update readme

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 [weightd bipartite graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
 The distinct TCRA and TCRB sequences form the two sets of vertices. Every TCRA/TCRB pair that share a well
 are connected by an edge, with the edge weight set to the number of wells in which both sequences appear.
 (Sequences present in *all* wells are filtered out prior to creating the graph, as there is no signal in their occupancy pattern.)
@@ -69,16 +69,26 @@ Please select an option:
 0) Exit
 ```
 
-### OUTPUT
+### 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
 
+These files are often generated in sequence. To save file I/O time, the most recent instance of each of these four
+files either generated or read from disk is cached in program memory. This is especially important for Graph/Data files,
+which can be several gigabytes in size. Since some simulations may require running multiple, 
+differntly-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached drastically reduces 
+execution time. 
+
+Subsequent uses of the same data file won't need to be read in again until another file of that type is used or generated.
+The program checks whether it needs to update its cached data by comparing filenames as entered by the user. On 
+encountering a new filename, the program flushes its cache and reads in the new file.
+
 When entering filenames, it is not necessary to include the file extension (.csv or .ser). When reading or
-writing files, the program will automatically add the correct extension to any filename without one.
+writing files, the program will automatically add the correct extension to any filename without one. 
 
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
@@ -121,7 +131,7 @@ 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 exponential with a lambda of approximately 0.6. (Howie, et al. 2015))*
 * Total number of wells on the plate
 * Number of sections on plate
 * Number of T cells per well
@@ -129,7 +139,7 @@ Options when making a Sample Plate file:
 * 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]`
@@ -155,14 +165,16 @@ Structure:
 
 ---
 
-#### Graph and Data Files
+#### Graph/Data Files
-Graph and Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
+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.
+Sample Plate file (to construct the associated occupancy graph).
-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 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.)
 
@@ -172,8 +184,8 @@ portable data format may be implemented in the future. The tricky part is encodi
 ---
 
 #### Matching Results Files 
-Matching results files consist of the results of a BiGpairSEQ matching simulation.
+Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a Graph and 
-Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
+Data file. Matching results files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
 Metadata about the matching simulation is included as comments. Comments are preceded by `#`.
 
 Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:

src/main/java/BiGpairSEQ.java

@@ -1,6 +1,13 @@
-//main class. Only job is to choose which interface to use, and hold graph data in memory
+import java.util.Random;
+
+//main class. For choosing interface type and caching file data
 public class BiGpairSEQ {
 
+    private static final Random rand = new Random();
+    private static CellSample cellSampleInMemory = null;
+    private static String cellFilename = null;
+    private static Plate plateInMemory = null;
+    private static String plateFilename = null;
     private static GraphWithMapData graphInMemory = null;
     private static String graphFilename = null;
 
@@ -15,18 +22,64 @@ public class BiGpairSEQ {
         }
     }
 
-    public static GraphWithMapData getGraph() {
+    public static Random getRand() {
+        return rand;
+    }
+
+    public static CellSample getCellSampleInMemory() {
+        return cellSampleInMemory;
+    }
+
+    public static void setCellSampleInMemory(CellSample cellSampleInMemory) {
+        BiGpairSEQ.cellSampleInMemory = cellSampleInMemory;
+    }
+
+    public static void clearCellSampleInMemory() {
+        cellSampleInMemory = null;
+        System.gc();
+    }
+
+    public static String getCellFilename() {
+        return cellFilename;
+    }
+
+    public static void setCellFilename(String cellFilename) {
+        BiGpairSEQ.cellFilename = cellFilename;
+    }
+
+    public static Plate getPlateInMemory() {
+        return plateInMemory;
+    }
+
+    public static void setPlateInMemory(Plate plateInMemory) {
+        BiGpairSEQ.plateInMemory = plateInMemory;
+    }
+
+    public static void clearPlateInMemory() {
+        plateInMemory = null;
+        System.gc();
+    }
+
+    public static String getPlateFilename() {
+        return plateFilename;
+    }
+
+    public static void setPlateFilename(String plateFilename) {
+        BiGpairSEQ.plateFilename = plateFilename;
+    }
+
+    public static GraphWithMapData getGraphInMemory() {
         return graphInMemory;
     }
 
-    public static void setGraph(GraphWithMapData g) {
+    public static void setGraphInMemory(GraphWithMapData g) {
         if (graphInMemory != null) {
-            clearGraph();
+            clearGraphInMemory();
         }
         graphInMemory = g;
     }
 
-    public static void clearGraph() {
+    public static void clearGraphInMemory() {
         graphInMemory = null;
         System.gc();
     }

src/main/java/CellFileReader.java

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

src/main/java/CellSample.java

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

src/main/java/CommandLineInterface.java

@@ -297,7 +297,7 @@ public class CommandLineInterface {
                                     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);
+        samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getListOfDistinctCellsDEPRECATED(), lambda);
         PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
         writer.writePlateFile();
     }
@@ -305,9 +305,9 @@ public class CommandLineInterface {
     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());
+        Double stdDev = Math.sqrt(cellReader.getCellCountDEPRECATED());
         Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
-        samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
+        samplePlate.fillWells(cellReader.getFilename(), cellReader.getListOfDistinctCellsDEPRECATED(), stdDev);
         PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
         writer.writePlateFile();
     }
@@ -316,7 +316,7 @@ public class CommandLineInterface {
                                  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);
+        samplePlate.fillWells(cellReader.getFilename(), cellReader.getListOfDistinctCellsDEPRECATED(), stdDev);
         PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
         writer.writePlateFile();
     }

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.

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

src/main/java/InteractiveInterface.java

@@ -1,14 +1,15 @@
 import java.io.IOException;
-import java.util.List;
+import java.util.*;
-import java.util.Scanner;
+import java.util.regex.Matcher;
-import java.util.InputMismatchException;
+import java.util.regex.Pattern;
 
 //
 public class InteractiveInterface {
 
-    final static Scanner sc = new Scanner(System.in);
+    private static final Random rand = BiGpairSEQ.getRand();
-    static int input;
+    private static final Scanner sc = new Scanner(System.in);
-    static boolean quit = false;
+    private static int input;
+    private static boolean quit = false;
 
     public static void startInteractive() {
 
@@ -73,9 +74,15 @@ public class InteractiveInterface {
         }
         CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
         assert filename != null;
+        System.out.println("Writing cells to file");
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
-        System.gc();
+        System.out.println("Cell sample written to: " + filename);
+        if(BiGpairSEQ.getCellSampleInMemory() != null) {
+            BiGpairSEQ.clearCellSampleInMemory();
+        }
+        BiGpairSEQ.setCellSampleInMemory(sample);
+        BiGpairSEQ.setCellFilename(filename);
     }
 
     //Output a CSV of sample plate
@@ -85,7 +92,7 @@ public class InteractiveInterface {
         Double stdDev = 0.0;
         Integer numWells = 0;
         Integer numSections;
-        Integer[] concentrations = {1};
+        Integer[] populations = {1};
         Double dropOutRate = 0.0;
         boolean poisson = false;
         boolean exponential = false;
@@ -124,10 +131,11 @@ public class InteractiveInterface {
                 }
                 case 3 -> {
                     exponential = true;
-                    System.out.println("Please enter lambda value for exponential distribution.");
+                    System.out.print("Please enter lambda value for exponential distribution: ");
                     lambda = sc.nextDouble();
                     if (lambda <= 0.0) {
-                        throw new InputMismatchException("Value must be positive.");
+                        lambda = 0.6;
+                        System.out.println("Value must be positive. Defaulting to 0.6.");
                     }
                 }
                 default -> {
@@ -140,22 +148,57 @@ public class InteractiveInterface {
             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");
+            //choose whether to make T cell population/well random
-            System.out.println("How many sections would you like to make (minimum 1)?");
+            boolean randomWellPopulations;
-            numSections = sc.nextInt();
+            System.out.println("Randomize number of T cells in each well? (y/n)");
-            if(numSections < 1) {
+            String ans = sc.next();
-                throw new InputMismatchException("Too few sections.");
+            Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
+            Matcher matcher = pattern.matcher(ans);
+            if(matcher.matches()){
+                randomWellPopulations = true;
             }
-            else if (numSections > numWells) {
+            else{
-                throw new InputMismatchException("Cannot have more sections than wells.");
+                randomWellPopulations = false;
             }
-            int i = 1;
+            if(randomWellPopulations) { //if T cell population/well is random
-            concentrations = new Integer[numSections];
+                numSections = numWells;
-            while(numSections > 0) {
+                Integer minPop;
-                System.out.print("Enter number of T-cells per well in section " + i +": ");
+                Integer maxPop;
-                concentrations[i - 1] = sc.nextInt();
+                System.out.print("Please enter minimum number of T cells in a well: ");
-                i++;
+                minPop = sc.nextInt();
-                numSections--;
+                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): ");
@@ -167,28 +210,40 @@ public class InteractiveInterface {
             System.out.println(ex);
             sc.next();
         }
-        System.out.println("Reading Cell Sample file: " + cellFile);
         assert cellFile != null;
-        CellFileReader cellReader = new CellFileReader(cellFile);
+        CellSample cells;
+        if (cellFile.equals(BiGpairSEQ.getCellFilename())){
+            cells = BiGpairSEQ.getCellSampleInMemory();
+        }
+        else {
+            System.out.println("Reading Cell Sample file: " + cellFile);
+            CellFileReader cellReader = new CellFileReader(cellFile);
+            cells = cellReader.getCellSample();
+            BiGpairSEQ.clearCellSampleInMemory();
+            BiGpairSEQ.setCellSampleInMemory(cells);
+            BiGpairSEQ.setCellFilename(cellFile);
+        }
+        assert filename != null;
+        Plate samplePlate;
+        PlateFileWriter writer;
         if(exponential){
-            Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
+            samplePlate = new Plate(numWells, dropOutRate, populations);
-            samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
+            samplePlate.fillWellsExponential(cellFile, cells.getCells(), lambda);
-            PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
+            writer = new PlateFileWriter(filename, samplePlate);
-            writer.writePlateFile();
         }
         else {
             if (poisson) {
-                stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
+                stdDev = Math.sqrt(cells.getCellCount()); //gaussian with square root of elements approximates poisson
             }
-            Plate samplePlate = new Plate(numWells, dropOutRate, concentrations);
+            samplePlate = new Plate(numWells, dropOutRate, populations);
-            samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
+            samplePlate.fillWells(cellFile, cells.getCells(), stdDev);
-            assert filename != null;
+            writer = new PlateFileWriter(filename, samplePlate);
-            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();
         }
+        System.out.println("Writing Sample Plate to file");
+        writer.writePlateFile();
+        System.out.println("Sample Plate written to file: " + filename);
+        BiGpairSEQ.setPlateInMemory(samplePlate);
+        BiGpairSEQ.setPlateFilename(filename);
     }
 
     //Output serialized binary of GraphAndMapData object
@@ -212,14 +267,37 @@ public class InteractiveInterface {
             System.out.println(ex);
             sc.next();
         }
-        System.out.println("Reading Cell Sample file: " + cellFile);
+
         assert cellFile != null;
-        CellFileReader cellReader = new CellFileReader(cellFile);
+        CellSample cellSample;
-        System.out.println("Reading Sample Plate file: " + plateFile);
+        //check if cells are already in memory
+        if(cellFile.equals(BiGpairSEQ.getCellFilename())) {
+            cellSample = BiGpairSEQ.getCellSampleInMemory();
+        }
+        else {
+            BiGpairSEQ.clearCellSampleInMemory();
+            System.out.println("Reading Cell Sample file: " + cellFile);
+            CellFileReader cellReader = new CellFileReader(cellFile);
+            cellSample = cellReader.getCellSample();
+            BiGpairSEQ.setCellSampleInMemory(cellSample);
+            BiGpairSEQ.setCellFilename(cellFile);
+        }
+
         assert plateFile != null;
-        PlateFileReader plateReader = new PlateFileReader(plateFile);
+        Plate plate;
-        Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
+        //check if plate is already in memory
-        if (cellReader.getCells().size() == 0){
+        if(plateFile.equals(BiGpairSEQ.getPlateFilename())){
+            plate = BiGpairSEQ.getPlateInMemory();
+        }
+        else {
+            BiGpairSEQ.clearPlateInMemory();
+            System.out.println("Reading Sample Plate file: " + plateFile);
+            PlateFileReader plateReader = new PlateFileReader(plateFile);
+            plate = new Plate(plateReader.getFilename(), plateReader.getWells());
+            BiGpairSEQ.setPlateInMemory(plate);
+            BiGpairSEQ.setPlateFilename(plateFile);
+        }
+        if (cellSample.getCells().size() == 0){
             System.out.println("No cell sample found.");
             System.out.println("Returning to main menu.");
         }
@@ -228,13 +306,15 @@ public class InteractiveInterface {
             System.out.println("Returning to main menu.");
         }
         else{
-            List<Integer[]> cells = cellReader.getCells();
+            List<Integer[]> cells = cellSample.getCells();
             GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
             assert filename != null;
             GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
             dataWriter.writeDataToFile();
             System.out.println("Graph and Data file written to: " + filename);
-            System.gc();
+            BiGpairSEQ.setGraphInMemory(data);
+            BiGpairSEQ.setGraphFilename(filename);
+            System.out.println("Graph and Data file " + filename + " cached.");
         }
     }
 
@@ -256,17 +336,28 @@ public class InteractiveInterface {
             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");
+                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();
-            System.out.println("\nWhat is the maximum difference in alpha/beta occupancy to attempt matching?");
+            if(highThreshold < lowThreshold) {
-            maxOccupancyDiff = sc.nextInt();
+                highThreshold = lowThreshold;
-            System.out.println("\nWell overlap percentage = pair overlap / sequence occupancy");
+                System.out.println("Value for high occupancy overlap threshold must be >= low overlap threshold");
-            System.out.println("What is the minimum well overlap percentage to attempt matching? (0 to 100)");
+                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) {
-                throw new InputMismatchException("Value outside range. Minimum percent set to 0");
+                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);
@@ -275,17 +366,17 @@ public class InteractiveInterface {
         assert graphFilename != null;
         //check if this is the same graph we already have in memory.
         GraphWithMapData data;
-        if(!(graphFilename.equals(BiGpairSEQ.getGraphFilename())) || BiGpairSEQ.getGraph() == null) {
+        if(!(graphFilename.equals(BiGpairSEQ.getGraphFilename())) || BiGpairSEQ.getGraphInMemory() == null) {
-            BiGpairSEQ.clearGraph();
+            BiGpairSEQ.clearGraphInMemory();
             //read object data from file
             GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
             data = dataReader.getData();
             //set new graph in memory and new filename
-            BiGpairSEQ.setGraph(data);
+            BiGpairSEQ.setGraphInMemory(data);
             BiGpairSEQ.setGraphFilename(graphFilename);
         }
         else {
-            data = BiGpairSEQ.getGraph();
+            data = BiGpairSEQ.getGraphInMemory();
         }
         //simulate matching
         MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
@@ -296,7 +387,6 @@ public class InteractiveInterface {
         System.out.println("Writing results to file");
         writer.writeResultsToFile();
         System.out.println("Results written to file: " + filename);
-        System.gc();
     }
 
     ///////

src/main/java/Plate.java

@@ -10,7 +10,7 @@ import java.util.*;
 public class Plate {
     private String sourceFile;
     private List<List<Integer[]>> wells;
-    private Random rand = new Random();
+    private final Random rand = BiGpairSEQ.getRand();
     private int size;
     private double error;
     private Integer[] populations;
@@ -51,7 +51,6 @@ public class Plate {
         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<>();
@@ -61,13 +60,6 @@ public class Plate {
                         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
@@ -80,7 +72,6 @@ public class Plate {
             }
             section++;
         }
-        System.out.println("Highest index: " +test);
     }
 
     public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {

src/main/java/PlateFileWriter.java

@@ -16,7 +16,7 @@ public class PlateFileWriter {
     private Double error;
     private String filename;
     private String sourceFileName;
-    private Integer[] concentrations;
+    private Integer[] populations;
     private boolean isExponential = false;
 
     public PlateFileWriter(String filename, Plate plate) {
@@ -35,8 +35,8 @@ public class PlateFileWriter {
         }
         this.error = plate.getError();
         this.wells = plate.getWells();
-        this.concentrations = plate.getPopulations();
+        this.populations = plate.getPopulations();
-        Arrays.sort(concentrations);
+        Arrays.sort(populations);
     }
 
     public void writePlateFile(){
@@ -73,14 +73,12 @@ public class PlateFileWriter {
 //            rows.add(tmp);
 //        }
 
-        //get list of well populations
+        //make string out of populations array
-        List<Integer> wellPopulations = Arrays.asList(concentrations);
-        //make string out of populations list
         StringBuilder populationsStringBuilder = new StringBuilder();
-        populationsStringBuilder.append(wellPopulations.remove(0).toString());
+        populationsStringBuilder.append(populations[0].toString());
-        for(Integer i: wellPopulations){
+        for(int i = 1; i < populations.length; i++){
             populationsStringBuilder.append(", ");
-            populationsStringBuilder.append(i.toString());
+            populationsStringBuilder.append(populations[i].toString());
         }
         String wellPopulationsString = populationsStringBuilder.toString();
 

src/main/java/Simulator.java

@@ -1,4 +1,3 @@
-import org.jgrapht.Graph;
 import org.jgrapht.alg.interfaces.MatchingAlgorithm;
 import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
 import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
@@ -14,6 +13,8 @@ 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 {
     private static final int cdr3AlphaIndex = 0;
@@ -247,10 +248,16 @@ public class Simulator {
         BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
         //rate of pairing error
         double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
-        BigDecimal pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
+        BigDecimal pairingErrorRateTrunc;
-        //get list of well concentrations
+        if(pairingErrorRate == NaN || pairingErrorRate == POSITIVE_INFINITY || pairingErrorRate == NEGATIVE_INFINITY) {
-        Integer[] wellPopulations = data.getWellConcentrations();
+            pairingErrorRateTrunc = new BigDecimal(-1, mc);
-        //make string out of concentrations list
+        }
+        else{
+            pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, 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++){
@@ -270,8 +277,8 @@ public class Simulator {
         metadata.put("total betas found", betaCount.toString());
         metadata.put("high overlap threshold", highThreshold.toString());
         metadata.put("low overlap threshold", lowThreshold.toString());
-        metadata.put("maximum occupancy difference", maxOccupancyDifference.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));