clarify help menu text

readme.md

@@ -20,8 +20,8 @@ The problem of pairing TCRA/TCRB sequences thus reduces to the "assignment probl
 matching on a bipartite graph--the subset of vertex-disjoint edges whose weights sum to the maximum possible value.
 
 This is a well-studied combinatorial optimization problem, with many known solutions.
-The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral weights
+The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral
-is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 
+weights is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N, 
 their algorithm runs in **O(m sqrt(n) log(N))** time. As the graph representation of a pairSEQ experiment is 
 bipartite with integer weights, this algorithm is ideal for BiGpairSEQ.
 
@@ -43,13 +43,13 @@ Run with the command:
 `java -jar BiGpairSEQ_Sim.jar`
 
 Processing sample plates with tens of thousands of sequences may require large amounts 
-of RAM. It is often desirable to increase the JVM maximum heap allocation with the -Xmx flag.
+of RAM. It is often desirable to increase the JVM maximum heap allocation with the `-Xmx` flag.
 For example, to run the program with 32 gigabytes of memory, use the command:
 
 `java -Xmx32G -jar BiGpairSEQ_Sim.jar`
 
 There are a number of command line options, to allow the program to be used in shell scripts. For a full list,
-use the -help flag:
+use the `-help` flag:
 
 `java -jar BiGpairSEQ_Sim.jar -help`
 
@@ -108,7 +108,7 @@ device-specific.)
 
 The program's caching behavior can be controlled in the Options menu. By default, all caching is OFF.
 
-The program can optionally output Graph/Data files in .GraphML format (.graphml) for data portability. This can be 
+The program can optionally output Graph/Data files in GraphML format (.graphml) for data portability. This can be 
 turned on in the Options menu. By default, GraphML output is OFF.
 
 ---
@@ -203,8 +203,13 @@ Options for creating a Graph/Data file:
 
 These files do not have a human-readable structure, and are not portable to other programs.
 
-(For portability to other software, turn on GraphML output in the Options menu. This will produce a .graphml file
+*Optional GraphML output*
-for the weighted graph, with vertex attributes sequence, type, and occupancy data.)
+
+For portability of graph data to other software, turn on [GraphML](http://graphml.graphdrawing.org/index.html) output 
+in the Options menu in interactive mode, or use the `-graphml`command line argument. This will produce a .graphml file 
+for the weighted graph, with vertex attributes for sequence, type, and occupancy data. This graph contains all the data 
+necessary for the BiGpairSEQ matching algorithm. It does not include the data to measure pairing accuracy; for that, 
+compare the matching results to the original Cell Sample .csv file.
 
 ---
 

src/main/java/BiGpairSEQ.java

@@ -16,6 +16,7 @@ public class BiGpairSEQ {
     private static String priorityQueueHeapType = "FIBONACCI";
     private static boolean outputBinary = true;
     private static boolean outputGraphML = false;
+    private static final String version = "version 2.0";
 
     public static void main(String[] args) {
         if (args.length == 0) {
@@ -172,5 +173,5 @@ public class BiGpairSEQ {
 
     public static boolean outputGraphML() {return outputGraphML;}
     public static void setOutputGraphML(boolean b) {outputGraphML = b;}
-
+    public static String getVersion() { return version; }
 }

src/main/java/CommandLineInterface.java

@@ -62,15 +62,18 @@ public class CommandLineInterface {
 
             if (line.hasOption("help")) {
                 HelpFormatter formatter = new HelpFormatter();
-                formatter.printHelp("BiGpairSEQ_Sim", mainOptions);
+                formatter.printHelp("BiGpairSEQ_Sim.jar", mainOptions);
                 System.out.println();
-                formatter.printHelp("BiGpairSEQ_SIM -cells", cellOptions);
+                formatter.printHelp("BiGpairSEQ_Sim.jar -cells", cellOptions);
                 System.out.println();
-                formatter.printHelp("BiGpairSEQ_Sim -plate", plateOptions);
+                formatter.printHelp("BiGpairSEQ_Sim.jar -plate", plateOptions);
                 System.out.println();
-                formatter.printHelp("BiGpairSEQ_Sim -graph", graphOptions);
+                formatter.printHelp("BiGpairSEQ_Sim.jar -graph", graphOptions);
                 System.out.println();
-                formatter.printHelp("BiGpairSEQ_Sim -match", matchOptions);
+                formatter.printHelp("BiGpairSEQ_Sim.jar -match", matchOptions);
+            }
+            else if (line.hasOption("version")) {
+                System.out.println("BiGpairSEQ_Sim " + BiGpairSEQ.getVersion());
             }
             else if (line.hasOption("cells")) {
                 line = parser.parse(cellOptions, Arrays.copyOfRange(args, 1, args.length));
@@ -153,17 +156,24 @@ public class CommandLineInterface {
             else if (line.hasOption("match")) { //can add a flag for which match type in future, spit this in two
                 line = parser.parse(matchOptions, Arrays.copyOfRange(args, 1, args.length));
                 String graphFilename = line.getOptionValue("g");
-                String outputFilename = line.getOptionValue("o");
+
+                String outputFilename;
+                if(line.hasOption("o")) {
+                    outputFilename = line.getOptionValue("o");
+                }
+                else {
+                    outputFilename = null;
+                }
                 Integer minThreshold = Integer.parseInt(line.getOptionValue("min"));
                 Integer maxThreshold = Integer.parseInt(line.getOptionValue("max"));
-                Integer minOverlapPct;
+                int minOverlapPct;
                 if (line.hasOption("minpct")) { //see if this filter is being used
                     minOverlapPct = Integer.parseInt(line.getOptionValue("minpct"));
                 }
                 else {
                     minOverlapPct = 0;
                 }
-                Integer maxOccupancyDiff;
+                int maxOccupancyDiff;
                 if (line.hasOption("maxdiff")) { //see if this filter is being used
                     maxOccupancyDiff = Integer.parseInt(line.getOptionValue("maxdiff"));
                 }
@@ -173,10 +183,17 @@ public class CommandLineInterface {
                 GraphWithMapData graph = getGraph(graphFilename);
                 MatchingResult result = Simulator.matchCDR3s(graph, graphFilename, minThreshold, maxThreshold,
                         maxOccupancyDiff, minOverlapPct, false);
-                MatchingFileWriter writer = new MatchingFileWriter(outputFilename, result);
+                if(outputFilename != null){
-                writer.writeResultsToFile();
+                    MatchingFileWriter writer = new MatchingFileWriter(outputFilename, result);
+                    writer.writeResultsToFile();
+                }
                 //can put a bunch of ifs for outputting various things from the MatchingResult to System.out here
                 //after I put those flags in the matchOptions
+                if(line.hasOption("print-metadata")) {
+                    for (String k : result.getMetadata().keySet()) {
+                        System.out.println(k + ": " + result.getMetadata().get(k));
+                    }
+                }
             }
         }
         catch (ParseException exp) {
@@ -216,8 +233,11 @@ public class CommandLineInterface {
                 .longOpt("match-cdr3")
                 .desc("Matches CDR3s. Requires a graph/data file.")
                 .build();
+        Option printVersion = Option.builder("version")
+                .desc("Prints the program version number to stdout").build();
         OptionGroup mainGroup = new OptionGroup();
         mainGroup.addOption(help);
+        mainGroup.addOption(printVersion);
         mainGroup.addOption(makeCells);
         mainGroup.addOption(makePlate);
         mainGroup.addOption(makeGraph);
@@ -297,7 +317,7 @@ public class CommandLineInterface {
                 .desc("Randomize well populations on sample plate. Takes two arguments: the minimum possible population and the maximum possible population.")
                 .hasArgs()
                 .numberOfArgs(2)
-                .argName("minimum maximum")
+                .argName("min> <max")
                 .build();
         Option specificWellPopulations = Option.builder("pop")
                 .desc("The well populations for each section of the sample plate. There will be as many sections as there are populations given.")
@@ -326,22 +346,22 @@ public class CommandLineInterface {
         Options graphOptions = new Options();
         Option cellFilename = Option.builder("c")
                 .longOpt("cell-file")
-                .desc("Cell sample file to use for checking accuracy")
+                .desc("Cell sample file to use for checking pairing accuracy")
                 .hasArg()
                 .argName("filename")
                 .required().build();
         Option plateFilename = Option.builder("p")
                 .longOpt("plate-filename")
-                .desc("Sample plate file (made from given cell sample file) to construct graph from")
+                .desc("Sample plate file from which to construct graph")
                 .hasArg()
                 .argName("filename")
                 .required().build();
         Option outputGraphML = Option.builder("graphml")
-                .desc("Output GraphML file")
+                .desc("(Optional) Output GraphML file")
                 .build();
         Option outputSerializedBinary = Option.builder("nb")
                 .longOpt("no-binary")
-                .desc("Don't output serialized binary file")
+                .desc("(Optional) Don't output serialized binary file")
                 .build();
         graphOptions.addOption(cellFilename);
         graphOptions.addOption(plateFilename);
@@ -379,15 +399,36 @@ public class CommandLineInterface {
                 .hasArg()
                 .argName("number")
                 .build();
-        matchCDR3options.addOption(graphFilename);
+        Option outputFile = Option.builder("o") //can't call the method this time, because this one's optional
-        matchCDR3options.addOption(minOccupancyOverlap);
+                .longOpt("output-file")
-        matchCDR3options.addOption(maxOccupancyOverlap);
+                .hasArg()
-        matchCDR3options.addOption(minOverlapPercent);
+                .argName("filename")
-        matchCDR3options.addOption(maxOccupancyDifference);
+                .desc("(Optional) Name of output the output file. If not present, no file will be written.")
-        matchCDR3options.addOption(outputFileOption());
+                .build();
-        //options for output to System.out
+        matchCDR3options.addOption(graphFilename)
-       //Option printPairingErrorRate = Option.builder()
+                .addOption(minOccupancyOverlap)
+                .addOption(maxOccupancyOverlap)
+                .addOption(minOverlapPercent)
+                .addOption(maxOccupancyDifference)
+                .addOption(outputFile);
 
+        //options for output to System.out
+//       Option printErrorRate = Option.builder().longOpt("print-error")
+//               .desc("(Optional) Print the pairing error rate to stdout").build();
+//       Option printAttempt = Option.builder().longOpt("print-attempt")
+//               .desc("(Optional) Print the pairing attempt rate to stdout").build();
+//       Option printCorrect = Option.builder().longOpt("print-correct")
+//               .desc("(Optional) Print the number of correct pairs to stdout").build();
+//       Option printIncorrect = Option.builder().longOpt("print-incorrect")
+//               .desc("(Optional) Print the number of incorrect pairs to stdout").build();
+       Option printMetadata = Option.builder().longOpt("print-metadata")
+                       .desc("(Optional) Print summary of matching results to stdout.").build();
+       matchCDR3options
+//               .addOption(printErrorRate)
+//               .addOption(printAttempt)
+//               .addOption(printCorrect)
+//               .addOption(printIncorrect)
+               .addOption(printMetadata);
         return matchCDR3options;
     }
 

src/main/java/GraphDataObjectReader.java

@@ -4,7 +4,7 @@ public class GraphDataObjectReader {
 
     private GraphWithMapData data;
     private String filename;
-    private boolean verbose = true;
+
 
     public GraphDataObjectReader(String filename, boolean verbose) throws IOException {
         if(!filename.matches(".*\\.ser")){
@@ -15,8 +15,10 @@ public class GraphDataObjectReader {
             BufferedInputStream fileIn = new BufferedInputStream(new FileInputStream(filename));
                 ObjectInputStream in = new ObjectInputStream(fileIn))
         {
-            System.out.println("Reading graph data from file. This may take some time");
+            if (verbose) {
-            System.out.println("File I/O time is not included in results");
+                System.out.println("Reading graph data from file. This may take some time");
+                System.out.println("File I/O time is not included in results");
+            }
             data = (GraphWithMapData) in.readObject();
         } catch (FileNotFoundException | ClassNotFoundException ex) {
             ex.printStackTrace();

src/main/java/InteractiveInterface.java

@@ -570,6 +570,8 @@ public class InteractiveInterface {
     }
 
     private static void acknowledge(){
+        System.out.println("BiGpairSEQ_Sim " + BiGpairSEQ.getVersion());
+        System.out.println();
         System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
         System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
         System.out.println();

src/main/java/Simulator.java

@@ -245,11 +245,11 @@ public class Simulator implements GraphModificationFunctions {
         //rate of pairing error
         double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
         BigDecimal pairingErrorRateTrunc;
-        if(pairingErrorRate == NaN || pairingErrorRate == POSITIVE_INFINITY || pairingErrorRate == NEGATIVE_INFINITY) {
+        if(Double.isFinite(pairingErrorRate)) {
-            pairingErrorRateTrunc = new BigDecimal(-1, mc);
+            pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
         }
         else{
-            pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
+            pairingErrorRateTrunc = new BigDecimal(-1, mc);
         }
         //get list of well populations
         Integer[] wellPopulations = data.getWellPopulations();