Cleanup file output, add UI verbosity

readme.md

@@ -190,24 +190,28 @@ Example output:
 
 ---
 ```
-# T cell counts in sample plate wells: 5000
+# Source Sample Plate file: 4MilCellsPlate.csv
-# Total alphas found: 3387
+# Source Graph and Data file: 4MilCellsPlateGraph.ser
-# Total betas found: 3396
+# T cell counts in sample plate wells: 30000
+# Total alphas found: 11813
+# Total betas found: 11808
 # High overlap threshold: 94
 # Low overlap threshold: 3
 # Minimum overlap percent: 0
-# Maximum occupancy difference: 50
+# Maximum occupancy difference: 96
-# Pairing attempt rate: 0.488
+# Pairing attempt rate: 0.438
-# Correct pairings: 1650
+# Correct pairings: 5151
-# Incorrect pairings: 4
+# Incorrect pairings: 18
-# Pairing error rate: 0.00242
+# Pairing error rate: 0.00348
-# Simulation time: 19 seconds
+# Simulation time: 862 seconds
 ```
 
 | Alpha | Alpha well count | Beta | Beta well count | Overlap count | Matched Correctly? | P-value |
 |---|---|---|---|---|---|---|
-|716809|31|20739|34|31.0|TRUE|4.99E-25|
+|5242972|17|1571520|18|17|true|1.41E-18|
-|753685|28|733213|27|27.0|TRUE|5.26E-23|
+|5161027|18|2072219|18|18|true|7.31E-20|
+|4145198|33|1064455|30|29|true|2.65E-21|
+|7700582|18|112748|18|18|true|7.31E-20|
 |...|...|...|...|...|...|...|
 
 ---

src/main/java/PlateFileWriter.java

@@ -73,6 +73,7 @@ public class PlateFileWriter {
             }
             rows.add(tmp);
         }
+        //build string of well concentrations
         StringBuilder concen = new StringBuilder();
         for(Integer i: concentrations){
             concen.append(i.toString());
@@ -80,7 +81,9 @@ public class PlateFileWriter {
         }
         String concenString = concen.toString();
 
-        CSVFormat plateFileFormat = CSVFormat.Builder.create().setCommentMarker('#').build();
+        CSVFormat plateFileFormat = CSVFormat.Builder.create()
+                .setCommentMarker('#')
+                .build();
 
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
             CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
@@ -96,7 +99,7 @@ public class PlateFileWriter {
             else {
                 printer.printComment("Std. dev.: " + stdDev);
             }
-            printer.printRecords(wellsAsStrings);
+            printer.printRecords(rows);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);
             System.err.println(ex);

src/main/java/Simulator.java

@@ -138,9 +138,9 @@ public class Simulator {
     }
 
     //match CDR3s.
-    public static MatchingResult matchCDR3s(GraphWithMapData data, Integer lowThreshold, Integer highThreshold,
+    public static MatchingResult matchCDR3s(GraphWithMapData data, String dataFilename, Integer lowThreshold,
-                                            Integer maxOccupancyDifference, Integer minOverlapPercent,
+                                            Integer highThreshold, Integer maxOccupancyDifference,
-                                            boolean verbose) {
+                                            Integer minOverlapPercent, boolean verbose) {
         Instant start = Instant.now();
         int numWells = data.getNumWells();
         Integer alphaCount = data.getAlphaCount();
@@ -250,6 +250,8 @@ public class Simulator {
         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);

src/main/java/UserInterface.java

@@ -256,7 +256,7 @@ public class UserInterface {
 //        }
 //        else {
             while (!quit) {
-                System.out.println("");
+                System.out.println();
                 System.out.println("--------BiGPairSEQ SIMULATOR--------");
                 System.out.println("ALPHA/BETA T-CELL RECEPTOR MATCHING");
                 System.out.println("  USING WEIGHTED BIPARTITE GRAPHS  ");
@@ -316,6 +316,7 @@ public class UserInterface {
             sc.next();
         }
         CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
+        assert filename != null;
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
     }
@@ -361,7 +362,7 @@ public class UserInterface {
         String filename = null;
         Double stdDev = 0.0;
         Integer numWells = 0;
-        Integer numSections = 0;
+        Integer numSections;
         Integer[] concentrations = {1};
         Double dropOutRate = 0.0;
         boolean poisson = false;
@@ -389,30 +390,29 @@ public class UserInterface {
             System.out.println("(Note: wider distributions are more memory intensive to match)");
             System.out.print("Enter selection value: ");
             input = sc.nextInt();
-            switch(input) {
+            switch (input) {
-                case 1:
+                case 1 -> poisson = true;
-                    poisson = true;
+                case 2 -> {
-                    break;
-                case 2:
                     System.out.println("How many distinct T-cells within one standard deviation of peak frequency?");
                     System.out.println("(Note: wider distributions are more memory intensive to match)");
                     stdDev = sc.nextDouble();
-                    if(stdDev <= 0.0){
+                    if (stdDev <= 0.0) {
                         throw new InputMismatchException("Value must be positive.");
                     }
-                    break;
+                }
-                case 3:
+                case 3 -> {
                     exponential = true;
                     System.out.println("Please enter lambda value for exponential distribution.");
                     lambda = sc.nextDouble();
-                    if(lambda <= 0.0){
+                    if (lambda <= 0.0) {
                         throw new InputMismatchException("Value must be positive.");
                     }
-                    break;
+                }
-                default:
+                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){
@@ -445,6 +445,8 @@ public class UserInterface {
             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);
@@ -458,8 +460,11 @@ public class UserInterface {
             }
             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);
         }
     }
 
@@ -484,7 +489,11 @@ public class UserInterface {
             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){
@@ -496,20 +505,21 @@ public class UserInterface {
             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);
         }
     }
 
     //Simulate matching and output CSV file of results
     private static void matchCDR3s() throws IOException {
         String filename = null;
-        String dataFile = null;
+        String dataFilename = null;
         Integer lowThreshold = 0;
         Integer highThreshold = Integer.MAX_VALUE;
         Integer maxOccupancyDiff = Integer.MAX_VALUE;
@@ -517,7 +527,7 @@ public class UserInterface {
         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: ");
-            dataFile = sc.next();
+            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();
@@ -543,17 +553,20 @@ public class UserInterface {
         //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");
-        GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFile);
+        assert dataFilename != null;
+        GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFilename);
         GraphWithMapData data = dataReader.getData();
         //set source file name
-        data.setSourceFilename(dataFile);
+        data.setSourceFilename(dataFilename);
         //simulate matching
-        MatchingResult results = Simulator.matchCDR3s(data, lowThreshold, highThreshold, maxOccupancyDiff,
+        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);
     }
 
     ///////
@@ -663,7 +676,7 @@ public class UserInterface {
     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();
         System.out.println("Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and compares");
         System.out.println("against a null distribution, BiGpairSEQ does not do any statistical calculations");
         System.out.println("directly. Instead, BiGpairSEQ creates a simple bipartite weighted graph representing");
@@ -674,12 +687,14 @@ public class UserInterface {
         System.out.println("pattern.) The problem of pairing TCRA/TCRB sequences thus reduces to the \"assignment");
         System.out.println("problem\" of finding a maximum weight matching on a bipartite graph--the subset of");
         System.out.println("vertex-disjoint edges whose weights sum to the maximum possible value.");
-        System.out.println("");
+        System.out.println();
+        System.out.println("For full documentation, see: https://gitea.ejsf.synology.me/efischer/BiGpairSEQ");
+        System.out.println();
         System.out.println("pairSEQ citation:");
         System.out.println("Howie, B., Sherwood, A. M., et. al.");
         System.out.println("High-throughput pairing of T cell receptor alpha and beta sequences.");
         System.out.println("Sci. Transl. Med. 7, 301ra131 (2015)");
-        System.out.println("");
+        System.out.println();
-        System.out.println("Simulation by Eugene Fischer, 2021-2022");
+        System.out.println("BiGpairSEQ_Sim by Eugene Fischer, 2021-2022");
     }
 }