Examples with Annotation org.dishevelled.bio.annotation.Annotation used on opensource projects

Example 16 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class ContainmentTest method setUp.

@Before
public void setUp() {
    container = Reference.valueOf("source+");
    contained = Reference.valueOf("target+");
    position = 42;
    overlap = "10M";
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 17 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class PafReaderTest method testRoundTrip.

@Test
public void testRoundTrip() throws Exception {
    Map<String, Annotation> annotations = new HashMap<String, Annotation>();
    annotations.put("NM", Annotation.valueOf("NM:i:0"));
    annotations.put("MD", Annotation.valueOf("MD:Z:101"));
    annotations.put("AS", Annotation.valueOf("AS:i:101"));
    annotations.put("XS", Annotation.valueOf("XS:i:55"));
    annotations.put("RG", Annotation.valueOf("RG:Z:NA12878-1"));
    annotations.put("MQ", Annotation.valueOf("MQ:i:60"));
    annotations.put("ms", Annotation.valueOf("ms:i:3614"));
    annotations.put("mc", Annotation.valueOf("mc:i:60612"));
    annotations.put("MC", Annotation.valueOf("MC:Z:101M"));
    annotations.put("ZB", Annotation.valueOf("ZB:B:i1,2"));
    annotations.put("ZT", Annotation.valueOf("ZT:B:f3.4,4.5"));
    PafRecord expected = new PafRecord("query", 100L, 10L, 20L, '-', "target", 200L, 20L, 30L, 42L, 10L, 32, annotations);
    File tmp = File.createTempFile("pafReaderTest", ".paf");
    tmp.deleteOnExit();
    try (PrintWriter writer = new PrintWriter(new FileWriter(tmp))) {
        PafWriter.write(expected, writer);
    }
    PafRecord observed = read(tmp).iterator().next();
    assertEquals(expected.getQueryName(), observed.getQueryName());
}

Example 18 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class PafWriterTest method setUp.

@Before
public void setUp() {
    Map<String, Annotation> annotations = new HashMap<String, Annotation>();
    annotations.put("NM", Annotation.valueOf("NM:i:0"));
    annotations.put("MD", Annotation.valueOf("MD:Z:101"));
    annotations.put("AS", Annotation.valueOf("AS:i:101"));
    annotations.put("XS", Annotation.valueOf("XS:i:55"));
    annotations.put("RG", Annotation.valueOf("RG:Z:NA12878-1"));
    annotations.put("MQ", Annotation.valueOf("MQ:i:60"));
    annotations.put("ms", Annotation.valueOf("ms:i:3614"));
    annotations.put("mc", Annotation.valueOf("mc:i:60612"));
    annotations.put("MC", Annotation.valueOf("MC:Z:101M"));
    annotations.put("ZB", Annotation.valueOf("ZB:B:i,1,2"));
    annotations.put("ZT", Annotation.valueOf("ZT:B:f,3.4,4.5"));
    record = new PafRecord("query", 100L, 10L, 20L, '-', "target", 200L, 20L, 30L, 42L, 10L, 32, annotations);
    records = ImmutableList.of(record);
    outputStream = new ByteArrayOutputStream();
    writer = new PrintWriter(outputStream);
}

Example 19 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class Link method valueOf.

/**
 * Parse a link GFA 1.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a link GFA 1.0 record parsed from the specified value
 */
public static Link valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("L"), "link value must start with L");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 6) {
        throw new IllegalArgumentException("link value must have at least six tokens, was " + tokens.size());
    }
    Reference source = Reference.splitValueOf(tokens.get(1), tokens.get(2));
    Reference target = Reference.splitValueOf(tokens.get(3), tokens.get(4));
    String overlap = "*".equals(tokens.get(5)) ? null : tokens.get(5);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 6; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Link(source, target, overlap, annotations.build());
}

Example 20 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class Segment method valueOf.

/**
 * Parse a segment GFA 1.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a segment GFA 1.0 record parsed from the specified value
 */
public static Segment valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("S"), "segment value must start with S");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 3) {
        throw new IllegalArgumentException("segment value must have at least three tokens, was " + tokens.size());
    }
    String id = tokens.get(1);
    String sequence = "*".equals(tokens.get(2)) ? null : tokens.get(2);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 3; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Segment(id, sequence, annotations.build());
}