Change plate reader/writer to use columns as wells

src/main/java/PlateFileReader.java

@@ -54,19 +54,16 @@ public class PlateFileReader {
                 if (record.hasComment()) {
                     continue;
                 }
-//                if (wells.size() == 0) {
-//                    int num = 0;
-//                    for (String s: record) {
-//                        num++;
-//                    }
-//                    for (int i = 0; i < num; i++) {
-//                        wells.add(new ArrayList<>());
-//                    }
-                if(wellNamesRecord){
-                    wellNamesRecord = false;
-                    continue;
+                if (wells.size() == 0) {
+                    int num = 0;
+                    for (String s: record) {
+                        num++;
+                    }
+                    for (int i = 0; i < num; i++) {
+                        wells.add(new ArrayList<>());
+                    }
                 } else {
-                    List<Integer[]> well = new ArrayList<>();
+                    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
@@ -79,10 +76,12 @@ public class PlateFileReader {
                             for (int j = 0; j < intsAsStrings.length; j++) {
                                 arr[j] = Integer.valueOf(intsAsStrings[j]);
                             }
-                            well.add(arr);
+                            //Add Integer array to the correct well
+                            wells.get(i).add(arr);
+                            i++;
                         }
                     }
-                    wells.add(well);
+
                 }
             }
         } catch(IOException ex){

src/main/java/PlateFileWriter.java

@@ -99,7 +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);