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

Example 6 with Annotation

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

the class LinkTest method setUp.

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

Example 7 with Annotation

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

the class Header method valueOf.

/**
 * Parse a header GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a header GFA 2.0 record parsed from the specified value
 */
public static Header valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("H"), "header value must start with H");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 1; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Header(annotations.build());
}

Example 8 with Annotation

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

the class Segment method valueOf.

/**
 * Parse a segment GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a segment GFA 2.0 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() < 4) {
        throw new IllegalArgumentException("segment value must have at least four tokens, was " + tokens.size());
    }
    String id = tokens.get(1);
    int length = Integer.parseInt(tokens.get(2));
    String sequence = "*".equals(tokens.get(3)) ? null : tokens.get(3);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 4; 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, length, sequence, annotations.build());
}

Example 9 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";
    length = 42;
    sequence = "actg";
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 10 with Annotation

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

the class FragmentTest method setUp.

@Before
public void setUp() {
    segmentId = "segmentId";
    external = Reference.valueOf("external+");
    segmentStart = Position.valueOf("1");
    segmentEnd = Position.valueOf("10");
    fragmentStart = Position.valueOf("101");
    fragmentEnd = Position.valueOf("110");
    alignment = Alignment.valueOf("10M");
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}