Revert attempt to switch plate output format. It worked, but introduced a bug in graph filtering I don't want to chase down

src/main/java/PlateFileReader.java

@@ -31,54 +31,23 @@ public class PlateFileReader {
             BufferedReader reader = Files.newBufferedReader(Path.of(filename));
             CSVParser parser = new CSVParser(reader, plateFileFormat);
         ){
-            //old code for wells as rows
-//            for(CSVRecord record: parser.getRecords()) {
-//                List<Integer[]> well = new ArrayList<>();
-//                for(String s: record) {
-//                    if(!"".equals(s)) {
-//                        String[] intString = s.replaceAll("\\[", "")
-//                                .replaceAll("]", "")
-//                                .replaceAll(" ", "")
-//                                .split(",");
-//                        //System.out.println(intString);
-//                        Integer[] arr = new Integer[intString.length];
-//                        for (int i = 0; i < intString.length; i++) {
-//                            arr[i] = Integer.valueOf(intString[i]);
-//                        }
-//                        well.add(arr);
-//                    }
-//                }
-//                wells.add(well);
             for(CSVRecord record: parser.getRecords()) {
-                if (wells.size() == 0) {
-                    int num = 0;
-                    for (String s: record) {
-                        num++;
-                    }
-                    for (int i = 0; i < num; i++) {
-                        wells.add(new ArrayList<>());
-                    }
-                } else {
-                    int i = 0;
-                    for (String s : record) {
-                        if (!"".equals(s)) { //if value isn't the empty string
-                            //get rid of brackets, split at commas into a string array
-                            String[] intsAsStrings = s.replaceAll("\\[", "")
-                                    .replaceAll("]", "")
-                                    .replaceAll(" ", "")
-                                    .split(",");
-                            //Make Integer array with the same values
-                            Integer[] arr = new Integer[intsAsStrings.length];
-                            for (int j = 0; j < intsAsStrings.length; j++) {
-                                arr[j] = Integer.valueOf(intsAsStrings[j]);
-                            }
-                            //Add Integer array to the correct well
-                            wells.get(i).add(arr);
-                            i++;
+                List<Integer[]> well = new ArrayList<>();
+                for(String s: record) {
+                    if(!"".equals(s)) {
+                        String[] intString = s.replaceAll("\\[", "")
+                                .replaceAll("]", "")
+                                .replaceAll(" ", "")
+                                .split(",");
+                        //System.out.println(intString);
+                        Integer[] arr = new Integer[intString.length];
+                        for (int i = 0; i < intString.length; i++) {
+                            arr[i] = Integer.valueOf(intString[i]);
                         }
+                        well.add(arr);
                     }
-
                 }
+                wells.add(well);
             }
         } catch(IOException ex){
             System.out.println("plate file " + filename + " not found.");

src/main/java/PlateFileWriter.java

@@ -59,7 +59,7 @@ public class PlateFileWriter {
             }
         }
 
-        //this took forever, and I don't use it, because it makes reading data in a huge pain
+        //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){
@@ -89,6 +89,7 @@ public class PlateFileWriter {
             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);
             printer.printComment("Concentrations: " + concenString);

src/main/java/UserInterface.java

@@ -319,7 +319,6 @@ public class UserInterface {
         assert filename != null;
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
-        System.gc();
     }
 
 //    //for calling from command line
@@ -466,7 +465,6 @@ public class UserInterface {
             System.out.println("Writing Sample Plate to file");
             writer.writePlateFile();
             System.out.println("Sample Plate written to file: " + filename);
-            System.gc();
         }
     }
 
@@ -515,7 +513,6 @@ public class UserInterface {
             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();
         }
     }
 
@@ -570,7 +567,6 @@ public class UserInterface {
         System.out.println("Writing results to file");
         writer.writeResultsToFile();
         System.out.println("Results written to file: " + filename);
-        System.gc();
     }
 
     ///////