Added metadata to MatchingResult to enable CLI options

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;
@@ -18,7 +17,7 @@ public class PlateFileWriter {
     private String filename;
     private String sourceFileName;
     private String[] headers;
-    private List<Integer> concentrations;
+    private Integer[] concentrations;
     private boolean isExponential = false;
 
     public PlateFileWriter(String filename, Plate plate) {
@@ -37,8 +36,8 @@ public class PlateFileWriter {
         }
         this.error = plate.getError();
         this.wells = plate.getWells();
-        this.concentrations = Arrays.asList(plate.getConcentrations());
-        concentrations.sort(Comparator.reverseOrder());
+        this.concentrations = plate.getPopulations();
+        Arrays.sort(concentrations);
     }
 
     public void writePlateFile(){
@@ -59,7 +58,7 @@ public class PlateFileWriter {
             }
         }
 
-        //this took forever
+        //this took forever and I don't use it
         List<List<String>> rows = new ArrayList<>();
         List<String> tmp = new ArrayList<>();
         for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
@@ -73,14 +72,19 @@ public class PlateFileWriter {
             }
             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();
 
+        //get list of well populations
+        List<Integer> wellPopulations = Arrays.asList(concentrations);
+        //make string out of populations list
+        StringBuilder populationsStringBuilder = new StringBuilder();
+        populationsStringBuilder.append(wellPopulations.remove(0).toString());
+        for(Integer i: wellPopulations){
+            populationsStringBuilder.append(", ");
+            populationsStringBuilder.append(i.toString());
+        }
+        String wellPopulationsString = populationsStringBuilder.toString();
+
+        //set CSV format
         CSVFormat plateFileFormat = CSVFormat.Builder.create()
                 .setCommentMarker('#')
                 .build();
@@ -92,7 +96,7 @@ 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);
             }