Java Arguments类代码示例

import dr.app.util.Arguments; //导入依赖的package包/类
/**
 * Generate a taxa block from these beast options
 *
 * @param writer    the writer
 * @param taxonList the taxon list to write
 * @throws dr.app.util.Arguments.ArgumentException
 *          ArgumentException
 */
private void writeTaxa(TaxonList taxonList, XMLWriter writer) throws Arguments.ArgumentException {
    // -1 (single taxa), 0 (1st gene of multi-taxa)

    writer.writeComment("The list of taxa to be analysed (can also include dates/ages).",
            "ntax=" + taxonList.getTaxonCount());
    writer.writeOpenTag(TaxaParser.TAXA, new Attribute[]{new Attribute.Default<String>(XMLParser.ID, TaxaParser.TAXA)});

    boolean hasAttr = options.traits.size() > 0;

    boolean firstDate = true;
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Taxon taxon = taxonList.getTaxon(i);

        boolean hasDate = false;
        if (options.clockModelOptions.isTipCalibrated()) {
            hasDate = TaxonList.Utils.hasAttribute(taxonList, i, dr.evolution.util.Date.DATE);
        }

        if (hasDate) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute(dr.evolution.util.Date.DATE);

            if (firstDate) {
                options.units = date.getUnits();
                firstDate = false;
            } else {
                if (options.units != date.getUnits()) {
                    System.err.println("Error: Units in dates do not match.");
                }
            }
        }

        writeTaxon(taxon, hasDate, hasAttr, writer);

    }

    writer.writeCloseTag(TaxaParser.TAXA);
}
 

import dr.app.util.Arguments; //导入依赖的package包/类
private void printUsage(Arguments arguments) {

        arguments.printUsage(
                "java -Djava.library.path=/usr/local/lib -jar buss.jar", " "
                + SPLIT_PARTITION + " " + "[<output-file-name>] [<seed>] [<true|false>] [<true|false>]");
        System.out.println();

        System.out
                .println("  Example: java -Djava.library.path=/usr/local/lib -jar pibuss.jar "
                        + "-treeFile SimTree.figtree -from 1 -to 500 -every 1 -branchSubstitutionModel HKY -HKYsubstitutionParameterValues 1.0"
                        + " "
                        + SPLIT_PARTITION
                        + " "
                        + "-treeFile SimTree.figtree -from 501 -to 1000 -every 1 -branchSubstitutionModel HKY -HKYsubstitutionParameterValues 10.0"
                        + " " + SPLIT_PARTITION + " " + "sequences.fasta");

        System.out.println();
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
/**
     * Generate a taxa block from these beast options
     *
     * @param writer    the writer
     * @param taxon the taxon to write
     * @throws dr.app.util.Arguments.ArgumentException
     *          ArgumentException
     */
    private void writeTaxon(Taxon taxon, boolean hasDate, boolean hasAttr, XMLWriter writer) throws Arguments.ArgumentException {

        writer.writeTag(TaxonParser.TAXON, new Attribute[]{
                        new Attribute.Default<String>(XMLParser.ID, taxon.getId())},
                !(hasDate || hasAttr)); // false if any of hasDate or hasAttr is true


        if (hasDate) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute(dr.evolution.util.Date.DATE);

            Attribute[] attributes;
            if (date.getUncertainty() > 0.0) {
                attributes = new Attribute[] {
                        new Attribute.Default<Double>(DateParser.VALUE, date.getTimeValue()),
                        new Attribute.Default<String>(DateParser.DIRECTION, date.isBackwards() ? DateParser.BACKWARDS : DateParser.FORWARDS),
                        new Attribute.Default<String>(DateParser.UNITS, Units.Utils.getDefaultUnitName(options.units)),
                        new Attribute.Default<Double>(DateParser.UNCERTAINTY, date.getUncertainty())
                };
            } else {
                attributes = new Attribute[] {
                        new Attribute.Default<Double>(DateParser.VALUE, date.getTimeValue()),
                        new Attribute.Default<String>(DateParser.DIRECTION, date.isBackwards() ? DateParser.BACKWARDS : DateParser.FORWARDS),
                        new Attribute.Default<String>(DateParser.UNITS, Units.Utils.getDefaultUnitName(options.units))
                        //new Attribute.Default("origin", date.getOrigin()+"")
                };
            }

            writer.writeTag(dr.evolution.util.Date.DATE, attributes, true);
        }

        for (TraitData trait : options.traits) {
            // there is no harm in allowing the species trait to be listed in the taxa
//                if (!trait.getName().equalsIgnoreCase(TraitData.TRAIT_SPECIES)) {
            writer.writeOpenTag(AttributeParser.ATTRIBUTE, new Attribute[]{
                    new Attribute.Default<String>(Attribute.NAME, trait.getName())});

            // denotes missing data using '?'
            writer.writeText(taxon.containsAttribute(trait.getName()) ? taxon.getAttribute(trait.getName()).toString() : "?");
            writer.writeCloseTag(AttributeParser.ATTRIBUTE);
//                }
        }

        generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_TAXON, taxon, writer);

        if (hasDate || hasAttr) writer.writeCloseTag(TaxonParser.TAXON);

    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static double[] parseVariableLengthDoubleArray(String inString) throws Arguments.ArgumentException {

        List<Double> returnList = new ArrayList<Double>();
        StringTokenizer st = new StringTokenizer(inString, ",");
        while (st.hasMoreTokens()) {
            try {
                returnList.add(Double.parseDouble(st.nextToken()));
            } catch (NumberFormatException e) {
                throw new Arguments.ArgumentException();
            }

        }

        if (returnList.size() > 0) {
            double[] doubleArray = new double[returnList.size()];
            for (int i = 0; i < doubleArray.length; i++)
                doubleArray[i] = returnList.get(i);

            return doubleArray;
        }
        return null;
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static double[] parseVariableLengthDoubleArray(String inString) throws Arguments.ArgumentException {

        List<Double> returnList = new ArrayList<Double>();
        StringTokenizer st = new StringTokenizer(inString,",");
        while(st.hasMoreTokens()) {
            try {
                returnList.add(Double.parseDouble(st.nextToken()));
            } catch (NumberFormatException e) {
                throw new Arguments.ArgumentException();
            }

        }

        if (returnList.size()>0) {
            double[] doubleArray = new double[returnList.size()];
            for(int i=0; i<doubleArray.length; i++)
                doubleArray[i] = returnList.get(i);
            return doubleArray;
        }
        return null;
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

		arguments.printUsage("densityplotter", "<input-file-name> [<output-file-name>]");
		System.out.println();
		System.out.println("  Example: densityplotter -burnin 100 -trait rate test.trees density.plot");
		System.out.println();
	}
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

        arguments.printUsage("GetAncestralSequenceFromSplitTrait", "[<*.tree file-name> [<output-file-name>]]");
        System.out.println();
        System.out.println("  Example: ...");
        System.out.println("  Example: ...");
        System.out.println();

    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

        arguments.printUsage(commandName, "<input-file-name> [<output-file-name>]");
        progressStream.println();
        progressStream.println("  Example: " + commandName + " indicator.log rates.out");
        progressStream.println();
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

        arguments.printUsage("beastgen", "<template-file-name> <input-file-name> [<output-file-name>]");
        System.out.println();
        System.out.println("  Example: beastgen template.beast test.nex test.xml");
        System.out.println("  Example: beastgen -help");
        System.out.println();
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

        arguments.printUsage("beast", "[<input-file-name>]");
        System.out.println();
        System.out.println("  Example: beast test.xml");
        System.out.println("  Example: beast -window test.xml");
        System.out.println("  Example: beast -help");
        System.out.println();
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

        arguments.printUsage("roottotip", "<input-file-name> [<output-file-name>]");
        System.out.println();
        System.out.println("  Example: roottotip -burnin 100 test.trees rootToTip.txt");
        System.out.println();
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void main(String[] args) throws IOException {

        String inputFileName = null;
        String outputFileName = null;

        printTitle();

        Arguments arguments = new Arguments(
                new Arguments.Option[]{
                        new Arguments.IntegerOption("burnin", "the number of trees to be ignored as 'burn-in' [default = 0]"),
                        new Arguments.StringOption("dateorder", "date_order", "order of date field in taxon name: first, last, 1, 2 etc. [default = last]"),
//                        new Arguments.StringOption("outgroup", "{taxon list}", "one or more taxa that will be used to root the tree(s) [default = find root]"),
                        new Arguments.Option("keeproot", "keep the existing root of the input trees [default = estimate root]"),
                        new Arguments.Option("writetree", "Write the optimally rooted tree to the output file"),
                        new Arguments.Option("help", "option to print this message"),
                });

        try {
            arguments.parseArguments(args);
        } catch (Arguments.ArgumentException ae) {
            System.out.println(ae);
            printUsage(arguments);
            System.exit(1);
        }

        if (arguments.hasOption("help")) {
            printUsage(arguments);
            System.exit(0);
        }

        int burnin = 0;
        if (arguments.hasOption("burnin")) {
            burnin = arguments.getIntegerOption("burnin");
        }

        String dateOrder = "LAST";
        if (arguments.hasOption("dateorder")) {
            dateOrder = arguments.getStringOption("dateorder").toUpperCase();
        }

        String outgroup = null;
        if (arguments.hasOption("outgroup")) {
            outgroup = arguments.getStringOption("dateorder").toUpperCase();
        }

        boolean keepRoot = arguments.hasOption("keeproot");

        boolean writeTree = arguments.hasOption("writetree");

        String[] args2 = arguments.getLeftoverArguments();

        if (args2.length > 2) {
            System.err.println("Unknown option: " + args2[2]);
            System.err.println();
            printUsage(arguments);
            System.exit(1);
        }

        if (args2.length == 0) {
            System.err.println("Missing input file name");
            printUsage(arguments);
            System.exit(1);
        }


        inputFileName = args2[0];
        if (args2.length == 2) {
            outputFileName = args2[1];
        }

        new RootToTip(burnin,
                dateOrder,
                keepRoot,
                outgroup,
                writeTree,
                inputFileName,
                outputFileName
        );

        System.exit(0);
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void printUsage(Arguments arguments) {

        arguments.printUsage("beauti", "[<input-file-name> ...]");
        System.out.println();
        System.out.println("  Example: beauti test.nex");
        System.out.println("  Example: beauti -help");
        System.out.println();
    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
public static void main(String[] args) throws java.io.IOException {

        // 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.StringOption("BEAST_XML", "FILENAME", "Specify a BEAST XML file"),
                        new Arguments.StringOption("load_dump", "FILENAME", "Specify a filename to load a dumped state from"),
                        new Arguments.StringOption("output_file", "FILENAME", "Specify a filename for the output file"),
                        new Arguments.StringOption("update_choice", "UPDATECHOICE", "Specify a function by which to update the tree"),
                        new Arguments.Option("help", "Print this information and stop")
                });

        try {
            arguments.parseArguments(args);
        } catch (Arguments.ArgumentException ae) {
            System.out.println();
            System.out.println(ae.getMessage());
            System.out.println();
            //printUsage(arguments);
            System.exit(1);
        }

        String inputFile = null;

        if (arguments.hasOption("BEAST_XML")) {
            inputFile = arguments.getStringOption("BEAST_XML");
        } else {
            throw new RuntimeException("No BEAST XML file specified.");
        }

        String debugStateFile;
        if (arguments.hasOption("load_dump")) {
            debugStateFile = arguments.getStringOption("load_dump");
            //pass on as argument
            System.setProperty(BeastCheckpointer.LOAD_STATE_FILE, debugStateFile);
        } else {
            throw new RuntimeException("No dump file specified.");
        }

        String choice = "";
        if (arguments.hasOption("update_choice")) {
            choice = arguments.getStringOption("update_choice");
        } else {
            throw new RuntimeException("Update mechanism needs to be specified.");
        }
        UpdateChoice chosen = null;
        for (UpdateChoice ch : UpdateChoice.values()) {
            if (choice.equals(ch.getName())) {
                chosen = ch;
                break;
            }
        }
        if (chosen == null) {
            throw new RuntimeException("Incorrect update mechanism specified.");
        }

        if (arguments.hasOption("output_file")) {
            String outputStateFile = arguments.getStringOption("output_file");
            //pass on as argument
            System.setProperty(BeastCheckpointer.SAVE_STATE_FILE, outputStateFile);
        } else {
            throw new RuntimeException("No output file specified.");
        }

        new CheckPointUpdaterApp(inputFile, debugStateFile, chosen);

        System.exit(0);

    }
 

import dr.app.util.Arguments; //导入依赖的package包/类
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.StringOption("BEAST_XML", "FILENAME", "Specify a BEAST XML file"),
                        new Arguments.StringOption("update_choice", "UPDATECHOICE", "Specify a function by which to update the tree"),
                        new Arguments.Option("help", "Print this information and stop")
                });

        try {
            arguments.parseArguments(args);
        } catch (Arguments.ArgumentException ae) {
            System.out.println();
            System.out.println(ae.getMessage());
            System.out.println();
            //printUsage(arguments);
            System.exit(1);
        }

        String inputFile = null;

        if (arguments.hasOption("BEAST_XML")) {
            inputFile = arguments.getStringOption("BEAST_XML");
        } else {
            throw new RuntimeException("No BEAST XML file specified.");
        }

        String choice = "";
        if (arguments.hasOption("update_choice")) {
            choice = arguments.getStringOption("update_choice");
        } else {
            throw new RuntimeException("Update mechanism needs to be specified.");
        }
        CheckPointUpdaterApp.UpdateChoice chosen = null;
        for (CheckPointUpdaterApp.UpdateChoice ch : CheckPointUpdaterApp.UpdateChoice.values()) {
            if (choice.equals(ch.getName())) {
                chosen = ch;
                break;
            }
        }
        if (chosen == null) {
            throw new RuntimeException("Incorrect update mechanism specified.");
        }

        //Create and set up the window.
        JFrame frame = new JFrame("Test distance matrix");
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

        DistanceMatrixInsertionTest test = new DistanceMatrixInsertionTest(inputFile, chosen);
        test.setOpaque(true);
        frame.setContentPane(test);

        //Display the window.
        frame.pack();
        frame.setVisible(true);

        //System.exit(0);

    }