Recording source file names in output files, allowing output of intermediate results

src/main/java/CellFileReader.java

@@ -11,17 +11,19 @@ import java.util.List;
 
 public class CellFileReader {
 
+    private String filename;
     private List<Integer[]> distinctCells = new ArrayList<>();
 
     public CellFileReader(String filename) {
-
         if(!filename.matches(".*\\.csv")){
             filename = filename + ".csv";
         }
+        this.filename = filename;
 
         CSVFormat cellFileFormat = CSVFormat.Builder.create()
                 .setHeader("Alpha CDR3", "Beta CDR3", "Alpha CDR1", "Beta CDR1")
                 .setSkipHeaderRecord(true)
+                .setCommentMarker('#')
                 .build();
 
         try(//don't need to close reader bc of try-with-resources auto-closing
@@ -42,6 +44,8 @@ public class CellFileReader {
         }
     }
 
+    public String getFilename() { return filename;}
+
     public List<Integer[]> getCells(){
         return distinctCells;
     }

src/main/java/MatchingFileWriter.java

@@ -12,18 +12,20 @@ import java.util.List;
 public class MatchingFileWriter {
 
     private String filename;
+    private String sourceFileName;
     private List<String> comments;
     private List<String> headers;
-    private List<List<String>> results;
+    private List<List<String>> allResults;
 
-    public MatchingFileWriter(String filename, List<String> comments, List<String> headers, List<List<String>> results){
+    public MatchingFileWriter(String filename, MatchingResult result){
         if(!filename.matches(".*\\.csv")){
             filename = filename + ".csv";
         }
         this.filename = filename;
-        this.comments = comments;
+        this.sourceFileName = result.getSourceFileName();
-        this.headers = headers;
+        this.comments = result.getComments();
-        this.results = results;
+        this.headers = result.getHeaders();
+        this.allResults = result.getAllResults();
     }
 
     public void writeResultsToFile(){
@@ -41,8 +43,8 @@ public class MatchingFileWriter {
             for(String comment: comments){
                 printer.printComment(comment);
             }
-            results.add(0, headers);
+            allResults.add(0, headers);
-            printer.printRecords(results);
+            printer.printRecords(allResults);
 
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);

src/main/java/MatchingResult.java

@@ -3,13 +3,15 @@ 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(List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap, 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;
         this.headers = headers;
         this.allResults = allResults;
@@ -37,4 +39,8 @@ public class MatchingResult {
     public Duration getTime() {
         return time;
     }
+
+    public String getSourceFileName() {
+        return sourceFile;
+    }
 }

src/main/java/Plate.java

@@ -5,6 +5,7 @@ TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
 public class Plate {
+    private String sourceFile;
     private List<List<Integer[]>> wells;
     private Random rand = new Random();
     private int size;
@@ -12,6 +13,7 @@ public class Plate {
     private Integer[] concentrations;
     private double stdDev;
 
+
     public Plate (int size, double error, Integer[] concentrations, double stdDev) {
         this.size = size;
         this.error = error;
@@ -20,12 +22,14 @@ public class Plate {
         wells = new ArrayList<>();
     }
 
-    public Plate(List<List<Integer[]>> wells){
+    public Plate(String sourceFileName, List<List<Integer[]>> wells){
+        this.sourceFile = sourceFileName;
         this.wells = wells;
         this.size = wells.size();
     }
 
-    public void fillWells(List<Integer[]> cells) {
+    public void fillWells(String sourceFileName, List<Integer[]> cells) {
+        sourceFile = sourceFileName;
         int numSections = concentrations.length;
         int section = 0;
         double m;
@@ -100,4 +104,8 @@ public class Plate {
             }
         }
     }
+
+    public String getSourceFileName() {
+        return sourceFile;
+    }
 }

src/main/java/PlateFileReader.java

@@ -14,12 +14,14 @@ import java.util.regex.Pattern;
 public class PlateFileReader {
 
     private List<List<Integer[]>> wells = new ArrayList<>();
+    private String filename;
 
     public PlateFileReader(String filename){
 
         if(!filename.matches(".*\\.csv")){
             filename = filename + ".csv";
         }
+        this.filename = filename;
 
         CSVFormat plateFileFormat = CSVFormat.Builder.create()
                 .setCommentMarker('#')
@@ -58,4 +60,7 @@ public class PlateFileReader {
         return wells;
     }
 
+    public String getFilename() {
+        return filename;
+    }
 }

src/main/java/PlateFileWriter.java

@@ -15,6 +15,7 @@ public class PlateFileWriter {
     private double stdDev;
     private Double error;
     private String filename;
+    private String sourceFileName;
     private String[] headers;
     private List<Integer> concentrations;
 
@@ -23,6 +24,7 @@ public class PlateFileWriter {
             filename = filename + ".csv";
         }
         this.filename = filename;
+        this.sourceFileName = plate.getSourceFileName();
         this.size = plate.getSize();
         this.stdDev = plate.getStdDev();
         this.error = plate.getError();
@@ -32,10 +34,6 @@ public class PlateFileWriter {
     }
 
     public void writePlateFile(){
-        //works as is, but too many columns in csv, need to make them all rows.
-
-        //will now redo it so that every column is a well, with well names as headers
-        //need to give plate error, sample pop size, stdDev, num sections, concentration per section as comments
         Comparator<List<Integer[]>> listLengthDescending = Comparator.comparingInt(List::size);
         wells.sort(listLengthDescending.reversed());
         int maxLength = wells.get(0).size();
@@ -79,6 +77,7 @@ public class PlateFileWriter {
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
             CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
         ){
+            printer.printComment("Cell source file name: " + sourceFileName);
             printer.printComment("Each row represents one well on the plate.");
             printer.printComment("Plate size: " + size);
             printer.printComment("Error rate: " + error);

src/main/java/Simulator.java

@@ -213,7 +213,7 @@ public class Simulator {
             System.out.println(s);
         }
 
-        return new MatchingResult(comments, header, allResults, matchMap, time);
+        return new MatchingResult(samplePlate.getSourceFileName(), comments, header, allResults, matchMap, time);
     }
 
     //Simulated matching of CDR1s to CDR3s. Requires MatchingResult from prior run of matchCDR3s.
@@ -466,7 +466,8 @@ public class Simulator {
         headers.add("second matched CDR1");
         headers.add("Correct match?");
 
-        MatchingResult firstTest = new MatchingResult(comments, headers, allResults, dualMatchesMap, time);
+        MatchingResult firstTest = new MatchingResult(samplePlate.getSourceFileName(),
+                comments, headers, allResults, dualMatchesMap, time);
 
         //results for dual map
         System.out.println("RESULTS FOR SECOND PASS MATCHING");
@@ -515,7 +516,8 @@ public class Simulator {
         }
 
         System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-        MatchingResult dualTest = new MatchingResult(comments, headers, allResults, dualMatchesMap, time);
+        MatchingResult dualTest = new MatchingResult(samplePlate.getSourceFileName(), comments, headers,
+                allResults, dualMatchesMap, time);
         MatchingResult[] output = {firstTest, dualTest};
         return output;
     }

src/main/java/UserInterface.java

@@ -1,6 +1,8 @@
 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 {
@@ -142,7 +144,7 @@ public class UserInterface {
             stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
         }
         Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
-        samplePlate.fillWells(cellReader.getCells());
+        samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells());
         PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
         writer.writePlateFile();
     }
@@ -175,7 +177,7 @@ public class UserInterface {
         }
         CellFileReader cellReader = new CellFileReader(cellFile);
         PlateFileReader plateReader = new PlateFileReader(plateFile);
-        Plate plate = new Plate(plateReader.getWells());
+        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.");
@@ -192,8 +194,7 @@ public class UserInterface {
             List<Integer[]> cells = cellReader.getCells();
             MatchingResult results = Simulator.matchCDR3s(cells, plate, lowThreshold, highThreshold);
             //result writer
-            MatchingFileWriter writer = new MatchingFileWriter(filename, results.getComments(),
+            MatchingFileWriter writer = new MatchingFileWriter(filename, results);
-                    results.getHeaders(), results.getAllResults());
             writer.writeResultsToFile();
         }
     }
@@ -205,12 +206,14 @@ public class UserInterface {
     match
      */
         String filename = null;
+        String preliminaryResultsFilename = null;
         String cellFile = null;
         String plateFile = null;
         Integer lowThresholdCDR3 = 0;
         Integer highThresholdCDR3 = Integer.MAX_VALUE;
         Integer lowThresholdCDR1 = 0;
         Integer highThresholdCDR1 = Integer.MAX_VALUE;
+        boolean outputCDR3Matches = false;
         try {
             System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
             System.out.print("Please enter name of an existing cell sample file: ");
@@ -234,13 +237,28 @@ public class UserInterface {
             }
             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.getWells());
+        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.");
@@ -261,14 +279,14 @@ public class UserInterface {
             MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3);
             MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
                     highThresholdCDR1, preliminaryResults);
-
+            MatchingFileWriter writer = new MatchingFileWriter(filename + "_FirstPass", results[0]);
-            //result writer
-            MatchingFileWriter writer = new MatchingFileWriter(filename + "First", results[0].getComments(),
-                    results[0].getHeaders(), results[0].getAllResults());
             writer.writeResultsToFile();
-            writer = new MatchingFileWriter(filename + "Dual", results[1].getComments(),
+            writer = new MatchingFileWriter(filename + "_SecondPass", results[1]);
-                    results[1].getHeaders(), results[1].getAllResults());
             writer.writeResultsToFile();
+            if(outputCDR3Matches){
+                writer = new MatchingFileWriter(preliminaryResultsFilename, preliminaryResults);
+                writer.writeResultsToFile();
+            }
         }
     }