Examples with DateGuesser dr.app.beauti.options.DateGuesser used on opensource projects

Example 1 with DateGuesser

use of dr.app.beauti.options.DateGuesser in project beast-mcmc by beast-dev.

the class BEASTGen method main.

public static void main(String[] args) {
    // There is a major issue with languages that use the comma as a decimal separator.
    // To ensure compatibility between programs in the package, enforce the US locale.
    Locale.setDefault(Locale.US);
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.IntegerOption("date_order", "The order of the date field (negative numbers from last)"), new Arguments.StringOption("date_prefix", "prefix", "A string that is the prefix to the date field"), new Arguments.StringOption("date_regex", "regex", "A string that gives the regular expression to match the date"), new Arguments.StringOption("date_format", "format", "A string that gives the date format for parsing"), new Arguments.Option("date_precision", "Specifies the date is a variable precision yyyy-MM-dd format"), new Arguments.StringOption("tree", "tree-file-name", "Read a tree from a file"), new Arguments.StringOption("D", "\"key=value,key=value...\"", "Properties for exchange in templates"), new Arguments.Option("version", "Print the version and credits and stop"), new Arguments.Option("help", "Print this information and stop") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        printTitle();
        System.out.println();
        System.out.println(ae.getMessage());
        System.out.println();
        printUsage(arguments);
        System.exit(1);
    }
    DateGuesser guesser = new DateGuesser();
    if (arguments.hasOption("date_order")) {
        guesser.guessDates = true;
        int order = arguments.getIntegerOption("date_order");
        if (order < 0) {
            guesser.order = 1 + order;
            guesser.fromLast = true;
        } else if (order > 0) {
            guesser.order = order - 1;
            guesser.fromLast = false;
        } else {
            guesser.order = 0;
            guesser.fromLast = false;
        }
    }
    if (arguments.hasOption("date_prefix")) {
        guesser.guessDates = true;
        guesser.prefix = arguments.getStringOption("date_prefix");
        guesser.guessType = DateGuesser.GuessType.PREFIX;
    }
    if (arguments.hasOption("date_regex")) {
        guesser.guessDates = true;
        guesser.regex = arguments.getStringOption("date_regex");
        guesser.guessType = DateGuesser.GuessType.REGEX;
    }
    if (arguments.hasOption("date_format")) {
        guesser.guessDates = true;
        guesser.calendarDateFormat = arguments.getStringOption("date_format");
        guesser.parseCalendarDates = true;
    }
    if (arguments.hasOption("date_precision")) {
        guesser.guessDates = true;
        guesser.parseCalendarDatesAndPrecision = true;
    }
    String treeFileName = null;
    if (arguments.hasOption("tree")) {
        treeFileName = arguments.getStringOption("tree");
    }
    Map argumentMap = new HashMap();
    if (arguments.hasOption("D")) {
        String properties = arguments.getStringOption("D");
        for (String property : properties.split("\\s*,\\s*")) {
            String[] keyValue = property.split("=");
            if (keyValue.length != 2) {
                System.err.println("Properties should take the form: key=value");
                System.exit(1);
            }
            String key = keyValue[0].trim();
            String value = keyValue[1].trim();
            if (key.isEmpty()) {
                System.err.println("Properties should take the form: key=value");
                System.exit(1);
            }
            argumentMap.put(key, value);
        }
    }
    if (arguments.hasOption("help")) {
        printTitle();
        printUsage(arguments);
        System.exit(0);
    }
    if (arguments.hasOption("version")) {
        printTitle();
    }
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length < 1) {
        printTitle();
        printUsage(arguments);
        System.exit(0);
    }
    if (args2.length < 2 || args2.length > 3) {
        System.err.println("Unknown option: " + args2[0]);
        System.err.println();
        printUsage(arguments);
        System.exit(1);
    }
    try {
        new BEASTGen(guesser, argumentMap, treeFileName, args2[0], args2[1], (args2.length == 3 ? args2[2] : null));
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
    }
}