use of org.sbolstandard.core2.MapsTo in project libSBOLj by SynBioDex.
the class MapsToTest method test_toString.
@Test
public void test_toString() throws SBOLValidationException {
MapsTo geneMapsTo = gene.createMapsTo("local_gene", RefinementType.USELOCAL, target_gene.getDisplayId(), protein.getDisplayId());
assertTrue(geneMapsTo.toString().length() != 0);
assertNotNull(geneMapsTo.toString());
assertTrue(geneMapsTo.toString().contains("identity="));
assertTrue(geneMapsTo.toString().contains("displayId="));
assertFalse(geneMapsTo.toString().contains("name="));
assertFalse(geneMapsTo.toString().contains("description="));
assertTrue(geneMapsTo.toString().contains("refinement="));
assertTrue(geneMapsTo.toString().contains("local="));
assertTrue(geneMapsTo.toString().contains("remote="));
}
use of org.sbolstandard.core2.MapsTo in project libSBOLj by SynBioDex.
the class ComponentTest method test_ComponentMapsTo.
@Test
public void test_ComponentMapsTo() throws SBOLValidationException {
MapsTo geneMapsTo = gene.createMapsTo("local_gene", RefinementType.USELOCAL, target_gene.getDisplayId(), protein.getDisplayId());
assertTrue(gene.getMapsTos().size() == 1);
assertNotNull(gene.getMapsTo("local_gene"));
assertEquals(gene.getMapsTo("local_gene"), geneMapsTo);
gene.removeMapsTo(geneMapsTo);
assertTrue(gene.getMapsTos().size() == 0);
geneMapsTo = gene.createMapsTo("local_gene", RefinementType.USELOCAL, target_gene.getIdentity(), protein.getIdentity());
assertNotNull(gene.getMapsTo(geneMapsTo.getIdentity()));
assertTrue(gene.getMapsTos().size() == 1);
gene.clearMapsTos();
assertTrue(gene.getMapsTos().size() == 0);
}
use of org.sbolstandard.core2.MapsTo in project libSBOLj by SynBioDex.
the class SBOLReader method parseFunctionalComponent.
/**
* @param functionalComponent
* @param nested
* @return
* @throws SBOLValidationException if either of the following conditions is satisfied:
* <ul>
* <li>any of the following SBOL validation rules was violated:
* 10203, 10204, 10206, 10208, 10212, 10213, 10602, 10607, 11606, 11802; or
* </li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
* <li>{@link FunctionalComponent#FunctionalComponent(URI, AccessType, URI, DirectionType)},</li>
* <li>{@link FunctionalComponent#setDisplayId(String)},</li>
* <li>{@link FunctionalComponent#setVersion(String)},</li>
* <li>{@link FunctionalComponent#setWasDerivedFrom(URI)},</li>
* <li>{@link FunctionalComponent#setMapsTos(Set)}, or</li>
* <li>{@link Identified#setAnnotations(List)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static FunctionalComponent parseFunctionalComponent(SBOLDocument SBOLDoc, NestedDocument<QName> functionalComponent, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
// URIcompliance.extractDisplayId(functionalComponent.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(functionalComponent.getIdentity()));
URI persistentIdentity = null;
String version = null;
AccessType access = null;
DirectionType direction = null;
URI functionalComponentURI = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
Set<MapsTo> mappings = new HashSet<>();
for (NamedProperty<QName> namedProperty : functionalComponent.getProperties()) {
if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10203", functionalComponent.getIdentity());
}
persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10206", functionalComponent.getIdentity());
}
version = ((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", functionalComponent.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access)) {
if (!(namedProperty.getValue() instanceof Literal) || access != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10607", functionalComponent.getIdentity());
}
String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
}
try {
access = AccessType.convertToAccessType(URI.create(accessTypeStr));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-10607", functionalComponent.getIdentity());
}
} else if (namedProperty.getName().equals(Sbol2Terms.FunctionalComponent.direction)) {
if (!(namedProperty.getValue() instanceof Literal) || direction != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-11802", functionalComponent.getIdentity());
}
String directionTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
if (directionTypeStr.startsWith("http://www.sbolstandard.org/")) {
System.err.println("Warning: namespace for direction types should be http://sbols.org/v2#");
directionTypeStr = directionTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
directionTypeStr = directionTypeStr.replace("input", "in");
directionTypeStr = directionTypeStr.replace("output", "out");
}
try {
direction = DirectionType.convertToDirectionType(URI.create(directionTypeStr));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-11802", functionalComponent.getIdentity());
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasMapsTo)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-10606", functionalComponent.getIdentity());
}
mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
NestedDocument<QName> nestedDocument = nested.get(uri);
if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-10606", functionalComponent.getIdentity());
}
mappings.add(parseMapsTo(nested.get(uri), false));
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasComponentDefinition)) {
if (functionalComponentURI != null) {
throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
}
functionalComponentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
ComponentDefinition componentDefinition = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
functionalComponentURI = componentDefinition.getIdentity();
} else {
throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
}
} 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", functionalComponent.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", functionalComponent.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10208", functionalComponent.getIdentity());
}
wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10221", functionalComponent.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
FunctionalComponent fc = new FunctionalComponent(functionalComponent.getIdentity(), access, functionalComponentURI, direction);
if (persistentIdentity != null)
fc.setPersistentIdentity(persistentIdentity);
if (version != null)
fc.setVersion(version);
if (displayId != null)
fc.setDisplayId(displayId);
if (!mappings.isEmpty())
fc.setMapsTos(mappings);
if (name != null)
fc.setName(name);
if (description != null)
fc.setDescription(description);
fc.setWasDerivedFroms(wasDerivedFroms);
fc.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
fc.setAnnotations(annotations);
return fc;
}
use of org.sbolstandard.core2.MapsTo in project libSBOLj by SynBioDex.
the class SBOLReader method parseModule.
/**
* @param module
* @param nested
* @return
* @throws SBOLValidationException if either of the following conditions is satisfied:
* <ul>
* <li>any of the following SBOL validation rules was violated:
* 10203, 10204, 10206, 10208, 10212, 10213, 11604, 11702; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
* <li>{@link Module#Module(URI, URI)},</li>
* <li>{@link Module#setDisplayId(String)},</li>
* <li>{@link Module#setVersion(String)},</li>
* <li>{@link Module#setWasDerivedFrom(URI)},</li>
* <li>{@link Identified#setAnnotations(List)}, or</li>
* <li>{@link Module#setMapsTos(Set)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static Module parseModule(SBOLDocument SBOLDoc, NestedDocument<QName> module, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
// URIcompliance.extractDisplayId(module.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(module.getIdentity()));
URI persistentIdentity = null;
String version = null;
URI definitionURI = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<MapsTo> mappings = new HashSet<>();
List<Annotation> annotations = new ArrayList<>();
for (NamedProperty<QName> namedProperty : module.getProperties()) {
if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10203", module.getIdentity());
}
persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10206", module.getIdentity());
}
version = ((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", module.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapsTo)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-11706", module.getIdentity());
}
mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
NestedDocument<QName> nestedDocument = nested.get(uri);
if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-11706", module.getIdentity());
}
mappings.add(parseMapsTo(nested.get(uri), false));
}
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapping)) {
System.err.println("Warning: tag should be sbol:mapTo, not sbol:mapping.");
if (namedProperty.getValue() instanceof NestedDocument) {
mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), true));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
mappings.add(parseMapsTo(nested.get(uri), true));
}
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasDefinition)) {
if (definitionURI != null) {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
definitionURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ModuleDefinition.ModuleDefinition)) {
ModuleDefinition moduleDefinition = parseModuleDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
definitionURI = moduleDefinition.getIdentity();
} else {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-11702", module.getIdentity());
}
} 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", module.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", module.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10208", module.getIdentity());
}
wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10221", module.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
Module submodule = new Module(module.getIdentity(), definitionURI);
if (persistentIdentity != null)
submodule.setPersistentIdentity(persistentIdentity);
if (version != null)
submodule.setVersion(version);
if (displayId != null)
submodule.setDisplayId(displayId);
if (!mappings.isEmpty())
submodule.setMapsTos(mappings);
if (name != null)
submodule.setName(name);
if (description != null)
submodule.setDescription(description);
submodule.setWasDerivedFroms(wasDerivedFroms);
submodule.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
submodule.setAnnotations(annotations);
return submodule;
}
use of org.sbolstandard.core2.MapsTo in project libSBOLj by SynBioDex.
the class SBOLReader method parseComponent.
/**
* @param component
* @param nested
* @return
* @throws SBOLValidationException if either of the following conditions is satisfied:
* <ul>
* <li>any of the following SBOL validation rules was violated:
* 10203, 10204, 10206, 10208, 10212, 10213, 10519, 10602, 10607; or
*</li>
* <li>an SBOL validation rule violation occurred in the following constructor or methods:
* <ul>
* <li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
* <li>{@link Component#Component(URI, AccessType, URI)},</li>
* <li>{@link Component#setVersion(String)},</li>
* <li>{@link Component#setDisplayId(String)},</li>
* <li>{@link Component#setAccess(AccessType)},</li>
* <li>{@link Component#setMapsTos(Set)},</li>
* <li>{@link Component#setDefinition(URI)},</li>
* <li>{@link Component#setWasDerivedFrom(URI)}, or</li>
* <li>{@link Identified#setAnnotations(List)}.</li>
* </ul>
* </li>
* </ul>
*/
@SuppressWarnings("unchecked")
private static Component parseComponent(SBOLDocument SBOLDoc, NestedDocument<QName> component, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
// URIcompliance.extractDisplayId(component.getIdentity());
String displayId = null;
String name = null;
String description = null;
// URI.create(URIcompliance.extractPersistentId(component.getIdentity()));
URI persistentIdentity = null;
String version = null;
URI subComponentURI = null;
AccessType access = null;
Set<URI> wasDerivedFroms = new HashSet<>();
Set<URI> wasGeneratedBys = new HashSet<>();
Set<URI> roles = new HashSet<>();
URI roleIntegration = null;
List<Annotation> annotations = new ArrayList<>();
Set<MapsTo> mapsTo = new HashSet<>();
for (NamedProperty<QName> namedProperty : component.getProperties()) {
if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10203", component.getIdentity());
}
persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10206", component.getIdentity());
}
version = ((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", component.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Component.roles)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10702", component.getIdentity());
}
roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Component.roleIntegration)) {
if (!(namedProperty.getValue() instanceof Literal) || roleIntegration != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10708", component.getIdentity());
}
roleIntegration = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access)) {
if (!(namedProperty.getValue() instanceof Literal) || access != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10607", component.getIdentity());
}
String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
}
try {
access = AccessType.convertToAccessType(URI.create(accessTypeStr));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-10607", component.getIdentity());
}
} else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapsTo)) {
if (namedProperty.getValue() instanceof NestedDocument) {
NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-10606", component.getIdentity());
}
mapsTo.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
} else {
URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
NestedDocument<QName> nestedDocument = nested.get(uri);
if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
throw new SBOLValidationException("sbol-10606", component.getIdentity());
}
mapsTo.add(parseMapsTo(nested.get(uri), false));
}
} else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasComponentDefinition)) {
if (subComponentURI != null) {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
subComponentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else if (namedProperty.getValue() instanceof IdentifiableDocument) {
if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
ComponentDefinition componentDefinition = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
subComponentURI = componentDefinition.getIdentity();
} else {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
} else {
throw new SBOLValidationException("sbol-10602", component.getIdentity());
}
} 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", component.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", component.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10208", component.getIdentity());
}
wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10221", component.getIdentity());
}
wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
} else {
annotations.add(new Annotation(namedProperty));
}
}
Component c = new Component(component.getIdentity(), access, subComponentURI);
if (persistentIdentity != null)
c.setPersistentIdentity(persistentIdentity);
if (version != null)
c.setVersion(version);
if (displayId != null)
c.setDisplayId(displayId);
if (access != null)
c.setAccess(access);
if (roleIntegration != null)
try {
c.setRoleIntegration(RoleIntegrationType.convertToRoleIntegrationType(roleIntegration));
} catch (SBOLValidationException e) {
throw new SBOLValidationException("sbol-10708", c);
}
if (!roles.isEmpty())
c.setRoles(roles);
if (!mapsTo.isEmpty())
c.setMapsTos(mapsTo);
if (subComponentURI != null)
c.setDefinition(subComponentURI);
if (name != null)
c.setName(name);
if (description != null)
c.setDescription(description);
c.setWasDerivedFroms(wasDerivedFroms);
c.setWasGeneratedBys(wasGeneratedBys);
if (!annotations.isEmpty())
c.setAnnotations(annotations);
return c;
}
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