Examples with NexusParser beast.util.NexusParser used on opensource projects

Example 1 with NexusParser

use of beast.util.NexusParser in project beast2 by CompEvol.

the class BeautiDoc method parseArgs.

public ActionOnExit parseArgs(String[] args) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    ActionOnExit endState = ActionOnExit.UNKNOWN;
    String outputFileName = "beast.xml";
    String xml = null;
    String templateXML = null;
    TraitSet traitset = null;
    int i = 0;
    try {
        while (i < args.length) {
            int old = i;
            if (args[i].equals("")) {
                i += 1;
            } else if (args[i].equals("-capture")) {
                // capture stderr and stdout
                // already done in beast.app.beauti.Beauti
                i += 1;
            } else if (args[i].equals("-xml")) {
                String fileName = args[i + 1];
                xml = load(fileName);
                // XMLParser parser = new XMLParser();
                // m_doc.m_mcmc.setValue(parser.parseFile(fileName),
                // m_doc);
                this.fileName = nameFromFile(fileName);
                i += 2;
            } else if (args[i].equals("-template")) {
                String fileName = args[i + 1];
                templateXML = processTemplate(fileName);
                templateFileName = fileName;
                templateName = nameFromFile(fileName);
                i += 2;
            } else if (args[i].equals("-nex")) {
                // NB: multiple -nex/-xmldata commands can be processed!
                String fileName = args[i + 1];
                NexusParser parser = new NexusParser();
                parser.parseFile(new File(fileName));
                if (parser.filteredAlignments.size() > 0) {
                    for (Alignment data : parser.filteredAlignments) {
                        alignments.add(data);
                    }
                } else {
                    alignments.add(parser.m_alignment);
                }
                i += 2;
                traitset = parser.traitSet;
            } else if (args[i].equals("-xmldata")) {
                // NB: multiple -xmldata/-nex commands can be processed!
                String fileName = args[i + 1];
                Alignment alignment = (Alignment) BeautiAlignmentProvider.getXMLData(new File(fileName));
                alignments.add(alignment);
                i += 2;
            } else if (args[i].equals("-exitaction")) {
                if (args[i + 1].equals("writexml")) {
                    endState = ActionOnExit.WRITE_XML;
                } else if (args[i + 1].equals("usetemplate")) {
                    endState = ActionOnExit.SHOW_DETAILS_USE_TEMPLATE;
                } else if (args[i + 1].equals("usexml")) {
                    endState = ActionOnExit.SHOW_DETAILS_USE_XML_SPEC;
                } else if (args[i + 1].equals("merge")) {
                    endState = ActionOnExit.MERGE_AND_WRITE_XML;
                } else {
                    throw new IllegalArgumentException("Expected one of 'writexml','usetemplate' or 'usexml', not " + args[i + 1]);
                }
                i += 2;
            } else if (args[i].equals("-out")) {
                outputFileName = args[i + 1];
                i += 2;
            } else if (args[i].equals("-noerr")) {
                System.setErr(new PrintStream(new OutputStream() {

                    @Override
                    public void write(int b) {
                    }
                }));
                i += 1;
            }
            if (i == old) {
                throw new IllegalArgumentException("Wrong argument: " + args[i]);
            }
        }
    } catch (Exception e) {
        JOptionPane.showMessageDialog(null, e.getMessage());
        e.printStackTrace();
        System.exit(1);
    }
    initialize(endState, xml, templateXML, outputFileName);
    addTraitSet(traitset);
    return endState;
}

Example 2 with NexusParser

use of beast.util.NexusParser in project beast2 by CompEvol.

the class LogCombinerTest method treeCount.

private int treeCount(String file) throws IOException {
    NexusParser analyser = new NexusParser();
    analyser.parseFile(new File(file));
    return analyser.trees.size();
}

Example 3 with NexusParser

use of beast.util.NexusParser in project beast2 by CompEvol.

the class AlignmentViewer method main.

public static void main(String[] args) {
    try {
        NexusParser parser = new NexusParser();
        parser.parseFile(new File(args[0]));
        Alignment data = parser.m_alignment;
        AlignmentViewer panel = new AlignmentViewer(data);
        panel.showInDialog();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 4 with NexusParser

use of beast.util.NexusParser in project beast2 by CompEvol.

the class XMLProducerTest method test_ThatNexusExamplesProduces.

// @Test
// public void test_ThatXmlExamplesProduces() {
// System.setProperty("java.only", "true");
// String dir = System.getProperty("user.dir") + "/examples";
// //String dir = "/tmp";
// List<String> exceptions = new ArrayList<String>();
// exceptions.add("testExponentialGrowth.xml");
// test_ThatXmlExamplesProduces(dir, exceptions);
// }
@Test
public void test_ThatNexusExamplesProduces() {
    try {
        String dirName = System.getProperty("user.dir") + "/examples/nexus";
        System.out.println("Test Nexus Examples in " + dirName);
        File exampleDir = new File(dirName);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".nex") || name.endsWith(".nxs");
            }
        });
        List<String> failedFiles = new ArrayList<>();
        for (String fileName : exampleFiles) {
            System.out.println("Processing " + fileName);
            NexusParser parser = new NexusParser();
            try {
                parser.parseFile(new File(dirName + "/" + fileName));
            } catch (Exception e) {
                System.out.println("ExampleNexusParsing::Failed for " + fileName + ": " + e.getMessage());
                failedFiles.add(fileName);
            }
            XMLProducer producer = new XMLProducer();
            BEASTInterface o = parser.m_alignment;
            if (o != null) {
                String xml = producer.toXML(o);
                // FileWriter outfile = new FileWriter(new File("/tmp/XMLProducerTest.xml"));
                // outfile.write(xml);
                // outfile.close();
                XMLParser parser2 = new XMLParser();
                try {
                    BEASTInterface o2 = parser2.parseFragment(xml, false);
                    System.out.println(o2);
                } catch (Exception e) {
                    System.out.println("test_ThatNexusExamplesProduces::Failed for " + fileName + ": " + e.getMessage());
                    failedFiles.add(fileName);
                }
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\test_ThatNexusExamplesProduces::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\test_ThatNexusExamplesProduces::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 5 with NexusParser

use of beast.util.NexusParser in project beast2 by CompEvol.

the class NexusParserTest method testTranslateBlock.

@Test
public void testTranslateBlock() {
    String nexusTreeWithTranslateBlock = "#NEXUS\n" + "\n" + "Begin trees;\n" + "\tTranslate\n" + "\t\t1 ID1,\n" + "\t\t2 ID0,\n" + "\t\t3 ID4,\n" + "\t\t4 ID2,\n" + "\t\t5 ID3,\n" + "\t\t6 ID5,\n" + "\t\t7 ID6\n" + "\t\t;\n" + "tree TREE1  = [&R] (((1[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.885354014841496E-17,height_range={0.0,8.881784197001252E-16}]:0.3500782084890231,2[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.885336674542856E-17,height_range={0.0,8.881784197001252E-16}]:0.3500782084890231)[&height_95%_HPD={0.07176417767165222,0.32897302210795143},height_median=0.1721780016900536,height=0.18167779468916231,posterior=0.9992003198720512,height_range={0.019500497296338903,0.472878180264112}]:0.9248218821607495,(3[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.9830145767837334E-17,height_range={0.0,4.440892098500626E-16}]:0.9953937953591572,(4[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=4.332577657073782E-17,height_range={0.0,8.881784197001252E-16}]:0.2885313407858645,5[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=4.332594997372422E-17,height_range={0.0,8.881784197001252E-16}]:0.2885313407858645)[&height_95%_HPD={0.03428997737185302,0.29384644242980307},height_median=0.13917660355071027,height=0.15063132242919447,posterior=0.9992003198720512,height_range={0.012135234424637736,0.43470259067266337}]:0.7068624545732927)[&height_95%_HPD={0.4703860181701143,1.2401041356897795},height_median=0.8841915264598103,height=0.8799641568544527,posterior=0.9668132746901239,height_range={0.2376833426394811,1.5008735971013971}]:0.2795062952906153)[&height_95%_HPD={0.871170115451148,1.736574411464855},height_median=1.3388341576137588,height=1.3419155689487607,posterior=0.8912435025989605,height_range={0.609339147487161,2.0082114277758554}]:0.1115505866359714,(6[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.805449918706939E-17,height_range={0.0,4.440892098500626E-16}]:0.1143648180955704,7[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.805449918706939E-17,height_range={0.0,4.440892098500626E-16}]:0.1143648180955704)[&height_95%_HPD={0.07189918035503462,0.3145415291508802},height_median=0.1807116511737813,height=0.18641149700061227,posterior=0.9996001599360256,height_range={0.0042543872372436675,0.4254547656747345}]:1.2720858591901736)[&height_95%_HPD={1.2498874674331548,2.2880779508436415},height_median=1.7581890486365315,height=1.7391129102773757,posterior=1.0,height_range={0.003684245207410762,2.42575160443681}];\n" + "End;\n";
    NexusParser parser = new NexusParser();
    try {
        Set<String> taxa = new TreeSet<>();
        taxa.add("ID0");
        taxa.add("ID1");
        taxa.add("ID2");
        taxa.add("ID3");
        taxa.add("ID4");
        taxa.add("ID5");
        taxa.add("ID6");
        parser.parseFile("testTranslateBlock", new StringReader(nexusTreeWithTranslateBlock));
        assertEquals(1, parser.trees.size());
        assertNotNull(parser.trees.get(0));
        assertEquals(7, parser.trees.get(0).getTaxaNames().length);
        for (String taxaName : parser.trees.get(0).getTaxaNames()) {
            assertNotNull(taxaName);
        }
        assertTrue(taxa.containsAll(Arrays.asList(parser.trees.get(0).getTaxaNames())));
    } catch (Exception e) {
        e.printStackTrace();
        assertTrue(false);
    }
}