low overlap threshold *
+         * maximum occupancy difference *
+         * minimum overlap percent *
+         * pairing attempt rate *
+         * correct pairing count *
+         * incorrect pairing count *
+         * pairing error rate *
+         * simulation time (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;
@@ -20,6 +43,8 @@ public class MatchingResult {

    }

+    public Map<String, String> getMetadata() {return metadata;}
+
    public List<String> getComments() {
        return comments;
    }
@@ -40,7 +65,48 @@ public class MatchingResult {
        return time;
    }

-    public String getSourceFileName() {
-        return sourceFile;
+    public String getPlateFilename() {
+        return metadata.get("sample plate filename");
    }
+
+    public String getGraphFilename() {
+        return metadata.get("graph filename");
+    }
+
+    public Integer[] getWellPopulations() {
+        List<Integer> wellPopulations = new ArrayList<>();
+        String popString = metadata.get("well populations");
+        for (String p : popString.split(", ")) {
+            wellPopulations.add(Integer.parseInt(p));
+        }
+        Integer[] popArray = new Integer[wellPopulations.size()];
+        return wellPopulations.toArray(popArray);
+    }
+
+    public Integer getAlphaCount() {
+        return Integer.parseInt(metadata.get("total alpha count"));
+    }
+
+    public Integer getBetaCount() {
+        return Integer.parseInt(metadata.get("total beta count"));
+    }
+
+    public Integer getHighOverlapThreshold() { return Integer.parseInt(metadata.get("high overlap threshold"));}
+
+    public Integer getLowOverlapThreshold() { return Integer.parseInt(metadata.get("low overlap threshold"));}
+
+    public Integer getMaxOccupancyDifference() { return Integer.parseInt(metadata.get("maximum occupancy difference"));}
+
+    public Integer getMinOverlapPercent() { return Integer.parseInt(metadata.get("minimum overlap percent"));}
+
+    public Double getPairingAttemptRate() { return Double.parseDouble(metadata.get("pairing attempt rate"));}
+
+    public Integer getCorrectPairingCount() { return Integer.parseInt(metadata.get("correct pairing count"));}
+
+    public Integer getIncorrectPairingCount() { return Integer.parseInt(metadata.get("incorrect pairing count"));}
+
+    public Double getPairingErrorRate() { return Double.parseDouble(metadata.get("pairing error rate"));}
+
+    public String getSimulationTime() { return metadata.get("simulation time (seconds)"); }
+
 }
--- a/src/main/java/Plate.java
+++ b/src/main/java/Plate.java
@@ -1,31 +1,55 @@
-import java.util.*;
+

 /*
 TODO: Implement exponential distribution using inversion method - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
 */

+import java.util.*;
+
 public class Plate {
+    private CellSample cells;
    private String sourceFile;
+    private String filename;
    private List<List<Integer[]>> wells;
-    private Random rand = new Random();
+    private final Random rand = BiGpairSEQ.getRand();
    private int size;
    private double error;
-    private Integer[] concentrations;
+    private Integer[] populations;
    private double stdDev;
    private double lambda;
    boolean exponential = false;

+    public Plate(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) {
-        this.sourceFile = sourceFileName;
+    //constructor for returning a Plate from a PlateFileReader
+    public Plate(String filename, List<List<Integer[]>> wells) {
+        this.filename = filename;
        this.wells = wells;
        this.size = wells.size();

@@ -35,37 +59,28 @@ public class Plate {
                concentrations.add(w.size());
            }
        }
-        this.concentrations = new Integer[concentrations.size()];
-        for (int i = 0; i < this.concentrations.length; i++) {
-            this.concentrations[i] = concentrations.get(i);
+        this.populations = new Integer[concentrations.size()];
+        for (int i = 0; i < this.populations.length; i++) {
+            this.populations[i] = concentrations.get(i);
        }
    }

-    public void fillWellsExponential(String sourceFileName, List<Integer[]> cells, double lambda){
+    private void fillWellsExponential(List<Integer[]> cells, double lambda){
        this.lambda = lambda;
        exponential = true;
-        sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.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<>();
-                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());
-                    // 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 seqeunce
@@ -78,20 +93,18 @@ public class Plate {
            }
            section++;
        }
-        System.out.println("Highest index: " +test);
    }

-    public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
+    private void fillWells( List<Integer[]> cells, double stdDev) {
        this.stdDev = stdDev;
-        sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.length;
        int section = 0;
        double m;
        int n;
        while (section < numSections){
            for (int i = 0; i < (size / numSections); i++) {
                List<Integer[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                    do {
                        m = (rand.nextGaussian() * stdDev) + (cells.size() / 2);
                    } while (m >= cells.size() || m < 0);
@@ -110,8 +123,8 @@ public class Plate {
        }
    }

-    public Integer[] getConcentrations(){
-        return concentrations;
+    public Integer[] getPopulations(){
+        return populations;
    }

    public int getSize(){
@@ -166,4 +179,6 @@ public class Plate {
    public String getSourceFileName() {
        return sourceFile;
    }
+
+    public String getFilename() { return filename; }
 }
--- a/src/main/java/PlateFileReader.java
+++ b/src/main/java/PlateFileReader.java
@@ -56,11 +56,8 @@ public class PlateFileReader {

    }

-    public List<List<Integer[]>> getWells() {
-        return wells;
+    public Plate getSamplePlate() {
+        return new Plate(filename, wells);
    }

-    public String getFilename() {
-        return filename;
-    }
 }
--- a/src/main/java/PlateFileWriter.java
+++ b/src/main/java/PlateFileWriter.java
@@ -7,7 +7,6 @@ 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;
@@ -17,8 +16,7 @@ public class PlateFileWriter {
    private Double error;
    private String filename;
    private String sourceFileName;
-    private String[] headers;
-    private List<Integer> concentrations;
+    private Integer[] populations;
    private boolean isExponential = false;

    public PlateFileWriter(String filename, Plate plate) {
@@ -37,8 +35,8 @@ public class PlateFileWriter {
        }
        this.error = plate.getError();
        this.wells = plate.getWells();
-        this.concentrations = Arrays.asList(plate.getConcentrations());
-        concentrations.sort(Comparator.reverseOrder());
+        this.populations = plate.getPopulations();
+        Arrays.sort(populations);
    }

    public void writePlateFile(){
@@ -59,28 +57,32 @@ public class PlateFileWriter {
            }
        }

-        //this took forever
-        List<List<String>> rows = new ArrayList<>();
-        List<String> tmp = new ArrayList<>();
-        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
-            tmp.add("well " + (i+1));
-        }
-        rows.add(tmp);
-        for(int row = 0; row < maxLength; row++){
-            tmp = new ArrayList<>();
-            for(List<String> c: wellsAsStrings){
-                tmp.add(c.get(row));
-            }
-            rows.add(tmp);
-        }
-        //build string of well concentrations
-        StringBuilder concen = new StringBuilder();
-        for(Integer i: concentrations){
-            concen.append(i.toString());
-            concen.append(" ");
-        }
-        String concenString = concen.toString();
+//        //this took forever and I don't use it
+//        //if I wanted to use it, I'd replace printer.printRecords(wellsAsStrings) with printer.printRecords(rows)
+//        List<List<String>> rows = new ArrayList<>();
+//        List<String> tmp = new ArrayList<>();
+//        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
+//            tmp.add("well " + (i+1));
+//        }
+//        rows.add(tmp);
+//        for(int row = 0; row < maxLength; row++){
+//            tmp = new ArrayList<>();
+//            for(List<String> c: wellsAsStrings){
+//                tmp.add(c.get(row));
+//            }
+//            rows.add(tmp);
+//        }

+        //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();
@@ -92,7 +94,7 @@ public class PlateFileWriter {
            printer.printComment("Each row represents one well on the plate.");
            printer.printComment("Plate size: " + size);
            printer.printComment("Error rate: " + error);
-            printer.printComment("Concentrations: " + concenString);
+            printer.printComment("Well populations: " + wellPopulationsString);
            if(isExponential){
                printer.printComment("Lambda: " + lambda);
            }
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -3,6 +3,7 @@ import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
 import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
 import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
+import org.jheaps.tree.FibonacciHeap;
 import org.jheaps.tree.PairingHeap;

 import java.math.BigDecimal;
@@ -13,42 +14,22 @@ import java.time.Duration;
 import java.util.*;
 import java.util.stream.IntStream;

+import static java.lang.Float.*;
+
 //NOTE: "sequence" in method and variable names refers to a peptide sequence from a simulated T cell
-public class Simulator {
+public class Simulator implements GraphModificationFunctions {
    private static final int cdr3AlphaIndex = 0;
    private static final int cdr3BetaIndex = 1;
    private static final int cdr1AlphaIndex = 2;
    private static final int cdr1BetaIndex = 3;

-    public static CellSample generateCellSample(Integer numDistinctCells, Integer cdr1Freq) {
-        //In real T cells, CDR1s have about one third the diversity of CDR3s
-        List<Integer> numbersCDR3 = new ArrayList<>();
-        List<Integer> numbersCDR1 = new ArrayList<>();
-        Integer numDistCDR3s = 2 * numDistinctCells + 1;
-        IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
-        IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
-        Collections.shuffle(numbersCDR3);
-        Collections.shuffle(numbersCDR1);
-
-        //Each cell represented by 4 values
-        //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
-        List<Integer[]> distinctCells = new ArrayList<>();
-        for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
-            Integer tmpCDR3a = numbersCDR3.get(i);
-            Integer tmpCDR3b = numbersCDR3.get(i+1);
-            Integer tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size());
-            Integer tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size());
-            Integer[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
-            distinctCells.add(tmp);
-        }
-        return new CellSample(distinctCells, cdr1Freq);
-    }
-
    //Make the graph needed for matching CDR3s
-    public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) {
+    public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
        Instant start = Instant.now();
+        List<Integer[]> distinctCells = cellSample.getCells();
        int[] alphaIndex = {cdr3AlphaIndex};
        int[] betaIndex = {cdr3BetaIndex};
+
        int numWells = samplePlate.getSize();

        if(verbose){System.out.println("Making cell maps");}
@@ -63,15 +44,11 @@ public class Simulator {
        if(verbose){System.out.println("All alphas count: " + alphaCount);}
        int betaCount = allBetas.size();
        if(verbose){System.out.println("All betas count: " + betaCount);}
-
        if(verbose){System.out.println("Well maps made");}

-        //Remove saturating-occupancy sequences because they have no signal value.
-        //Remove sequences with total occupancy below minimum pair overlap threshold
-        if(verbose){System.out.println("Removing sequences present in all wells.");}
-        //if(verbose){System.out.println("Removing sequences with occupancy below the minimum overlap threshold");}
-        filterByOccupancyThreshold(allAlphas, 1, numWells - 1);
-        filterByOccupancyThreshold(allBetas, 1, numWells - 1);
+        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
+        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
+        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
        if(verbose){System.out.println("Sequences removed");}
        int pairableAlphaCount = allAlphas.size();
        if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
@@ -131,10 +108,15 @@ public class Simulator {

        Instant stop = Instant.now();
        Duration time = Duration.between(start, stop);
-        //return GraphWithMapData object
-        return new GraphWithMapData(graph, numWells, samplePlate.getConcentrations(), alphaCount, betaCount,
+
+        //create GraphWithMapData object
+        GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), alphaCount, betaCount,
                distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
                plateBtoVMap, alphaWellCounts, betaWellCounts, time);
+        //Set source file name in graph to name of sample plate
+        output.setSourceFilename(samplePlate.getFilename());
+        //return GraphWithMapData object
+        return output;
    }

    //match CDR3s.
@@ -142,6 +124,8 @@ public class Simulator {
                                            Integer highThreshold, Integer maxOccupancyDifference,
                                            Integer minOverlapPercent, boolean verbose) {
        Instant start = Instant.now();
+        List<Integer[]> removedEdges = new ArrayList<>();
+        boolean saveEdges = BiGpairSEQ.cacheGraph();
        int numWells = data.getNumWells();
        Integer alphaCount = data.getAlphaCount();
        Integer betaCount = data.getBetaCount();
@@ -152,33 +136,51 @@ public class Simulator {
        Map<Integer, Integer> betaWellCounts = data.getBetaWellCounts();
        SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = data.getGraph();

-        //remove weights outside given overlap thresholds
+        //remove edges with weights outside given overlap thresholds, add those to removed edge list
        if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
-        filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
-        if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
+        removedEdges.addAll(GraphModificationFunctions.filterByOverlapThresholds(graph, lowThreshold, highThreshold, saveEdges));
+        if(verbose){System.out.println("Over- and under-weight edges removed");}

-        //Filter by overlap size
+        //remove edges between vertices with too small an overlap size, add those to removed edge list
        if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
                " percent of vertex occupancy value.");}
-        filterByOverlapSize(graph, alphaWellCounts, betaWellCounts, plateVtoAMap, plateVtoBMap, minOverlapPercent);
-        if(verbose){System.out.println("Edges with weights too far below vertex occupancy values set to 0.0");}
+        removedEdges.addAll(GraphModificationFunctions.filterByOverlapPercent(graph, alphaWellCounts, betaWellCounts,
+                plateVtoAMap, plateVtoBMap, minOverlapPercent, saveEdges));
+        if(verbose){System.out.println("Edges with weights too far below a vertex occupancy value removed");}

        //Filter by relative occupancy
        if(verbose){System.out.println("Eliminating edges between vertices with occupancy difference > "
                + maxOccupancyDifference);}
-        filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts, plateVtoAMap, plateVtoBMap,
-                maxOccupancyDifference);
+        removedEdges.addAll(GraphModificationFunctions.filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts,
+                plateVtoAMap, plateVtoBMap, maxOccupancyDifference, saveEdges));
        if(verbose){System.out.println("Edges between vertices of with excessively different occupancy values " +
-                "set to 0.0");}
+                "removed");}
+
        //Find Maximum Weighted Matching
-        //using jheaps library class PairingHeap for improved efficiency
        if(verbose){System.out.println("Finding maximum weighted matching");}
-        //Attempting to use addressable heap to improve performance
-        MaximumWeightBipartiteMatching maxWeightMatching =
-                new MaximumWeightBipartiteMatching(graph,
+        MaximumWeightBipartiteMatching maxWeightMatching;
+        //Use correct heap type for priority queue
+        String heapType = BiGpairSEQ.getPriorityQueueHeapType();
+        switch (heapType) {
+            case "PAIRING" -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
                        plateVtoAMap.keySet(),
                        plateVtoBMap.keySet(),
                        i -> new PairingHeap(Comparator.naturalOrder()));
+            }
+            case "FIBONACCI" -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
+                        plateVtoAMap.keySet(),
+                        plateVtoBMap.keySet(),
+                        i -> new FibonacciHeap(Comparator.naturalOrder()));
+            }
+            default -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
+                        plateVtoAMap.keySet(),
+                        plateVtoBMap.keySet());
+            }
+        }
+        //get the matching
        MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = maxWeightMatching.getMatching();
        if(verbose){System.out.println("Matching completed");}
        Instant stop = Instant.now();
@@ -233,351 +235,385 @@ public class Simulator {
            allResults.add(result);
        }

-        //Metadate comments for CSV file
+        //Metadata comments for CSV file
+        String algoType = "LEDA book with heap: " + heapType;
        int min = Math.min(alphaCount, betaCount);
+        //rate of attempted matching
        double attemptRate = (double) (trueCount + falseCount) / min;
        BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
+        //rate of pairing error
        double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
-        BigDecimal pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
-        //get list of well concentrations
-        List<Integer> wellConcentrations = Arrays.asList(data.getWellConcentrations());
-        //make string out of concentrations list
-        StringBuilder concentrationStringBuilder = new StringBuilder();
-        for(Integer i: wellConcentrations){
-            concentrationStringBuilder.append(i.toString());
-            concentrationStringBuilder.append(" ");
+        BigDecimal pairingErrorRateTrunc;
+        if(Double.isFinite(pairingErrorRate)) {
+            pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
        }
-        String concentrationString = concentrationStringBuilder.toString();
-
-        List<String> comments = new ArrayList<>();
-        comments.add("Source Sample Plate filename: " + data.getSourceFilename());
-        comments.add("Source Graph and Data filename: " + dataFilename);
-        comments.add("T cell counts in sample plate wells: " + concentrationString);
-        comments.add("Total alphas found: " + alphaCount);
-        comments.add("Total betas found: " + betaCount);
-        comments.add("High overlap threshold: " + highThreshold);
-        comments.add("Low overlap threshold: " + lowThreshold);
-        comments.add("Minimum overlap percent: " + minOverlapPercent);
-        comments.add("Maximum occupancy difference: " + maxOccupancyDifference);
-        comments.add("Pairing attempt rate: " + attemptRateTrunc);
-        comments.add("Correct pairings: " + trueCount);
-        comments.add("Incorrect pairings: " + falseCount);
-        comments.add("Pairing error rate: " + pairingErrorRateTrunc);
+        else{
+            pairingErrorRateTrunc = new BigDecimal(-1, mc);
+        }
+        //get list of well populations
+        Integer[] wellPopulations = data.getWellPopulations();
+        //make string out of populations list
+        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();
+        //total simulation time
        Duration time = Duration.between(start, stop);
        time = time.plus(data.getTime());
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+
+        Map<String, String> metadata = new LinkedHashMap<>();
+        metadata.put("sample plate filename", data.getSourceFilename());
+        metadata.put("graph filename", dataFilename);
+        metadata.put("algorithm type", algoType);
+        metadata.put("well populations", wellPopulationsString);
+        metadata.put("total alphas found", alphaCount.toString());
+        metadata.put("total betas found", betaCount.toString());
+        metadata.put("high overlap threshold", highThreshold.toString());
+        metadata.put("low overlap threshold", lowThreshold.toString());
+        metadata.put("minimum overlap percent", minOverlapPercent.toString());
+        metadata.put("maximum occupancy difference", maxOccupancyDifference.toString());
+        metadata.put("pairing attempt rate", attemptRateTrunc.toString());
+        metadata.put("correct pairing count", Integer.toString(trueCount));
+        metadata.put("incorrect pairing count", Integer.toString(falseCount));
+        metadata.put("pairing error rate", pairingErrorRateTrunc.toString());
+        metadata.put("simulation time (seconds)", nf.format(time.toSeconds()));
+        //create MatchingResult object
+        MatchingResult output = new MatchingResult(metadata, header, allResults, matchMap, time);
        if(verbose){
-            for(String s: comments){
+            for(String s: output.getComments()){
                System.out.println(s);
            }
        }
-        return new MatchingResult(data.getSourceFilename(), comments, header, allResults, matchMap, time);
-    }

-    //Simulated matching of CDR1s to CDR3s. Requires MatchingResult from prior run of matchCDR3s.
-    public static MatchingResult[] matchCDR1s(List<Integer[]> distinctCells,
-                                  Plate samplePlate, Integer lowThreshold,
-                                            Integer highThreshold, MatchingResult priorResult){
-        Instant start = Instant.now();
-        Duration previousTime = priorResult.getTime();
-        Map<Integer, Integer> previousMatches = priorResult.getMatchMap();
-        int numWells = samplePlate.getSize();
-        int[] cdr3Indices = {cdr3AlphaIndex, cdr3BetaIndex};
-        int[] cdr1Indices = {cdr1AlphaIndex, cdr1BetaIndex};
-
-        System.out.println("Making previous match maps");
-        Map<Integer, Integer> cdr3AtoBMap = previousMatches;
-        Map<Integer, Integer> cdr3BtoAMap = invertVertexMap(cdr3AtoBMap);
-        System.out.println("Previous match maps made");
-
-        System.out.println("Making cell maps");
-        Map<Integer, Integer> alphaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr1AlphaIndex);
-        Map<Integer, Integer> betaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3BetaIndex, cdr1BetaIndex);
-        System.out.println("Cell maps made");
-
-        System.out.println("Making well maps");
-        Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
-        Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
-        int CDR3Count = allCDR3s.size();
-        System.out.println("all CDR3s count: " + CDR3Count);
-        int CDR1Count = allCDR1s.size();
-        System.out.println("all CDR1s count: " + CDR1Count);
-        System.out.println("Well maps made");
-
-        System.out.println("Removing unpaired CDR3s from well maps");
-        List<Integer> unpairedCDR3s = new ArrayList<>();
-        for(Integer i: allCDR3s.keySet()){
-            if(!(cdr3AtoBMap.containsKey(i) || cdr3BtoAMap.containsKey(i))){
-                unpairedCDR3s.add(i);
-            }
+        if(saveEdges) {
+            //put the removed edges back on the graph
+            System.out.println("Restoring removed edges to graph.");
+            GraphModificationFunctions.addRemovedEdges(graph, removedEdges);
        }
-        for(Integer i: unpairedCDR3s){
-            allCDR3s.remove(i);
-        }
-        System.out.println("Unpaired CDR3s removed.");
-        System.out.println("Remaining CDR3 count: " + allCDR3s.size());
-
-        System.out.println("Removing below-minimum-overlap-threshold and saturating-occupancy CDR1s");
-        filterByOccupancyThreshold(allCDR1s, lowThreshold, numWells - 1);
-        System.out.println("CDR1s removed.");
-        System.out.println("Remaining CDR1 count: " + allCDR1s.size());
-
-        System.out.println("Making vertex maps");
-
-        //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
-        // distinct numbers associated with them. Since I'm using a 2D array, that means
-        // distinct indices between the rows and columns. vertexStartValue lets me track where I switch
-        // from numbering rows to columns, so I can assign unique numbers to every vertex, and then
-        // subtract the vertexStartValue from CDR1s to use their vertex labels as array indices
-        Integer vertexStartValue = 0;
-        //keys are sequential integer vertices, values are CDR3s
-        Map<Integer, Integer> plateVtoCDR3Map = makeVertexToSequenceMap(allCDR3s, vertexStartValue);
-        //New start value for vertex to CDR1 map should be one more than final vertex value in CDR3 map
-        vertexStartValue += plateVtoCDR3Map.size();
-        //keys are sequential integers vertices, values are CDR1s
-        Map<Integer, Integer> plateVtoCDR1Map = makeVertexToSequenceMap(allCDR1s, vertexStartValue);
-        //keys are CDR3s, values are sequential integer vertices from previous map
-        Map<Integer, Integer> plateCDR3toVMap = invertVertexMap(plateVtoCDR3Map);
-        //keys are CDR1s, values are sequential integer vertices from previous map
-        Map<Integer, Integer> plateCDR1toVMap = invertVertexMap(plateVtoCDR1Map);
-        System.out.println("Vertex maps made");
-
-        System.out.println("Creating adjacency matrix");
-        //Count how many wells each CDR3 appears in
-        Map<Integer, Integer> cdr3WellCounts = new HashMap<>();
-        //count how many wells each CDR1 appears in
-        Map<Integer, Integer> cdr1WellCounts = new HashMap<>();
-        //add edges, where weights are number of wells the peptides share in common.
-        //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
-        Map<Integer, Integer> wellNCDR3s = null;
-        Map<Integer, Integer> wellNCDR1s = null;
-        double[][] weights = new double[plateVtoCDR3Map.size()][plateVtoCDR1Map.size()];
-        countSequencesAndFillMatrix(samplePlate, allCDR3s, allCDR1s, plateCDR3toVMap, plateCDR1toVMap,
-                cdr3Indices, cdr1Indices, cdr3WellCounts, cdr1WellCounts, weights);
-        System.out.println("Matrix created");
-
-        System.out.println("Creating graph");
-        SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
-                new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
-
-        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
-        List<Integer> cdr3Vertices = new ArrayList<>(plateVtoCDR3Map.keySet()); //This will work because LinkedHashMap preserves order of entry
-        graphGenerator.first(cdr3Vertices);
-        List<Integer> cdr1Vertices = new ArrayList<>(plateVtoCDR1Map.keySet());
-        graphGenerator.second(cdr1Vertices); //This will work because LinkedHashMap preserves order of entry
-        graphGenerator.weights(weights);
-        graphGenerator.generateGraph(graph);
-        System.out.println("Graph created");
-
-        System.out.println("Removing edges outside of weight thresholds");
-        filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
-        System.out.println("Over- and under-weight edges set to 0.0");
-
-        System.out.println("Finding first maximum weighted matching");
-        MaximumWeightBipartiteMatching firstMaxWeightMatching =
-                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
-        MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = firstMaxWeightMatching.getMatching();
-        System.out.println("First maximum weighted matching found");
-
-
-        //first processing run
-        Map<Integer, Integer> firstMatchCDR3toCDR1Map = new HashMap<>();
-        Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
-        DefaultWeightedEdge e;
-        while(weightIter.hasNext()){
-            e = weightIter.next();
-//            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
-//                continue;
-//            }
-            Integer source = graph.getEdgeSource(e);
-            Integer target = graph.getEdgeTarget(e);
-            firstMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
-        }
-        System.out.println("First pass matches: " + firstMatchCDR3toCDR1Map.size());
-
-        System.out.println("Removing edges from first maximum weighted matching");
-        //zero out the edge weights in the matching
-        weightIter = graphMatching.iterator();
-        while(weightIter.hasNext()){
-            graph.removeEdge(weightIter.next());
-        }
-        System.out.println("Edges removed");
-
-        //Generate a new matching
-        System.out.println("Finding second maximum weighted matching");
-        MaximumWeightBipartiteMatching secondMaxWeightMatching =
-                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
-        graphMatching = secondMaxWeightMatching.getMatching();
-        System.out.println("Second maximum weighted matching found");
-
-
-        //second processing run
-        Map<Integer, Integer> secondMatchCDR3toCDR1Map = new HashMap<>();
-        weightIter = graphMatching.iterator();
-        while(weightIter.hasNext()){
-            e = weightIter.next();
-//            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
-//                continue;
-//            }
-            Integer source = graph.getEdgeSource(e);
-//            if(!(CDR3AtoBMap.containsKey(source) || CDR3BtoAMap.containsKey(source))){
-//                continue;
-//            }
-            Integer target = graph.getEdgeTarget(e);
-            secondMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
-        }
-        System.out.println("Second pass matches: " + secondMatchCDR3toCDR1Map.size());
-
-        System.out.println("Mapping first pass CDR3 alpha/beta pairs");
-        //get linked map for first matching attempt
-        Map<Integer, Integer> firstMatchesMap = new LinkedHashMap<>();
-        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
-            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
-                continue;
-            }
-            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
-            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
-                continue;
-            }
-            firstMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
-            firstMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
-        }
-        System.out.println("First pass CDR3 alpha/beta pairs mapped");
-
-        System.out.println("Mapping second pass CDR3 alpha/beta pairs.");
-        System.out.println("Finding CDR3 pairs that swapped CDR1 matches between first pass and second pass.");
-        //Look for matches that simply swapped already-matched alpha and beta CDR3s
-        Map<Integer, Integer> dualMatchesMap = new LinkedHashMap<>();
-        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
-            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3) && secondMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
-                continue;
-            }
-            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
-            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3) && secondMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
-                continue;
-            }
-            if(firstMatchCDR3toCDR1Map.get(alphaCDR3).equals(secondMatchCDR3toCDR1Map.get(betaCDR3))){
-                if(firstMatchCDR3toCDR1Map.get(betaCDR3).equals(secondMatchCDR3toCDR1Map.get(alphaCDR3))){
-                    dualMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
-                    dualMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
-                }
-            }
-        }
-        System.out.println("Second pass mapping made. Dual CDR3/CDR1 pairings found.");
-
-        Instant stop = Instant.now();
-        //results for first map
-        System.out.println("RESULTS FOR FIRST PASS MATCHING");
-        List<List<String>> allResults = new ArrayList<>();
-        Integer trueCount = 0;
-        Iterator iter = firstMatchesMap.keySet().iterator();
-
-        while(iter.hasNext()){
-            Boolean proven = false;
-            List<String> tmp = new ArrayList<>();
-            tmp.add(iter.next().toString());
-            tmp.add(iter.next().toString());
-            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
-            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
-            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
-                    proven = true;
-                }
-            }
-            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
-                    proven = true;
-                }
-            }
-            tmp.add(proven.toString());
-            allResults.add(tmp);
-            if(proven){
-                trueCount++;
-            }
-        }
-
-        List<String> comments = new ArrayList<>();
-        comments.add("Plate size: " + samplePlate.getSize() + " wells");
-        comments.add("Previous pairs found: " + previousMatches.size());
-        comments.add("CDR1 matches attempted: " + allResults.size());
-        double attemptRate = (double) allResults.size() / previousMatches.size();
-        comments.add("Matching attempt rate: " + attemptRate);
-        comments.add("Number of correct matches: " + trueCount);
-        double correctRate = (double) trueCount / allResults.size();
-        comments.add("Correct matching rate: " + correctRate);
-        NumberFormat nf = NumberFormat.getInstance(Locale.US);
-        Duration time = Duration.between(start, stop);
-        time = time.plus(previousTime);
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-        for(String s: comments){
-            System.out.println(s);
-        }
-
-
-
-        List<String> headers = new ArrayList<>();
-        headers.add("CDR3 alpha");
-        headers.add("CDR3 beta");
-        headers.add("first matched CDR1");
-        headers.add("second matched CDR1");
-        headers.add("Correct match?");
-
-        MatchingResult firstTest = new MatchingResult(samplePlate.getSourceFileName(),
-                comments, headers, allResults, dualMatchesMap, time);
-
-        //results for dual map
-        System.out.println("RESULTS FOR SECOND PASS MATCHING");
-        allResults = new ArrayList<>();
-        trueCount = 0;
-        iter = dualMatchesMap.keySet().iterator();
-        while(iter.hasNext()){
-            Boolean proven = false;
-            List<String> tmp = new ArrayList<>();
-            tmp.add(iter.next().toString());
-            tmp.add(iter.next().toString());
-            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
-            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
-            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
-                    proven = true;
-                }
-            }
-            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
-                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
-                    proven = true;
-                }
-            }
-            tmp.add(proven.toString());
-            allResults.add(tmp);
-            if(proven){
-                trueCount++;
-            }
-        }
-
-        comments = new ArrayList<>();
-        comments.add("Plate size: " + samplePlate.getSize() + " wells");
-        comments.add("Previous pairs found: " + previousMatches.size());
-        comments.add("High overlap threshold: " + highThreshold);
-        comments.add("Low overlap threshold: " + lowThreshold);
-        comments.add("CDR1 matches attempted: " + allResults.size());
-        attemptRate = (double) allResults.size() / previousMatches.size();
-        comments.add("Matching attempt rate: " + attemptRate);
-        comments.add("Number of correct matches: " + trueCount);
-        correctRate = (double) trueCount / allResults.size();
-        comments.add("Correct matching rate: " + correctRate);
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-
-        for(String s: comments){
-            System.out.println(s);
-        }
-
-        System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-        MatchingResult dualTest = new MatchingResult(samplePlate.getSourceFileName(), comments, headers,
-                allResults, dualMatchesMap, time);
-        MatchingResult[] output = {firstTest, dualTest};
+        //return MatchingResult object
        return output;
    }

+    //Commented out CDR1 matching until it's time to re-implement it
+//    //Simulated matching of CDR1s to CDR3s. Requires MatchingResult from prior run of matchCDR3s.
+//    public static MatchingResult[] matchCDR1s(List<Integer[]> distinctCells,
+//                                  Plate samplePlate, Integer lowThreshold,
+//                                            Integer highThreshold, MatchingResult priorResult){
+//        Instant start = Instant.now();
+//        Duration previousTime = priorResult.getTime();
+//        Map<Integer, Integer> previousMatches = priorResult.getMatchMap();
+//        int numWells = samplePlate.getSize();
+//        int[] cdr3Indices = {cdr3AlphaIndex, cdr3BetaIndex};
+//        int[] cdr1Indices = {cdr1AlphaIndex, cdr1BetaIndex};
+//
+//        System.out.println("Making previous match maps");
+//        Map<Integer, Integer> cdr3AtoBMap = previousMatches;
+//        Map<Integer, Integer> cdr3BtoAMap = invertVertexMap(cdr3AtoBMap);
+//        System.out.println("Previous match maps made");
+//
+//        System.out.println("Making cell maps");
+//        Map<Integer, Integer> alphaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr1AlphaIndex);
+//        Map<Integer, Integer> betaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3BetaIndex, cdr1BetaIndex);
+//        System.out.println("Cell maps made");
+//
+//        System.out.println("Making well maps");
+//        Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
+//        Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
+//        int CDR3Count = allCDR3s.size();
+//        System.out.println("all CDR3s count: " + CDR3Count);
+//        int CDR1Count = allCDR1s.size();
+//        System.out.println("all CDR1s count: " + CDR1Count);
+//        System.out.println("Well maps made");
+//
+//        System.out.println("Removing unpaired CDR3s from well maps");
+//        List<Integer> unpairedCDR3s = new ArrayList<>();
+//        for(Integer i: allCDR3s.keySet()){
+//            if(!(cdr3AtoBMap.containsKey(i) || cdr3BtoAMap.containsKey(i))){
+//                unpairedCDR3s.add(i);
+//            }
+//        }
+//        for(Integer i: unpairedCDR3s){
+//            allCDR3s.remove(i);
+//        }
+//        System.out.println("Unpaired CDR3s removed.");
+//        System.out.println("Remaining CDR3 count: " + allCDR3s.size());
+//
+//        System.out.println("Removing below-minimum-overlap-threshold and saturating-occupancy CDR1s");
+//        filterByOccupancyThreshold(allCDR1s, lowThreshold, numWells - 1);
+//        System.out.println("CDR1s removed.");
+//        System.out.println("Remaining CDR1 count: " + allCDR1s.size());
+//
+//        System.out.println("Making vertex maps");
+//
+//        //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
+//        // distinct numbers associated with them. Since I'm using a 2D array, that means
+//        // distinct indices between the rows and columns. vertexStartValue lets me track where I switch
+//        // from numbering rows to columns, so I can assign unique numbers to every vertex, and then
+//        // subtract the vertexStartValue from CDR1s to use their vertex labels as array indices
+//        Integer vertexStartValue = 0;
+//        //keys are sequential integer vertices, values are CDR3s
+//        Map<Integer, Integer> plateVtoCDR3Map = makeVertexToSequenceMap(allCDR3s, vertexStartValue);
+//        //New start value for vertex to CDR1 map should be one more than final vertex value in CDR3 map
+//        vertexStartValue += plateVtoCDR3Map.size();
+//        //keys are sequential integers vertices, values are CDR1s
+//        Map<Integer, Integer> plateVtoCDR1Map = makeVertexToSequenceMap(allCDR1s, vertexStartValue);
+//        //keys are CDR3s, values are sequential integer vertices from previous map
+//        Map<Integer, Integer> plateCDR3toVMap = invertVertexMap(plateVtoCDR3Map);
+//        //keys are CDR1s, values are sequential integer vertices from previous map
+//        Map<Integer, Integer> plateCDR1toVMap = invertVertexMap(plateVtoCDR1Map);
+//        System.out.println("Vertex maps made");
+//
+//        System.out.println("Creating adjacency matrix");
+//        //Count how many wells each CDR3 appears in
+//        Map<Integer, Integer> cdr3WellCounts = new HashMap<>();
+//        //count how many wells each CDR1 appears in
+//        Map<Integer, Integer> cdr1WellCounts = new HashMap<>();
+//        //add edges, where weights are number of wells the peptides share in common.
+//        //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
+//        Map<Integer, Integer> wellNCDR3s = null;
+//        Map<Integer, Integer> wellNCDR1s = null;
+//        double[][] weights = new double[plateVtoCDR3Map.size()][plateVtoCDR1Map.size()];
+//        countSequencesAndFillMatrix(samplePlate, allCDR3s, allCDR1s, plateCDR3toVMap, plateCDR1toVMap,
+//                cdr3Indices, cdr1Indices, cdr3WellCounts, cdr1WellCounts, weights);
+//        System.out.println("Matrix created");
+//
+//        System.out.println("Creating graph");
+//        SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
+//                new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
+//
+//        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
+//        List<Integer> cdr3Vertices = new ArrayList<>(plateVtoCDR3Map.keySet()); //This will work because LinkedHashMap preserves order of entry
+//        graphGenerator.first(cdr3Vertices);
+//        List<Integer> cdr1Vertices = new ArrayList<>(plateVtoCDR1Map.keySet());
+//        graphGenerator.second(cdr1Vertices); //This will work because LinkedHashMap preserves order of entry
+//        graphGenerator.weights(weights);
+//        graphGenerator.generateGraph(graph);
+//        System.out.println("Graph created");
+//
+//        System.out.println("Removing edges outside of weight thresholds");
+//        filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
+//        System.out.println("Over- and under-weight edges set to 0.0");
+//
+//        System.out.println("Finding first maximum weighted matching");
+//        MaximumWeightBipartiteMatching firstMaxWeightMatching =
+//                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
+//        MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = firstMaxWeightMatching.getMatching();
+//        System.out.println("First maximum weighted matching found");
+//
+//
+//        //first processing run
+//        Map<Integer, Integer> firstMatchCDR3toCDR1Map = new HashMap<>();
+//        Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
+//        DefaultWeightedEdge e;
+//        while(weightIter.hasNext()){
+//            e = weightIter.next();
+////            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
+////                continue;
+////            }
+//            Integer source = graph.getEdgeSource(e);
+//            Integer target = graph.getEdgeTarget(e);
+//            firstMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
+//        }
+//        System.out.println("First pass matches: " + firstMatchCDR3toCDR1Map.size());
+//
+//        System.out.println("Removing edges from first maximum weighted matching");
+//        //zero out the edge weights in the matching
+//        weightIter = graphMatching.iterator();
+//        while(weightIter.hasNext()){
+//            graph.removeEdge(weightIter.next());
+//        }
+//        System.out.println("Edges removed");
+//
+//        //Generate a new matching
+//        System.out.println("Finding second maximum weighted matching");
+//        MaximumWeightBipartiteMatching secondMaxWeightMatching =
+//                new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
+//        graphMatching = secondMaxWeightMatching.getMatching();
+//        System.out.println("Second maximum weighted matching found");
+//
+//
+//        //second processing run
+//        Map<Integer, Integer> secondMatchCDR3toCDR1Map = new HashMap<>();
+//        weightIter = graphMatching.iterator();
+//        while(weightIter.hasNext()){
+//            e = weightIter.next();
+////            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
+////                continue;
+////            }
+//            Integer source = graph.getEdgeSource(e);
+////            if(!(CDR3AtoBMap.containsKey(source) || CDR3BtoAMap.containsKey(source))){
+////                continue;
+////            }
+//            Integer target = graph.getEdgeTarget(e);
+//            secondMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
+//        }
+//        System.out.println("Second pass matches: " + secondMatchCDR3toCDR1Map.size());
+//
+//        System.out.println("Mapping first pass CDR3 alpha/beta pairs");
+//        //get linked map for first matching attempt
+//        Map<Integer, Integer> firstMatchesMap = new LinkedHashMap<>();
+//        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
+//                continue;
+//            }
+//            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
+//                continue;
+//            }
+//            firstMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
+//            firstMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
+//        }
+//        System.out.println("First pass CDR3 alpha/beta pairs mapped");
+//
+//        System.out.println("Mapping second pass CDR3 alpha/beta pairs.");
+//        System.out.println("Finding CDR3 pairs that swapped CDR1 matches between first pass and second pass.");
+//        //Look for matches that simply swapped already-matched alpha and beta CDR3s
+//        Map<Integer, Integer> dualMatchesMap = new LinkedHashMap<>();
+//        for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3) && secondMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
+//                continue;
+//            }
+//            Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
+//            if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3) && secondMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
+//                continue;
+//            }
+//            if(firstMatchCDR3toCDR1Map.get(alphaCDR3).equals(secondMatchCDR3toCDR1Map.get(betaCDR3))){
+//                if(firstMatchCDR3toCDR1Map.get(betaCDR3).equals(secondMatchCDR3toCDR1Map.get(alphaCDR3))){
+//                    dualMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
+//                    dualMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
+//                }
+//            }
+//        }
+//        System.out.println("Second pass mapping made. Dual CDR3/CDR1 pairings found.");
+//
+//        Instant stop = Instant.now();
+//        //results for first map
+//        System.out.println("RESULTS FOR FIRST PASS MATCHING");
+//        List<List<String>> allResults = new ArrayList<>();
+//        Integer trueCount = 0;
+//        Iterator iter = firstMatchesMap.keySet().iterator();
+//
+//        while(iter.hasNext()){
+//            Boolean proven = false;
+//            List<String> tmp = new ArrayList<>();
+//            tmp.add(iter.next().toString());
+//            tmp.add(iter.next().toString());
+//            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
+//            tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
+//            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
+//                    proven = true;
+//                }
+//            }
+//            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
+//                    proven = true;
+//                }
+//            }
+//            tmp.add(proven.toString());
+//            allResults.add(tmp);
+//            if(proven){
+//                trueCount++;
+//            }
+//        }
+//
+//        List<String> comments = new ArrayList<>();
+//        comments.add("Plate size: " + samplePlate.getSize() + " wells");
+//        comments.add("Previous pairs found: " + previousMatches.size());
+//        comments.add("CDR1 matches attempted: " + allResults.size());
+//        double attemptRate = (double) allResults.size() / previousMatches.size();
+//        comments.add("Matching attempt rate: " + attemptRate);
+//        comments.add("Number of correct matches: " + trueCount);
+//        double correctRate = (double) trueCount / allResults.size();
+//        comments.add("Correct matching rate: " + correctRate);
+//        NumberFormat nf = NumberFormat.getInstance(Locale.US);
+//        Duration time = Duration.between(start, stop);
+//        time = time.plus(previousTime);
+//        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+//        for(String s: comments){
+//            System.out.println(s);
+//        }
+//
+//
+//
+//        List<String> headers = new ArrayList<>();
+//        headers.add("CDR3 alpha");
+//        headers.add("CDR3 beta");
+//        headers.add("first matched CDR1");
+//        headers.add("second matched CDR1");
+//        headers.add("Correct match?");
+//
+//        MatchingResult firstTest = new MatchingResult(samplePlate.getSourceFileName(),
+//                comments, headers, allResults, dualMatchesMap, time);
+//
+//        //results for dual map
+//        System.out.println("RESULTS FOR SECOND PASS MATCHING");
+//        allResults = new ArrayList<>();
+//        trueCount = 0;
+//        iter = dualMatchesMap.keySet().iterator();
+//        while(iter.hasNext()){
+//            Boolean proven = false;
+//            List<String> tmp = new ArrayList<>();
+//            tmp.add(iter.next().toString());
+//            tmp.add(iter.next().toString());
+//            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
+//            tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
+//            if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
+//                    proven = true;
+//                }
+//            }
+//            else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
+//                if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
+//                    proven = true;
+//                }
+//            }
+//            tmp.add(proven.toString());
+//            allResults.add(tmp);
+//            if(proven){
+//                trueCount++;
+//            }
+//        }
+//
+//        comments = new ArrayList<>();
+//        comments.add("Plate size: " + samplePlate.getSize() + " wells");
+//        comments.add("Previous pairs found: " + previousMatches.size());
+//        comments.add("High overlap threshold: " + highThreshold);
+//        comments.add("Low overlap threshold: " + lowThreshold);
+//        comments.add("CDR1 matches attempted: " + allResults.size());
+//        attemptRate = (double) allResults.size() / previousMatches.size();
+//        comments.add("Matching attempt rate: " + attemptRate);
+//        comments.add("Number of correct matches: " + trueCount);
+//        correctRate = (double) trueCount / allResults.size();
+//        comments.add("Correct matching rate: " + correctRate);
+//        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+//
+//        for(String s: comments){
+//            System.out.println(s);
+//        }
+//
+//        System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
+//        MatchingResult dualTest = new MatchingResult(samplePlate.getSourceFileName(), comments, headers,
+//                allResults, dualMatchesMap, time);
+//        MatchingResult[] output = {firstTest, dualTest};
+//        return output;
+//    }
+
+    //Remove sequences based on occupancy
+    public static void filterByOccupancyThresholds(Map<Integer, Integer> wellMap, int low, int high){
+        List<Integer> noise = new ArrayList<>();
+        for(Integer k: wellMap.keySet()){
+            if((wellMap.get(k) > high) || (wellMap.get(k) < low)){
+                noise.add(k);
+            }
+        }
+        for(Integer k: noise) {
+            wellMap.remove(k);
+        }
+    }

    //Counts the well occupancy of the row peptides and column peptides into given maps, and
    //fills weights in the given 2D array
@@ -621,62 +657,6 @@ public class Simulator {
        }
    }

-
-    private static void filterByOccupancyThreshold(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
-                                                   int low, int high) {
-        for(DefaultWeightedEdge e: graph.edgeSet()){
-            if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)){
-                graph.setEdgeWeight(e, 0.0);
-            }
-        }
-    }
-    private static void filterByOccupancyThreshold(Map<Integer, Integer> wellMap, int low, int high){
-        List<Integer> noise = new ArrayList<>();
-        for(Integer k: wellMap.keySet()){
-            if((wellMap.get(k) > high) || (wellMap.get(k) < low)){
-                noise.add(k);
-            }
-        }
-        for(Integer k: noise) {
-            wellMap.remove(k);
-        }
-    }
-
-    //Remove edges for pairs with large occupancy discrepancy
-    private static void filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
-                                                  Map<Integer, Integer> alphaWellCounts,
-                                                  Map<Integer, Integer> betaWellCounts,
-                                                  Map<Integer, Integer> plateVtoAMap,
-                                                  Map<Integer, Integer> plateVtoBMap,
-                                                  Integer maxOccupancyDifference) {
-        for (DefaultWeightedEdge e : graph.edgeSet()) {
-            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
-            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
-            //Adjust this to something cleverer later
-            if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
-                graph.setEdgeWeight(e, 0.0);
-            }
-        }
-    }
-
-    //Remove edges for pairs where overlap size is significantly lower than the well occupancy
-    private static void filterByOverlapSize(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
-                                            Map<Integer, Integer> alphaWellCounts,
-                                            Map<Integer, Integer> betaWellCounts,
-                                            Map<Integer, Integer> plateVtoAMap,
-                                            Map<Integer, Integer> plateVtoBMap,
-                                            Integer minOverlapPercent) {
-        for (DefaultWeightedEdge e : graph.edgeSet()) {
-            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
-            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
-            double weight = graph.getEdgeWeight(e);
-            double min = minOverlapPercent / 100.0;
-            if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
-                graph.setEdgeWeight(e, 0.0);
-            }
-        }
-    }
-
    private static Map<Integer, Integer> makeSequenceToSequenceMap(List<Integer[]> cells, int keySequenceIndex,
                                                                   int valueSequenceIndex){
        Map<Integer, Integer> keySequenceToValueSequenceMap = new HashMap<>();
@@ -688,7 +668,7 @@ public class Simulator {

    private static Map<Integer, Integer> makeVertexToSequenceMap(Map<Integer, Integer> sequences, Integer startValue) {
        Map<Integer, Integer> map = new LinkedHashMap<>(); //LinkedHashMap to preserve order of entry
-        Integer index = startValue;
+        Integer index = startValue; //is this necessary? I don't think I use this.
        for (Integer k: sequences.keySet()) {
            map.put(index, k);
            index++;
--- a/src/main/java/UserInterface.java
+++ b/src/main/java/UserInterface.java
@@ -1,694 +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("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");
-    }
-}
--- a/src/main/java/Vertex.java
+++ b/src/main/java/Vertex.java
@@ -1,14 +1,20 @@
+
+
 public class Vertex {
-    private final Integer peptide;
+    private final Integer vertexLabel;
+    private final Integer sequence;
    private final Integer occupancy;

-    public Vertex(Integer peptide, Integer occupancy) {
-        this.peptide = peptide;
+    public Vertex(Integer vertexLabel, Integer sequence, Integer occupancy) {
+        this.vertexLabel = vertexLabel;
+        this.sequence = sequence;
        this.occupancy = occupancy;
    }

-    public Integer getPeptide() {
-        return peptide;
+    public Integer getVertexLabel() { return vertexLabel; }
+
+    public Integer getSequence() {
+        return sequence;
    }

    public Integer getOccupancy() {
Author	SHA1	Message	Date
efischer	96ba57d653	Remove singleton sequences from wells in initial filtering	2022-03-04 16:14:17 -06:00
efischer	b602fb02f1	Remove obsolete comments	2022-03-02 23:35:24 -06:00
efischer	325e1ebe2b	Add data on randomized well population behavior	2022-03-02 23:21:56 -06:00
efischer	df047267ee	Add data on randomized well population behavior	2022-03-02 22:54:17 -06:00
efischer	03e8d31210	Add data on randomized well population behavior	2022-03-02 18:55:19 -06:00
efischer	582dc3ef40	Update readme	2022-03-02 12:39:40 -06:00
efischer	4c872ed48e	Add optional stdout print flags	2022-03-01 15:27:04 -06:00
efischer	3fc39302c7	Add detail to error message	2022-03-01 15:24:14 -06:00
efischer	578bdc0fbf	clarify help menu text	2022-03-01 15:08:43 -06:00
efischer	8275cf7740	Check for finite pairing error rate	2022-03-01 09:01:53 -06:00
efischer	64209691f0	Check for finite pairing error rate	2022-03-01 09:00:58 -06:00
efischer	1886800873	update readme	2022-03-01 08:54:32 -06:00
efischer	bedf0894bc	update readme	2022-03-01 08:45:40 -06:00
efischer	2ac3451842	update readme	2022-03-01 08:43:48 -06:00
efischer	67ec3f3764	update readme	2022-03-01 08:43:18 -06:00
efischer	b5a8b7e2d5	update readme	2022-03-01 08:41:57 -06:00
efischer	9fb3095f0f	Clarify help text	2022-03-01 08:40:34 -06:00
efischer	25acf920c2	Add version information	2022-03-01 08:34:35 -06:00
efischer	f301327693	Update readme with -graphml flag	2022-03-01 08:24:43 -06:00
efischer	e04d2d6777	Fix typos in help menu	2022-03-01 08:16:06 -06:00
efischer	3e41afaa64	bugfix	2022-02-27 19:08:29 -06:00
efischer	bc5d67680d	Add flag to print metadata to stdout	2022-02-27 17:36:23 -06:00
efischer	f2347e8fc2	check verbose flag	2022-02-27 17:35:50 -06:00
efischer	c8364d8a6e	check verbose flag	2022-02-27 17:34:20 -06:00
efischer	6f5afbc6ec	Update readme with CLI arguments	2022-02-27 17:01:12 -06:00
efischer	fb4d22e7a4	Update readme with CLI arguments	2022-02-27 17:00:54 -06:00
efischer	e10350c214	Update readme with CLI arguments	2022-02-27 16:56:58 -06:00
efischer	b1155f8100	Format -help CLI option	2022-02-27 16:53:46 -06:00
efischer	12b003a69f	Add -help CLI option	2022-02-27 16:45:30 -06:00
efischer	32c5bcaaff	Deactivate file I/O announcement for CLI	2022-02-27 16:16:24 -06:00
efischer	2485ac4cf6	Add getters to MatchingResult	2022-02-27 16:15:26 -06:00
efischer	05556bce0c	Add units to metadata	2022-02-27 16:08:59 -06:00
efischer	a822f69ea4	Control verbose output	2022-02-27 16:07:17 -06:00
efischer	3d1f8668ee	Control verbose output	2022-02-27 16:03:57 -06:00
efischer	40c743308b	Initialize wells	2022-02-27 15:54:47 -06:00
efischer	5246cc4a0c	Re-implement command line options	2022-02-27 15:35:07 -06:00
efischer	a5f7c0641d	Refactor for better encapsulation with CellSamples	2022-02-27 14:51:53 -06:00
efischer	8ebfc1469f	Refactor plate to fill its own wells in its constructor	2022-02-27 14:25:53 -06:00
efischer	b53f5f1cc0	Refactor plate to fill its own wells in its constructor	2022-02-27 14:17:16 -06:00
efischer	974d2d650c	Refactor plate to fill its own wells in its constructor	2022-02-27 14:17:11 -06:00
efischer	6b5837e6ce	Add Vose's alias method to to-dos	2022-02-27 11:46:11 -06:00
efischer	b4cc240048	Update Readme	2022-02-26 11:03:31 -06:00
efischer	ff72c9b359	Update Readme	2022-02-26 11:02:23 -06:00
efischer	88eb8aca50	Update Readme	2022-02-26 11:01:44 -06:00
efischer	98bf452891	Update Readme	2022-02-26 11:01:20 -06:00
efischer	c2db4f87c1	Update Readme	2022-02-26 11:00:18 -06:00
efischer	8935407ade	Get rid of GraphML reader, those files are larger than serialized files	2022-02-26 10:38:10 -06:00
efischer	9fcc20343d	Fix GraphML writer	2022-02-26 10:36:00 -06:00
efischer	e4d094d796	Adding GraphML output to options menu	2022-02-24 17:22:07 -06:00
efischer	f385ebc31f	Update vertex class	2022-02-24 16:25:01 -06:00
efischer	8745550e11	add MWM algorithm type to matching metadata	2022-02-24 16:24:48 -06:00
efischer	41805135b3	remove unused import	2022-02-24 16:04:30 -06:00
efischer	373a5e02f9	Refactor to make CellSample class more self-contained	2022-02-24 16:03:49 -06:00
efischer	7f18311054	fix typos	2022-02-24 15:55:32 -06:00
efischer	bcb816c3e6	Reformat TODO	2022-02-24 15:48:10 -06:00
efischer	dad0fd35fd	Update readme to reflect wells with random population implemented	2022-02-24 15:47:08 -06:00
efischer	35d580cfcf	Update readme to reflect wells with random population implemented	2022-02-24 15:45:03 -06:00
efischer	ab8d98ed81	Update readme to reflect new default caching behavior.	2022-02-24 15:39:15 -06:00
efischer	3d9890e16a	Change GraphModificationFunctions to only save edges if graph data is cached	2022-02-24 15:32:27 -06:00
efischer	dd64ac2731	Change GraphModificationFunctions to interface	2022-02-24 15:18:09 -06:00
efischer	a5238624f1	Change default graph caching behavior to false	2022-02-24 15:14:28 -06:00
efischer	d8ba42b801	Fix Algorithm Options menu output	2022-02-24 14:59:08 -06:00
efischer	8edd89d784	Added heap type selection, fixed error handling	2022-02-24 14:48:19 -06:00
efischer	2829b88689	Update readme to reflect caching changes	2022-02-24 12:47:26 -06:00
efischer	108b0ec13f	Improve options menu wording	2022-02-24 12:42:09 -06:00
efischer	a8b58d3f79	Output new setting when changing options	2022-02-24 12:38:15 -06:00
efischer	bf64d57731	implement option menu for file caching	2022-02-24 12:30:47 -06:00
efischer	c068c3db3c	implement option menu for file caching	2022-02-23 20:35:31 -06:00
efischer	4bcda9b66c	update readme	2022-02-23 13:22:04 -06:00
efischer	17ae763c6c	Generate populations correctly	2022-02-23 10:37:40 -06:00
efischer	decdb147a9	Cache everything	2022-02-23 10:30:42 -06:00
efischer	74ffbfd8ac	make everything use same random number generator	2022-02-23 09:29:21 -06:00
efischer	08699ce8ce	Change output order to match interactive UI	2022-02-23 08:56:09 -06:00
efischer	69b0cc535c	Error checking	2022-02-23 08:55:07 -06:00
efischer	e58f7b0a55	checking for possible divide by zero error.	2022-02-23 08:54:14 -06:00
efischer	dd2164c250	implement sample plates with random well populations	2022-02-23 08:14:17 -06:00
efischer	7323093bdc	change "getRandomNumber" to "getRandomInt" for consistency.	2022-02-23 08:13:52 -06:00
efischer	f904cf6672	add more data caching code	2022-02-23 08:13:06 -06:00
efischer	3ccee9891b	change "concentrations" to "populations" for consistency	2022-02-23 08:12:48 -06:00
efischer	40c2be1cfb	create populations string correctly	2022-02-23 08:11:01 -06:00
efischer	4b597c4e5e	remove old testing code	2022-02-23 08:10:35 -06:00
efischer	b2398531a3	Update readme	2022-02-23 05:11:36 +00:00
efischer	8e9a250890	Cache graph data on creation	2022-02-22 22:23:55 -06:00
efischer	e2a996c997	update readme	2022-02-22 22:23:40 -06:00
efischer	a5db89cb0b	update readme	2022-02-22 22:13:01 -06:00
efischer	1630f9ccba	Moved I/O alert to file reader	2022-02-22 22:11:50 -06:00
efischer	d785aa0da2	Moved I/O alert to file reader	2022-02-22 22:10:31 -06:00
efischer	a7afeb6119	bugfixes	2022-02-22 22:10:09 -06:00
efischer	f8167b0774	Add .jar manifest to repo	2022-02-22 21:45:46 -06:00
efischer	68ee9e4bb6	Implemented storing graphs in memory for multiple pairing experiments	2022-02-22 21:30:00 -06:00
efischer	fd2ec76b71	Realized how to store graph in memory	2022-02-22 19:42:35 -06:00
efischer	875f457a2d	reimplement CLI (in progress)	2022-02-22 19:42:23 -06:00
efischer	906c06062f	Added metadata to MatchingResult to enable CLI options	2022-02-22 18:36:30 -06:00
efischer	90ae2ff474	Re-implemeting CLI options (in progress)	2022-02-22 17:37:00 -06:00
efischer	7d983076f3	Add link to releases page for download	2022-02-22 16:34:24 -06:00