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

Example 26 with Annotation

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

the class Gap method valueOf.

/**
 * Parse a gap GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a gap GFA 2.0 record parsed from the specified value
 */
public static Gap valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("G"), "gap value must start with G");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 6) {
        throw new IllegalArgumentException("gap value must have at least six tokens, was " + tokens.size());
    }
    String id = "*".equals(tokens.get(1)) ? null : tokens.get(1);
    Reference source = Reference.valueOf(tokens.get(2));
    Reference target = Reference.valueOf(tokens.get(3));
    int distance = Integer.parseInt(tokens.get(4));
    Integer variance = "*".equals(tokens.get(5)) ? null : Integer.parseInt(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 Gap(id, source, target, distance, variance, annotations.build());
}

Example 27 with Annotation

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

the class SetTest method setUp.

@Before
public void setUp() {
    id = "id";
    ids = ImmutableSet.of("source", "target");
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 28 with Annotation

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

the class PathTest method setUp.

@Before
public void setUp() {
    name = "name";
    segments = ImmutableList.of(Reference.valueOf("source+"), Reference.valueOf("target+"));
    overlaps = ImmutableList.of("10M");
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 29 with Annotation

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

the class SegmentTest method setUp.

@Before
public void setUp() {
    id = "id";
    sequence = "actg";
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 30 with Annotation

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

the class TraversalTest method setUp.

@Before
public void setUp() {
    pathName = "pathName";
    ordinal = 0;
    source = Reference.valueOf("1+");
    target = Reference.valueOf("2-");
    overlap = "0M";
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}