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

Example 21 with Annotation

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

the class Traversal method valueOf.

/**
 * Parse a traversal GFA 1.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a traversal GFA 1.0 record parsed from the specified value
 */
public static Traversal valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("t"), "traversal value must start with t");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 8) {
        throw new IllegalArgumentException("traversal value must have at least eight tokens, was " + tokens.size());
    }
    String name = tokens.get(1);
    int ordinal = Integer.parseInt(tokens.get(2));
    Reference source = Reference.splitValueOf(tokens.get(3), tokens.get(4));
    Reference target = Reference.splitValueOf(tokens.get(5), tokens.get(6));
    String overlap = "*".equals(tokens.get(7)) ? null : tokens.get(7);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 8; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(tokens.get(i));
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Traversal(name, ordinal, source, target, overlap, annotations.build());
}

Example 22 with Annotation

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

the class SamWriterTest method setUp.

@Before
public void setUp() {
    header = SamHeader.builder().withHeaderLine(SamHeaderLine.valueOf(SAM_HEADER)).build();
    Map<String, Annotation> annotations = ImmutableMap.<String, Annotation>builder().put("NM", Annotation.valueOf("NM:i:0")).put("MD", Annotation.valueOf("MD:Z:101")).put("AS", Annotation.valueOf("AS:i:101")).put("XS", Annotation.valueOf("XS:i:55")).put("RG", Annotation.valueOf("RG:Z:NA12878-1")).put("MQ", Annotation.valueOf("MQ:i:60")).put("ms", Annotation.valueOf("ms:i:3614")).put("mc", Annotation.valueOf("mc:i:60612")).put("MC", Annotation.valueOf("MC:Z:101M")).put("ZB", Annotation.valueOf("ZB:B:i,1,2")).put("ZT", Annotation.valueOf("ZT:B:f,3.4,4.5")).build();
    record = new SamRecord("ERR194147.765130386", 99, "chr20", 60250, 60, "101M", "=", 60512, 363, "ACTCCATCCCATTCCATTCCACTCCCTTCATTTCCATTCCAGTCCATTCCATTCCATTCCATTCCATTCCACTCCACTCCATTCCATTCCACTGCACTCCA", "CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIIJJJJJJJJJJJJJHIIJIJGIJJJJJJJJJJJJJIJJJJJJJJJJJGGHHHFF@", annotations);
    records = ImmutableList.of(record);
    outputStream = new ByteArrayOutputStream();
    writer = new PrintWriter(outputStream);
}

Example 23 with Annotation

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

the class Containment method valueOf.

/**
 * Parse a containment GFA 1.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a containment GFA 1.0 record parsed from the specified value
 */
public static Containment valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("C"), "containment value must start with C");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 7) {
        throw new IllegalArgumentException("containment value must have at least seven tokens, was " + tokens.size());
    }
    Reference container = Reference.splitValueOf(tokens.get(1), tokens.get(2));
    Reference contained = Reference.splitValueOf(tokens.get(3), tokens.get(4));
    int position = Integer.parseInt(tokens.get(5));
    String overlap = "*".equals(tokens.get(6)) ? null : tokens.get(6);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 7; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Containment(container, contained, position, overlap, annotations.build());
}

Example 24 with Annotation

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

the class Edge method valueOf.

/**
 * Parse an edge GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return an edge GFA 2.0 record parsed from the specified value
 */
public static Edge valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("E"), "edge value must start with E");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 9) {
        throw new IllegalArgumentException("edge value must have at least nine 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));
    Position sourceStart = Position.valueOf(tokens.get(4));
    Position sourceEnd = Position.valueOf(tokens.get(5));
    Position targetStart = Position.valueOf(tokens.get(6));
    Position targetEnd = Position.valueOf(tokens.get(7));
    Alignment alignment = Alignment.valueOf(tokens.get(8));
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 9; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Edge(id, source, target, sourceStart, sourceEnd, targetStart, targetEnd, alignment, annotations.build());
}

Example 25 with Annotation

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

the class Fragment method valueOf.

/**
 * Parse a fragment GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a fragment GFA 2.0 record parsed from the specified value
 */
public static Fragment valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("F"), "fragment value must start with F");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 8) {
        throw new IllegalArgumentException("fragment value must have at least eight tokens, was " + tokens.size());
    }
    String segmentId = tokens.get(1);
    Reference external = Reference.valueOf(tokens.get(2));
    Position segmentStart = Position.valueOf(tokens.get(3));
    Position segmentEnd = Position.valueOf(tokens.get(4));
    Position fragmentStart = Position.valueOf(tokens.get(5));
    Position fragmentEnd = Position.valueOf(tokens.get(6));
    Alignment alignment = Alignment.valueOf(tokens.get(7));
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 8; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Fragment(segmentId, external, segmentStart, segmentEnd, fragmentStart, fragmentEnd, alignment, annotations.build());
}