Examples with Sequence org.sbolstandard.core2.Sequence used on opensource projects

Example 6 with Sequence

use of org.sbolstandard.core2.Sequence in project libSBOLj by SynBioDex.

the class GettingStartedExample method main.

public static void main(String[] args) throws IOException, SBOLValidationException, SBOLConversionException {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    String myersLabURI = "http://www.async.ece.utah.edu/";
    String myersLabPrefix = "myersLab";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    document.setComplete(true);
    document.setCreateDefaults(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    document.addNamespace(URI.create(myersLabURI), myersLabPrefix);
    // Creating a Top-level SBOL Data Object
    HashSet<URI> types = new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA, URI.create("http://identifiers.org/chebi/CHEBI:4705")));
    ComponentDefinition TetR_promoter = document.createComponentDefinition("BBa_R0040", types);
    ComponentDefinition LacI_repressor = document.createComponentDefinition("BBa_C0012", types);
    ComponentDefinition pIKELeftCassette = document.createComponentDefinition("pIKELeftCassette", types);
    Sequence seq_187 = document.createSequence("partseq_187", "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac", Sequence.IUPAC_DNA);
    String element2 = "atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtc" + "tcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcggga" + "aaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactgg" + "cgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcg" + "caaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgat" + "ggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcg" + "tcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcc" + "tgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattat" + "tttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagc" + "aaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctgg" + "cataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgc" + "catgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgc" + "tggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgc" + "gttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatccc" + "gccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgc" + "tgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaa" + "agaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcatt" + "aatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaact" + "acgctttagtagcttaataa";
    Sequence seq_153 = document.createSequence("partseq_153", element2, Sequence.IUPAC_DNA);
    // Setting and editing optional fields
    TetR_promoter.setName("p(tetR)");
    LacI_repressor.setName("lacI");
    TetR_promoter.setDescription("TetR repressible promoter");
    LacI_repressor.setDescription("lacI repressor from E. coli (+LVA)");
    if (TetR_promoter.isSetName()) {
        TetR_promoter.unsetName();
    }
    TetR_promoter.setName("p(tetR)");
    TetR_promoter.addRole(SequenceOntology.PROMOTER);
    LacI_repressor.addRole(SequenceOntology.CDS);
    URI TetR_promoter_role2 = URI.create("http://identifiers.org/so/SO:0000613");
    TetR_promoter.addRole(TetR_promoter_role2);
    if (TetR_promoter.containsRole(TetR_promoter_role2)) {
        TetR_promoter.removeRole(TetR_promoter_role2);
    }
    TetR_promoter.clearRoles();
    if (!TetR_promoter.getRoles().isEmpty()) {
        System.out.println("TetR_promoter set is not empty");
    }
    TetR_promoter.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
    // Creating and editing references
    TetR_promoter.addSequence(seq_187);
    LacI_repressor.addSequence(seq_153);
    pIKELeftCassette.addSequence(seq_187);
    pIKELeftCassette.clearSequences();
    // Adding the sequence below causes an exception because it cannot be found
    // pIKELeftCassette.addSequence(URI.create("http://partsregistry.org/seq/partseq_154"));
    // Creating Annotations
    TetR_promoter.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/Part:BBa_R0040"));
    // Creating Generic TopLevel Object
    GenericTopLevel datasheet = document.createGenericTopLevel("datasheet", "1.0", new QName(myersLabURI, "datasheet", myersLabPrefix));
    datasheet.setName("Datasheet for Custom Parameters");
    datasheet.createAnnotation(new QName(myersLabURI, "characterizationData", myersLabPrefix), URI.create(myersLabURI + "/measurement/Part:BBa_R0040"));
    datasheet.createAnnotation(new QName(myersLabURI, "transcriptionRate", myersLabPrefix), "0.75");
    TetR_promoter.createAnnotation(new QName(myersLabURI, "datasheet", myersLabPrefix), datasheet.getIdentity());
    // Creating and editing Child Objects
    // For pIKELeftCassette, create sequence constraint that says BBa_R0040 precedes BBa_C0012.
    // Note that with CreateDefaults that components get created automatically.
    // The position of the subject Component MUST precede that of the object Component.
    pIKELeftCassette.createSequenceConstraint("pIKELeftCassette_sc", RestrictionType.PRECEDES, TetR_promoter.getDisplayId(), LacI_repressor.getDisplayId());
    if (pIKELeftCassette.getComponent("BBa_R0040") == null) {
        System.out.println("TetR_promoter component is missing");
    }
    if (pIKELeftCassette.getComponent("BBa_C0012") == null) {
        System.out.println("LacI_repressor component is missing");
    }
    // Removing the subject component below causes an exception.
    // pIKELeftCassette.removeComponent(pIKELeftCassette.getComponent("BBa_R0040"));
    // Copying objects
    ComponentDefinition TetR_promoter_copy = (ComponentDefinition) document.createCopy(TetR_promoter, "BBa_K137046");
    Sequence seq = document.createSequence("seq_K137046", "gtgctcagtatctctatcactgatagggatgtcaatctctatcactgatagggactctagtatat" + "aaacgcagaaaggcccacccgaaggtgagccagtgtgactctagtagagagcgttcaccgaca" + "aacaacagataaaacgaaaggc", Sequence.IUPAC_DNA);
    TetR_promoter_copy.addSequence(seq);
    SBOLWriter.write(document, "GettingStartedExample.rdf");
    writeThenRead(document);
}

Example 7 with Sequence

use of org.sbolstandard.core2.Sequence in project libSBOLj by SynBioDex.

the class ComponentDefinitionOutput method createComponentDefinitionOutput.

public static SBOLDocument createComponentDefinitionOutput() throws SBOLValidationException {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    SBOLDocument document = new SBOLDocument();
    document.setTypesInURIs(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    document.setDefaultURIprefix(prURI);
    Sequence seqpTetR = document.createSequence("BBa_R0040", "", "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqRbs = document.createSequence("BBa_B0034", "", "aaagaggagaaa", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqCds = document.createSequence("BBa_C0062", "", "atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcac", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqTer = document.createSequence("BBa_B0015", "", "ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqPluxR = document.createSequence("BBa_R0062", "", "acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    ComponentDefinition pTetR = document.createComponentDefinition("BBa_R0040", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    pTetR.addRole(SequenceOntology.PROMOTER);
    pTetR.setName("pTetR");
    pTetR.setDescription("TetR repressible promoter");
    pTetR.addSequence(seqpTetR.getIdentity());
    ComponentDefinition rbs = document.createComponentDefinition("BBa_B0034", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    rbs.addRole(SequenceOntology.RIBOSOME_ENTRY_SITE);
    rbs.setName("BBa_B0034");
    rbs.setDescription("RBS based on Elowitz repressilator");
    rbs.addSequence(seqRbs.getIdentity());
    ComponentDefinition cds = document.createComponentDefinition("BBa_C0062", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    cds.addRole(SequenceOntology.CDS);
    cds.setName("luxR");
    cds.setDescription("luxR coding sequence");
    cds.addSequence(seqCds.getIdentity());
    ComponentDefinition ter = document.createComponentDefinition("BBa_B0015", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    ter.addRole(URI.create("http://identifiers.org/so/SO:0000141"));
    ter.setName("BBa_B0015");
    ter.setDescription("Double terminator");
    ter.addSequence(seqTer.getIdentity());
    ComponentDefinition pluxR = document.createComponentDefinition("BBa_R0062", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    // 
    pluxR.addRole(SequenceOntology.PROMOTER);
    pluxR.setName("pLuxR");
    pluxR.setDescription("LuxR inducible promoter");
    pluxR.addSequence(seqPluxR.getIdentity());
    ComponentDefinition device = document.createComponentDefinition("BBa_F2620", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    // biological region
    device.addRole(URI.create("http://identifiers.org/so/SO:00001411"));
    device.setName("BBa_F2620");
    device.setDescription("3OC6HSL -> PoPS Receiver");
    Component comPtetR = device.createComponent("pTetR", AccessType.PUBLIC, pTetR.getIdentity());
    Component comRbs = device.createComponent("rbs", AccessType.PUBLIC, rbs.getIdentity());
    Component comCds = device.createComponent("luxR", AccessType.PUBLIC, cds.getIdentity());
    Component comTer = device.createComponent("ter", AccessType.PUBLIC, ter.getIdentity());
    Component comPluxR = device.createComponent("pLuxR", AccessType.PUBLIC, pluxR.getIdentity());
    int start = 1;
    int end = seqPluxR.getElements().length();
    SequenceAnnotation anno = device.createSequenceAnnotation("anno1", "location1", start, end, OrientationType.INLINE);
    anno.setComponent(comPtetR.getIdentity());
    start = end + 1;
    end = seqRbs.getElements().length() + end + 1;
    SequenceAnnotation anno2 = device.createSequenceAnnotation("anno2", "location2", start, end, OrientationType.INLINE);
    anno2.setComponent(comRbs.getIdentity());
    start = end + 1;
    end = seqCds.getElements().length() + end + 1;
    SequenceAnnotation anno3 = device.createSequenceAnnotation("anno3", "location3", start, end, OrientationType.INLINE);
    anno3.setComponent(comCds.getIdentity());
    start = end + 1;
    end = seqTer.getElements().length() + end + 1;
    SequenceAnnotation anno4 = device.createSequenceAnnotation("anno4", "location4", start, end, OrientationType.INLINE);
    anno4.setComponent(comTer.getIdentity());
    start = end + 1;
    end = seqPluxR.getElements().length() + end + 1;
    SequenceAnnotation anno5 = device.createSequenceAnnotation("anno5", "location5", start, end, OrientationType.INLINE);
    anno5.setComponent(comPluxR.getIdentity());
    return document;
}

Example 8 with Sequence

use of org.sbolstandard.core2.Sequence in project libSBOLj by SynBioDex.

the class SequenceTest method test_deep_copy.

@Test
public void test_deep_copy() throws SBOLValidationException {
    Sequence gen_seq = doc.createSequence("CRa_U6_seq", CRa_U6_seq, Sequence.IUPAC_DNA);
    Sequence copy_seq = (Sequence) doc.createCopy(gen_seq, "copy_seq");
    // assertTrue(copy_seq.equals(gen_seq));
    assertTrue(copy_seq.getElements().equals(CRa_U6_seq));
}

Example 9 with Sequence

use of org.sbolstandard.core2.Sequence in project libSBOLj by SynBioDex.

the class SBOLReader method parseDnaSequenceV1.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String, String, boolean)},</li>
 * 		<li>{@link Sequence#Sequence(URI, String, URI)},</li>
 * 		<li>{@link Sequence#setVersion(String)},</li>
 * 		<li>{@link Sequence#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link Sequence#setDisplayId(String)},</li>
 * 		<li>{@link Identified#setAnnotations(List)},</li>
 * 		<li>{@link Sequence#setIdentity(URI)}, or </li>
 * 		<li>{@link SBOLDocument#addSequence(Sequence)}; or</li>
 * 	</ul>
 * </li>
 * <li>any of the following SBOL validation rules was violated: 10202, 10204, 10212, 10213.</li>
 * </ul>
 */
private static Sequence parseDnaSequenceV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException {
    String elements = null;
    String displayId = null;
    String name = null;
    String description = null;
    URI identity = topLevel.getIdentity();
    URI persistentIdentity = topLevel.getIdentity();
    URI encoding = Sequence.IUPAC_DNA;
    List<Annotation> annotations = new ArrayList<>();
    if (URIPrefix != null) {
        displayId = URIcompliance.findDisplayId(topLevel.getIdentity().toString());
        identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
        persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
    }
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.DNASequence.nucleotides)) {
            elements = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            if (URIPrefix != null) {
                identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Sequence sequence = new Sequence(identity, elements, encoding);
    if (persistentIdentity != null) {
        sequence.setPersistentIdentity(persistentIdentity);
        sequence.setVersion(version);
    }
    if (identity != topLevel.getIdentity())
        sequence.addWasDerivedFrom(topLevel.getIdentity());
    if (displayId != null)
        sequence.setDisplayId(displayId);
    if (name != null)
        sequence.setName(name);
    if (description != null)
        sequence.setDescription(description);
    if (!annotations.isEmpty())
        sequence.setAnnotations(annotations);
    Sequence oldS = SBOLDoc.getSequence(identity);
    if (oldS == null) {
        SBOLDoc.addSequence(sequence);
    } else if (sequence.getWasDerivedFroms().size() > 0 && oldS.getWasDerivedFroms().size() > 0 && !sequence.getWasDerivedFroms().equals(oldS.getWasDerivedFroms())) {
        URI wasDerivedFrom = (URI) sequence.getWasDerivedFroms().toArray()[0];
        Set<TopLevel> topLevels = SBOLDoc.getByWasDerivedFrom(wasDerivedFrom);
        for (TopLevel top : topLevels) {
            if (top instanceof Sequence) {
                return (Sequence) top;
            }
        }
        do {
            displayId = displayId + "_";
            identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
            persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
        } while (SBOLDoc.getSequence(identity) != null);
        sequence.setIdentity(identity);
        sequence.setDisplayId(displayId);
        sequence.setPersistentIdentity(persistentIdentity);
        SBOLDoc.addSequence(sequence);
    } else if (dropObjectsWithDuplicateURIs) {
        return oldS;
    } else {
        if (!sequence.equals(oldS)) {
            throw new SBOLValidationException("sbol-10202", sequence);
        }
    }
    return sequence;
}

Example 10 with Sequence

use of org.sbolstandard.core2.Sequence in project libSBOLj by SynBioDex.

the class ComponentDefinition method getImpliedNucleicAcidSequence.

/**
 *  Return the elements of a nucleic acid sequence implied by the hierarchically included components.
 *  <p>
 *  This method first tries to obtain the length of a nucleic acid sequence from the set of sequences referenced by this component definition
 *  that has an {@link Sequence#IUPAC_DNA} encoding. It then iterates through this component defintion's
 *  sequence annotations, and update the length with the ending locations that have a larger value than the current length. It then populates
 *  the elements with this length with unknown bases. This method iterates through this component defintion's sequence annotations to recursively
 *  search for bases implied by the hierarchically included components, and fills the elements with these known bases.
 *
 *  @return the elements of a nucleic sequence implied by the hierarchically included components
 */
public String getImpliedNucleicAcidSequence() {
    URI type = null;
    if (this.getTypes().contains(ComponentDefinition.DNA)) {
        type = ComponentDefinition.DNA;
    } else if (this.getTypes().contains(ComponentDefinition.RNA)) {
        type = ComponentDefinition.RNA;
    } else {
        return null;
    }
    String elements = "";
    int length = 0;
    if (this.getSequenceByEncoding(Sequence.IUPAC_DNA) != null) {
        length = this.getSequenceByEncoding(Sequence.IUPAC_DNA).getElements().length();
    }
    for (SequenceAnnotation sequenceAnnotation : this.getSequenceAnnotations()) {
        for (Location location : sequenceAnnotation.getLocations()) {
            if (location instanceof Range) {
                Range range = (Range) location;
                if (range.getEnd() > length) {
                    length = range.getEnd();
                }
            }
        }
    }
    for (int i = 0; i < length; i++) {
        elements += "N";
    }
    char[] elementsArray = elements.toCharArray();
    for (SequenceAnnotation sequenceAnnotation : this.getSequenceAnnotations()) {
        String subElements = null;
        if (!sequenceAnnotation.isSetComponent())
            continue;
        if (sequenceAnnotation.getComponent().getDefinition() != null) {
            ComponentDefinition compDef = sequenceAnnotation.getComponent().getDefinition();
            if (compDef.getSequenceByEncoding(Sequence.IUPAC_DNA) != null) {
                subElements = compDef.getSequenceByEncoding(Sequence.IUPAC_DNA).getElements();
            } else {
                subElements = compDef.getImpliedNucleicAcidSequence();
            }
            for (Location location : sequenceAnnotation.getLocations()) {
                if (location instanceof Range) {
                    Range range = (Range) location;
                    if (range.isSetOrientation() && range.getOrientation().equals(OrientationType.REVERSECOMPLEMENT)) {
                        subElements = Sequence.reverseComplement(subElements, type);
                    }
                    for (int i = 0; i < subElements.length(); i++) {
                        // TODO: need to deal with when start index out of range
                        elementsArray[(range.getStart() + i) - 1] = subElements.charAt(i);
                    }
                }
            }
        }
    }
    elements = String.valueOf(elementsArray);
    return elements;
}