Add flag to print metadata to stdout

src/main/java/CommandLineInterface.java

@@ -153,17 +153,24 @@ 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 +180,17 @@ public class CommandLineInterface {
                 GraphWithMapData graph = getGraph(graphFilename);
                 MatchingResult result = Simulator.matchCDR3s(graph, graphFilename, minThreshold, maxThreshold,
                         maxOccupancyDiff, minOverlapPct, false);
-                MatchingFileWriter writer = new MatchingFileWriter(outputFilename, result);
-                writer.writeResultsToFile();
+                if(outputFilename != null){
+                    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) {
@@ -297,7 +311,7 @@ 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 +340,22 @@ 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 +393,36 @@ public class CommandLineInterface {
                 .hasArg()
                 .argName("number")
                 .build();
-        matchCDR3options.addOption(graphFilename);
-        matchCDR3options.addOption(minOccupancyOverlap);
-        matchCDR3options.addOption(maxOccupancyOverlap);
-        matchCDR3options.addOption(minOverlapPercent);
-        matchCDR3options.addOption(maxOccupancyDifference);
-        matchCDR3options.addOption(outputFileOption());
-        //options for output to System.out
-       //Option printPairingErrorRate = Option.builder()
+        Option outputFile = Option.builder("o") //can't call the method this time, because this one's optional
+                .longOpt("output-file")
+                .hasArg()
+                .argName("filename")
+                .desc("(Optional) Name of output the output file. If not present, no file will be written.")
+                .build();
+        matchCDR3options.addOption(graphFilename)
+                .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 all metadata to stdout").build();
+       matchCDR3options
+//               .addOption(printErrorRate)
+//               .addOption(printAttempt)
+//               .addOption(printCorrect)
+//               .addOption(printIncorrect)
+               .addOption(printMetadata);
         return matchCDR3options;
     }
 

src/main/java/GraphDataObjectReader.java

@@ -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");
-            System.out.println("File I/O time is not included in results");
+            if (this.verbose) {
+                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();