code: public static void main(String[] args) throws FileParsingException {
      if (args.length == 0)
        System.err.println("Supply arguments that are paths to pepxml files");
      List<Path> paths = Arrays.stream(args).map(s -> Paths.get(s)).collect(Collectors.toList());
      if (paths.stream().anyMatch(p -> !Files.exists(p)))
        System.err.println("Not all input files exist");
  
      for (Path p : paths) {
        System.out.println("\nParsing: " + p.toString());
        MsmsPipelineAnalysis pepxml = PepXmlParser.parse(p);
        int sum = pepxml.getMsmsRunSummary().stream()
            .flatMapToInt(msmsRunSummary -> msmsRunSummary.getSpectrumQuery().stream()
                .flatMapToInt(spectrumQuery -> spectrumQuery.getSearchResult().stream()
                    .mapToInt(value -> value.getSearchHit().size()))
            ).sum();
        System.out.printf("Done, found %d PSMs\n", sum);
      }
    }
docs: This entry point may be used to test if JAXB is functioning properly after all
  the java packaging and minification.<br/>
  To run use `java -cp path-to.jar umich.ms.fileio.filetypes.pepxml.PepXmlParser`.<br/>
  @param args List of existing filesystem paths.