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

Example 6 with NexusParser

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

the class NexusParserTest method testAssumptionsParse.

@Test
public void testAssumptionsParse() {
    try {
        String fileName = System.getProperty("user.dir") + "/examples/nexus/Primates.nex";
        NexusParser parser = new NexusParser();
        parser.parseFile(new File(fileName));
        assertEquals(2, parser.filteredAlignments.size());
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 7 with NexusParser

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

the class BeautiDoc method importNexus.

public void importNexus(File file) throws IOException {
    NexusParser parser = new NexusParser();
    parser.parseFile(file);
    if (parser.filteredAlignments.size() > 0) {
        for (Alignment data : parser.filteredAlignments) {
            addAlignmentWithSubnet(data, beautiConfig.partitionTemplate.get());
        }
    } else {
        addAlignmentWithSubnet(parser.m_alignment, beautiConfig.partitionTemplate.get());
    }
    // connectModel();
    addTraitSet(parser.traitSet);
// fireDocHasChanged();
}

Example 8 with NexusParser

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

the class NexusParserTest method testThatNexusExamplesParse.

@Test
public void testThatNexusExamplesParse() {
    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);
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\ntest_ThatNexusExamplesParse::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\ntest_ThatNexusExamplesParse::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 9 with NexusParser

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

the class NexusParserTest method testTranslateBlock2.

@Test
public void testTranslateBlock2() {
    String nexusTreeWithTranslateBlock = "#NEXUS\n" + "\n" + "Begin trees;\n" + "\tTranslate\n" + "\t\t1 C,\n" + "\t\t2 B,\n" + "\t\t3 A\n" + "\t\t;\n" + "tree TREE1  = [&R] (1:10,(3:30,2:20):10);\n" + "End;\n";
    NexusParser parser = new NexusParser();
    try {
        List<String> taxa = new ArrayList<>();
        taxa.add("2");
        taxa.add("0");
        taxa.add("1");
        parser.parseFile("testTranslateBlock", new StringReader(nexusTreeWithTranslateBlock));
        assertEquals(1, parser.trees.size());
        assertNotNull(parser.trees.get(0));
        String t = parser.trees.get(0).getRoot().toNewick();
        System.out.println(t);
        assertEquals("(C:10.0,(B:20.0,A:30.0):10.0):0.0", t);
    } catch (Exception e) {
        e.printStackTrace();
        assertTrue(false);
    }
}