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

Example 31 with Annotation

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

the class EdgeTest method setUp.

@Before
public void setUp() {
    id = "id";
    source = Reference.valueOf("source+");
    target = Reference.valueOf("target+");
    sourceStart = Position.valueOf("1");
    sourceEnd = Position.valueOf("10");
    targetStart = Position.valueOf("101");
    targetEnd = Position.valueOf("110");
    alignment = Alignment.valueOf("10M");
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 32 with Annotation

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

the class GapTest method setUp.

@Before
public void setUp() {
    id = "id";
    source = Reference.valueOf("source+");
    target = Reference.valueOf("target+");
    distance = 42;
    variance = Integer.valueOf(2);
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 33 with Annotation

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

the class SamRecord method valueOf.

/**
 * Parse a SAM record from the specified value.
 *
 * @param value value, must not be null
 * @return a SAM record parsed from the specified value
 */
public static SamRecord valueOf(final String value) {
    checkNotNull(value);
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 11) {
        throw new IllegalArgumentException("invalid record, expected 11 or more tokens, found " + tokens.size());
    }
    // QNAME String [!-?A-~]{1,254} Query template NAME
    String qname = "*".equals(tokens.get(0)) ? null : tokens.get(0);
    // FLAG Int [0,2^16-1] bitwise FLAG
    int flag = Integer.parseInt(tokens.get(1));
    // RNAME String \*|[!-()+-<>-~][!-~]* Reference sequence NAME
    String rname = "*".equals(tokens.get(2)) ? null : tokens.get(2);
    // POS Int [0,2^31-1] 1-based leftmost mapping POSition
    int pos = Integer.parseInt(tokens.get(3));
    // MAPQ Int [0,28-1] MAPping Quality
    int mapq = Integer.parseInt(tokens.get(4));
    // CIGAR String \*|([0-9]+[MIDNSHPX=])+ CIGAR string
    String cigar = "*".equals(tokens.get(5)) ? null : tokens.get(5);
    // RNEXT String \*|=|[!-()+-<>-~][!-~]* Ref. name of the mate/next read
    String rnext = "*".equals(tokens.get(6)) ? null : tokens.get(6);
    // PNEXT Int [0,2^31-1] Position of the mate/next read
    int pnext = Integer.parseInt(tokens.get(7));
    // TLEN Int [-2^31+1,2^31-1] observed Template LENgth
    int tlen = Integer.parseInt(tokens.get(8));
    // SEQ String \*|[A-Za-z=.]+ segment SEQuence
    String seq = "*".equals(tokens.get(9)) ? null : tokens.get(9);
    // QUAL String [!-~]+ ASCII of Phred-scaled base QUALity+33
    String qual = "*".equals(tokens.get(10)) ? null : tokens.get(10);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 11; 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 SamRecord(qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual, annotations.build());
}

Example 34 with Annotation

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

the class PafRecord method valueOf.

/**
 * Parse a PAF record from the specified value.
 *
 * @param value value, must not be null
 * @return a PAF record parsed from the specified value
 */
public static PafRecord valueOf(final String value) {
    checkNotNull(value);
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 12) {
        throw new IllegalArgumentException("PAF record value must have at least twelve tokens, was " + tokens.size());
    }
    String queryName = tokens.get(0);
    long queryLength = Long.parseLong(tokens.get(1));
    long queryStart = Long.parseLong(tokens.get(2));
    long queryEnd = Long.parseLong(tokens.get(3));
    char strand = tokens.get(4).charAt(0);
    String targetName = tokens.get(5);
    long targetLength = Long.parseLong(tokens.get(6));
    long targetStart = Long.parseLong(tokens.get(7));
    long targetEnd = Long.parseLong(tokens.get(8));
    long matches = Long.parseLong(tokens.get(9));
    long alignmentBlockLength = Long.parseLong(tokens.get(10));
    int mappingQuality = Integer.parseInt(tokens.get(11));
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 12; 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 PafRecord(queryName, queryLength, queryStart, queryEnd, strand, targetName, targetLength, targetStart, targetEnd, matches, alignmentBlockLength, mappingQuality, annotations.build());
}