reimplement CLI (in progress)

src/main/java/CommandLineInterface.java

@@ -1,6 +1,45 @@
 import org.apache.commons.cli.*;
 
-//Class for parsing options passed to program from command line
+/*
+ * Class for parsing options passed to program from command line
+ *
+ * Top-level flags:
+ * cells : to make a cell sample file
+ * plate : to make a sample plate file
+ * graph : to make a graph and data file
+ * match : to do a cdr3 matching (WITH OR WITHOUT MAKING A RESULTS FILE. May just want to print summary for piping.)
+ *
+ * Cell flags:
+ * count : number of cells to generate
+ * diversity factor : factor by which CDR3s are more diverse than CDR1s
+ * output : name of the output file
+ *
+ * Plate flags:
+ * cellfile : name of the cell sample file to use as input
+ * wells : the number of wells on the plate
+ * dist : the statistical distribution to use
+ *      (if exponential) lambda : the lambda value of the exponential distribution
+ *      (if gaussian) stddev : the standard deviation of the gaussian distribution
+ * rand : randomize well populations, take a minimum argument and a maximum argument
+ * populations : number of t cells per well per section (number of arguments determines number of sections)
+ * dropout : plate dropout rate, double from 0.0 to 1.0
+ * output : name of the output file
+ *
+ * Graph flags:
+ * cellfile : name of the cell sample file to use as input
+ * platefile : name of the sample plate file to use as input
+ * output : name of the output file
+ *
+ * Match flags:
+ * graphFile : name of graph and data file to use as input
+ * min : minimum number of overlap wells to attempt a matching
+ * max : the maximum number of overlap wells to attempt a matching
+ * maxdiff : (optional) the maximum difference in occupancy to attempt a matching
+ * minpercent : (optional) the minimum percent overlap to attempt a matching.
+ * writefile : (optional) the filename to write results to
+ * output : the values to print to System.out for piping
+ *
+ */
 public class CommandLineInterface {
 
     public static void startCLI(String[] args) {
@@ -20,7 +59,7 @@ public class CommandLineInterface {
                 .longOpt("make-plates")
                 .desc("Makes a sample plate file")
                 .build();
-        Option makeGraph = Option.builder("graoh")
+        Option makeGraph = Option.builder("graph")
                 .longOpt("make-graph")
                 .desc("Makes a graph and data file")
                 .build();

src/main/java/InteractiveInterface.java

@@ -31,10 +31,10 @@ public class InteractiveInterface {
                 try {
                     input = sc.nextInt();
                     switch (input) {
-                        case 1 -> makeCellsInteractive();
+                        case 1 -> makeCells();
-                        case 2 -> makePlateInteractive();
+                        case 2 -> makePlate();
-                        case 3 -> makeCDR3GraphInteractive();
+                        case 3 -> makeCDR3Graph();
-                        case 4 -> matchCDR3sInteractive();
+                        case 4 -> matchCDR3s();
                         //case 6 -> matchCellsCDR1();
                         case 9 -> acknowledge();
                         case 0 -> quit = true;
@@ -48,7 +48,7 @@ public class InteractiveInterface {
             sc.close();
     }
 
-    private static void makeCellsInteractive() {
+    private static void makeCells() {
         String filename = null;
         Integer numCells = 0;
         Integer cdr1Freq = 1;
@@ -79,7 +79,7 @@ public class InteractiveInterface {
     }
 
     //Output a CSV of sample plate
-    private static void makePlateInteractive() {
+    private static void makePlate() {
         String cellFile = null;
         String filename = null;
         Double stdDev = 0.0;
@@ -192,7 +192,7 @@ public class InteractiveInterface {
     }
 
     //Output serialized binary of GraphAndMapData object
-    private static void makeCDR3GraphInteractive() {
+    private static void makeCDR3Graph() {
         String filename = null;
         String cellFile = null;
         String plateFile = null;
@@ -241,7 +241,7 @@ public class InteractiveInterface {
     }
 
     //Simulate matching and output CSV file of results
-    private static void matchCDR3sInteractive() throws IOException {
+    private static void matchCDR3s() throws IOException {
         String filename = null;
         String dataFilename = null;
         Integer lowThreshold = 0;

src/main/java/PlateFileWriter.java

@@ -16,7 +16,6 @@ public class PlateFileWriter {
     private Double error;
     private String filename;
     private String sourceFileName;
-    private String[] headers;
     private Integer[] concentrations;
     private boolean isExponential = false;
 
@@ -58,20 +57,21 @@ public class PlateFileWriter {
             }
         }
 
-        //this took forever and I don't use it
+//        //this took forever and I don't use it
-        List<List<String>> rows = new ArrayList<>();
+//        //if I wanted to use it, I'd replace printer.printRecords(wellsAsStrings) with printer.printRecords(rows)
-        List<String> tmp = new ArrayList<>();
+//        List<List<String>> rows = new ArrayList<>();
-        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
+//        List<String> tmp = new ArrayList<>();
-            tmp.add("well " + (i+1));
+//        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
-        }
+//            tmp.add("well " + (i+1));
-        rows.add(tmp);
+//        }
-        for(int row = 0; row < maxLength; row++){
+//        rows.add(tmp);
-            tmp = new ArrayList<>();
+//        for(int row = 0; row < maxLength; row++){
-            for(List<String> c: wellsAsStrings){
+//            tmp = new ArrayList<>();
-                tmp.add(c.get(row));
+//            for(List<String> c: wellsAsStrings){
-            }
+//                tmp.add(c.get(row));
-            rows.add(tmp);
+//            }
-        }
+//            rows.add(tmp);
+//        }
 
         //get list of well populations
         List<Integer> wellPopulations = Arrays.asList(concentrations);