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

Example 26 with Sequence

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

the class CutExample method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.addRole(URI.create("http://identifiers.org/so/SO:0000613"));
    promoter.setName("J23119 promoter");
    promoter.setDescription("Constitutive promoter");
    promoter.addWasDerivedFrom(URI.create("http://partsregistry.org/Part:BBa_J23119"));
    document.setDefaultURIprefix(prURI);
    Sequence seq = document.createSequence("BBa_J23119", "", "ttgacagctagctcagtcctaggtataatgctagc", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    seq.addWasDerivedFrom(URI.create("http://parts.igem.org/Part:BBa_J23119:Design"));
    promoter.addSequence(seq.getIdentity());
    promoter.createSequenceAnnotation("cutat10", "cut1", 10, OrientationType.INLINE);
    promoter.createSequenceAnnotation("cutat12", "cut2", 12, OrientationType.INLINE);
    SBOLWriter.write(document, (System.out));
}

Example 27 with Sequence

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

the class SequenceAnnotation method addRange.

/**
 * Creates a range with the given arguments and then adds it to this sequence annotation's
 * list of locations.
 * <p>
 * This method first creates a compliant URI for the range to be created.
 * It starts with this sequence annotation's persistent identity URI,
 * followed by the given display ID, and ends an empty string for version.
 *
 * @param displayId the display ID for the range to be created
 * @param start the start index for the range to be created
 * @param end the end index for the range to be created
 * @return the created range
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206, 11102, 11103, 11104.
 */
public Range addRange(String displayId, int start, int end) throws SBOLValidationException {
    URI identity = createCompliantURI(this.getPersistentIdentity().toString(), displayId, this.getVersion());
    Range range = new Range(identity, start, end);
    range.setPersistentIdentity(createCompliantURI(this.getPersistentIdentity().toString(), displayId, ""));
    range.setDisplayId(displayId);
    range.setVersion(this.getVersion());
    addLocation(range);
    return range;
}

Example 28 with Sequence

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

the class SequenceAnnotation method setComponent.

/**
 * Sets this sequence annotation's reference component (its identity URI) to the one matching
 * the given display ID.
 * <p>
 * This method first creates a compliant URI for the reference component. It starts with this sequence
 * annotation's parent component defintion's persistent identity URI, followed by the given display ID,
 * and ends with this sequence annotation's parent component defintion's version.
 *
 * @param displayId the given display ID for the reference component
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>either of the following SBOL validation rules was violated: 10204, 10206; or</li>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link ComponentDefinition#createComponent(String, AccessType, String, String)}, or</li>
 * 		<li>{@link #setComponent(URI)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
public void setComponent(String displayId) throws SBOLValidationException {
    URI componentURI = URIcompliance.createCompliantURI(componentDefinition.getPersistentIdentity().toString(), displayId, componentDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && componentDefinition != null && componentDefinition.getComponent(componentURI) == null) {
        componentDefinition.createComponent(displayId, AccessType.PUBLIC, displayId, "");
    }
    setComponent(componentURI);
}

Example 29 with Sequence

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

the class SequenceAnnotation method addGenericLocation.

/**
 * Creates a generic location with the given arguments and then adds it to this sequence annotation's
 * list of locations.
 * <p>
 * This method first creates a compliant URI for the generic location to be created.
 * It starts with this sequence annotation's persistent identity URI,
 * followed by the given display ID, and ends an empty string for version.
 *
 * @param displayId the display ID for the generic location to be created
 * @param orientation the orientation type
 * @return the created generic location instance
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206.
 */
public GenericLocation addGenericLocation(String displayId, OrientationType orientation) throws SBOLValidationException {
    URI identity = createCompliantURI(this.getPersistentIdentity().toString(), displayId, this.getVersion());
    GenericLocation genericLocation = new GenericLocation(identity);
    genericLocation.setPersistentIdentity(createCompliantURI(this.getPersistentIdentity().toString(), displayId, ""));
    genericLocation.setDisplayId(displayId);
    genericLocation.setVersion(this.getVersion());
    genericLocation.setOrientation(orientation);
    addLocation(genericLocation);
    return genericLocation;
}

Example 30 with Sequence

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

the class SequenceAnnotation method addRange.

/**
 * Creates a range with the given arguments and then adds it to this sequence annotation's
 * list of locations.
 * <p>
 * This method first creates a compliant URI for the range to be created.
 * It starts with this sequence annotation's persistent identity URI,
 * followed by the given display ID, and ends an empty string for version.
 *
 * @param displayId the display ID for the range to be created
 * @param start the start index for the range to be created
 * @param end the end index for the range to be created
 * @param orientation the orientation type
 * @return the created range
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206, 11102, 11103, 11104.
 */
public Range addRange(String displayId, int start, int end, OrientationType orientation) throws SBOLValidationException {
    URI identity = createCompliantURI(this.getPersistentIdentity().toString(), displayId, this.getVersion());
    Range range = new Range(identity, start, end);
    range.setPersistentIdentity(createCompliantURI(this.getPersistentIdentity().toString(), displayId, ""));
    range.setDisplayId(displayId);
    range.setVersion(this.getVersion());
    range.setOrientation(orientation);
    addLocation(range);
    return range;
}