Example 1 with SBOLConversionException
use of org.sbolstandard.core2.SBOLConversionException in project libSBOLj by SynBioDex.
the class RepressionModel method main.
public static void main(String[] args) throws SBOLValidationException, SBOLConversionException, IOException {
SBOLDocument doc = new SBOLDocument();
doc.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
doc.setComplete(true);
doc.setCreateDefaults(true);
String version = "1.0.0";
// Create ComponentDefinition for cas9_generic protein
doc.createComponentDefinition("cas9_generic", version, ComponentDefinition.PROTEIN);
// Create ComponentDefinition for gRNA_generic RNA
doc.createComponentDefinition("gRNA_generic", version, ComponentDefinition.RNA).addRole(SequenceOntology.SGRNA);
// Create ComponentDefinition for cas9_gRNA_complex
doc.createComponentDefinition("cas9_gRNA_complex", version, ComponentDefinition.COMPLEX);
// Create ComponentDefinition for target gene
doc.createComponentDefinition("target_gene", version, ComponentDefinition.DNA).addRole(SequenceOntology.PROMOTER);
// Create ComponentDefinition for target protein
doc.createComponentDefinition("target", version, ComponentDefinition.PROTEIN);
// Create ModuleDefinition for CRISPR_Repression_Template
ModuleDefinition CRISPR_Template = doc.createModuleDefinition("CRISPR_Template", version);
// Complex Formation Interaction for Cas9m_BFP and gRNA
Interaction Cas9Complex_Formation = CRISPR_Template.createInteraction("cas9_complex_formation", SystemsBiologyOntology.NON_COVALENT_BINDING);
Cas9Complex_Formation.createParticipation("cas9_generic", "cas9_generic", SystemsBiologyOntology.REACTANT);
Cas9Complex_Formation.createParticipation("gRNA_generic", "gRNA_generic", SystemsBiologyOntology.REACTANT);
Cas9Complex_Formation.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.PRODUCT);
// Production of target from target gene
Interaction EYFP_production = CRISPR_Template.createInteraction("target_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
EYFP_production.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
EYFP_production.createParticipation("target", "target", SystemsBiologyOntology.PRODUCT);
// Inhibition of target by cas9m_BFP_gRNA
Interaction target_generic_gene_inhibition = CRISPR_Template.createInteraction("target_gene_inhibition", SystemsBiologyOntology.INHIBITION);
target_generic_gene_inhibition.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.INHIBITOR);
target_generic_gene_inhibition.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
// Create Sequence for CRa_U6 promoter
String CRa_U6_seq_elements = "GGTTTACCGAGCTCTTATTGGTTTTCAAACTTCATTGACTGTGCC" + "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAATATAGAACCG" + "ATCCTCCCATTGGTATATATTATAGAACCGATCCTCCCATTGGCT" + "TGTGGAAAGGACGAAACACCGTACCTCATCAGGAACATGTGTTTA" + "AGAGCTATGCTGGAAACAGCAGAAATAGCAAGTTTAAATAAGGCT" + "AGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT" + "TTGGTGCGTTTTTATGCTTGTAGTATTGTATAATGTTTTT";
doc.createSequence("CRa_U6_seq", version, CRa_U6_seq_elements, Sequence.IUPAC_DNA);
// Create Sequence for gRNA_b coding sequence
String gRNA_b_elements = "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGAT" + "TTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTACCT" + "CATCAGGAACATGTGTTTAAGAGCTATGCTGGAAACAGCAGAAAT" + "AGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGG" + "CACCGAGTCGGTGCTTTTTTT";
doc.createSequence("gRNA_b_seq", version, gRNA_b_elements, Sequence.IUPAC_DNA);
// Create Sequence for mKate
String mKate_seq_elements = "TCTAAGGGCGAAGAGCTGATTAAGGAGAACATGCACATGAAGCTG" + "TACATGGAGGGCACCGTGAACAACCACCACTTCAAGTGCACATCC" + "GAGGGCGAAGGCAAGCCCTACGAGGGCACCCAGACCATGAGAATC" + "AAGGTGGTCGAGGGCGGCCCTCTCCCCTTCGCCTTCGACATCCTG" + "GCTACCAGCTTCATGTACGGCAGCAAAACCTTCATCAACCACACC" + "CAGGGCATCCCCGACTTCTTTAAGCAGTCCTTCCCTGAGGTAAGT" + "GGTCCTACCTCATCAGGAACATGTGTTTTAGAGCTAGAAATAGCA" + "AGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACC" + "GAGTCGGTGCTACTAACTCTCGAGTCTTCTTTTTTTTTTTCACAG" + "GGCTTCACATGGGAGAGAGTCACCACATACGAAGACGGGGGCGTG" + "CTGACCGCTACCCAGGACACCAGCCTCCAGGACGGCTGCCTCATC" + "TACAACGTCAAGATCAGAGGGGTGAACTTCCCATCCAACGGCCCT" + "GTGATGCAGAAGAAAACACTCGGCTGGGAGGCCTCCACCGAGATG" + "CTGTACCCCGCTGACGGCGGCCTGGAAGGCAGAAGCGACATGGCC" + "CTGAAGCTCGTGGGCGGGGGCCACCTGATCTGCAACTTGAAGACC" + "ACATACAGATCCAAGAAACCCGCTAAGAACCTCAAGATGCCCGGC" + "GTCTACTATGTGGACAGAAGACTGGAAAGAATCAAGGAGGCCGAC" + "AAAGAGACCTACGTCGAGCAGCACGAGGTGGCTGTGGCCAGATAC" + "TGCG";
doc.createSequence("mKate_seq", version, mKate_seq_elements, Sequence.IUPAC_DNA);
// Create Sequence for CRP_b promoter
String CRP_b_seq_elements = "GCTCCGAATTTCTCGACAGATCTCATGTGATTACGCCAAGCTACG" + "GGCGGAGTACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAG" + "TACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAGTTCTGTC" + "CTCCGAGCGGAGACTCTAGATACCTCATCAGGAACATGTTGGAAT" + "TCTAGGCGTGTACGGTGGGAGGCCTATATAAGCAGAGCTCGTTTA" + "GTGAACCGTCAGATCGCCTCGAGTACCTCATCAGGAACATGTTGG" + "ATCCAATTCGACC";
doc.createSequence("CRP_b_seq", version, CRP_b_seq_elements, Sequence.IUPAC_DNA);
// Create ComponentDefinition for a Constitutive Promoter
doc.createComponentDefinition("pConst", version, ComponentDefinition.DNA).addRole(SequenceOntology.PROMOTER);
// Create ComponentDefinition for cas9m_BFP coding sequence
doc.createComponentDefinition("cas9m_BFP_cds", version, ComponentDefinition.DNA).addRole(SequenceOntology.CDS);
// Create ComponentDefinition for cas9m_BFP gene
ComponentDefinition cas9m_BFP_gene = doc.createComponentDefinition("cas9m_BFP_gene", version, ComponentDefinition.DNA);
cas9m_BFP_gene.addRole(SequenceOntology.PROMOTER);
cas9m_BFP_gene.createSequenceConstraint("cas9m_BFP_gene_constraint", RestrictionType.PRECEDES, "pConst", "cas9m_BFP_cds");
// Create ComponentDefintion for cas9m_BFP protein
doc.createComponentDefinition("cas9m_BFP", version, ComponentDefinition.PROTEIN);
// Create ComponentDefintion for CRa_U6 promoter
ComponentDefinition CRa_U6 = doc.createComponentDefinition("CRa_U6", version, ComponentDefinition.DNA);
CRa_U6.addRole(SequenceOntology.PROMOTER);
CRa_U6.addSequence("CRa_U6_seq");
// Create ComponentDefintion for gRNA_b coding sequence
ComponentDefinition gRNA_b_nc = doc.createComponentDefinition("gRNA_b_nc", version, ComponentDefinition.DNA);
gRNA_b_nc.addRole(SequenceOntology.CDS);
gRNA_b_nc.addSequence("gRNA_b_seq");
// Create ComponentDefinition for gRNA_b terminator
doc.createComponentDefinition("gRNA_b_terminator", version, ComponentDefinition.DNA).addRole(SequenceOntology.TERMINATOR);
// Create ComponentDefinition for gRNA_b gene
ComponentDefinition gRNA_b_gene = doc.createComponentDefinition("gRNA_b_gene", version, ComponentDefinition.DNA);
gRNA_b_gene.addRole(SequenceOntology.PROMOTER);
gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint1", RestrictionType.PRECEDES, "CRa_U6", "gRNA_b_nc");
gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint2", RestrictionType.PRECEDES, "gRNA_b_nc", "gRNA_b_terminator");
// Create ComponentDefinition for gRNA_b RNA
doc.createComponentDefinition("gRNA_b", version, ComponentDefinition.RNA).addRole(SequenceOntology.SGRNA);
SequenceOntology so = new SequenceOntology();
URI sgrna = so.getURIbyName("sgRNA");
// Create ComponentDefinition for cas9m_BFP gRNA_b complex
doc.createComponentDefinition("cas9m_BFP_gRNA_b", version, ComponentDefinition.COMPLEX);
// Create ComponentDefinition for mKate coding sequence
ComponentDefinition mKate_cds = doc.createComponentDefinition("mKate_cds", version, ComponentDefinition.DNA);
mKate_cds.addRole(SequenceOntology.CDS);
mKate_cds.addSequence("mKate_seq");
// Create ComponentDefinition for mKate gene
ComponentDefinition mKate_gene = doc.createComponentDefinition("mKate_gene", version, ComponentDefinition.DNA);
mKate_gene.addRole(SequenceOntology.PROMOTER);
mKate_gene.createSequenceConstraint("mKate_gene_constraint", RestrictionType.PRECEDES, "pConst", "mKate_cds");
// Create ComponentDefinition for mKate protein
doc.createComponentDefinition("mKate", version, ComponentDefinition.PROTEIN);
// Create ComponentDefinition for Gal4VP16 coding sequence
ComponentDefinition Gal4VP16_cds = doc.createComponentDefinition("Gal4VP16_cds", version, ComponentDefinition.DNA);
Gal4VP16_cds.addRole(SequenceOntology.CDS);
// Create ComponentDefintion for Gal4VP16 gene
ComponentDefinition Gal4VP16_gene = doc.createComponentDefinition("Gal4VP16_gene", version, ComponentDefinition.DNA);
Gal4VP16_gene.addRole(SequenceOntology.PROMOTER);
Gal4VP16_gene.createSequenceConstraint("GAL4VP16_gene_constraint", RestrictionType.PRECEDES, "pConst", "Gal4VP16_cds");
// Create ComponentDefintion for Gal4VP16 protein
doc.createComponentDefinition("Gal4VP16", version, ComponentDefinition.PROTEIN);
// Create ComponentDefinition for CRP_b promoter
ComponentDefinition CRP_b = doc.createComponentDefinition("CRP_b", version, ComponentDefinition.DNA);
CRP_b.addRole(SequenceOntology.PROMOTER);
CRP_b.addSequence("CRP_b_seq");
// Create ComponentDefintiion for EYFP coding sequence
ComponentDefinition EYFP_cds = doc.createComponentDefinition("EYFP_cds", version, ComponentDefinition.DNA);
EYFP_cds.addRole(SequenceOntology.CDS);
// Create ComponentDefinition for EYFP gene
ComponentDefinition EYFP_gene = doc.createComponentDefinition("EYFP_gene", version, ComponentDefinition.DNA);
EYFP_gene.addRole(SequenceOntology.PROMOTER);
EYFP_gene.createSequenceConstraint("EYFP_gene_constraint", RestrictionType.PRECEDES, "CRP_b", "EYFP_cds");
// Create ComponentDefintiion for EYFP protein
doc.createComponentDefinition("EYFP", version, ComponentDefinition.PROTEIN);
// Create ModuleDefintion for CRISPR Repression
ModuleDefinition CRPb_circuit = doc.createModuleDefinition("CRPb_characterization_circuit", version);
// Create the FunctionalComponents for the ModuleDefinition CRISPR_Repression
CRPb_circuit.createFunctionalComponent("cas9m_BFP", AccessType.PRIVATE, "cas9m_BFP", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("cas9m_BFP_gene", AccessType.PRIVATE, "cas9m_BFP_gene", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("gRNA_b", AccessType.PRIVATE, "gRNA_b", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("gRNA_b_gene", AccessType.PRIVATE, "gRNA_b_gene", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("mKate", AccessType.PRIVATE, "mKate", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("mKate_gene", AccessType.PRIVATE, "mKate_gene", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("Gal4VP16", AccessType.PRIVATE, "Gal4VP16", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("Gal4VP16_gene", AccessType.PRIVATE, "Gal4VP16_gene", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("EYFP", AccessType.PRIVATE, "EYFP", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("EYFP_gene", AccessType.PRIVATE, "EYFP_gene", version, DirectionType.NONE);
CRPb_circuit.createFunctionalComponent("cas9m_BFP_gRNA_b", AccessType.PRIVATE, "cas9m_BFP_gRNA_b", version, DirectionType.NONE);
/* Production of mKate from the mKate gene */
Interaction mKate_production = CRPb_circuit.createInteraction("mKate_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
mKate_production.createParticipation("mKate", "mKate", SystemsBiologyOntology.PRODUCT);
mKate_production.createParticipation("mKate_gene", "mKate_gene", SystemsBiologyOntology.PROMOTER);
// Production of GAL4VP16 from the GAL4VP16 gene
Interaction GAL4VP16_production = CRPb_circuit.createInteraction("Gal4VP16_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
GAL4VP16_production.createParticipation("Gal4VP16_gene", "Gal4VP16_gene", SystemsBiologyOntology.PROMOTER);
GAL4VP16_production.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.PRODUCT);
// Production of cas9m_BFP from the cas9m_BFP gene
Interaction cas9m_BFP_production = CRPb_circuit.createInteraction("cas9m_BFP_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
cas9m_BFP_production.createParticipation("cas9m_BFP_gene", "cas9m_BFP_gene", SystemsBiologyOntology.PROMOTER);
cas9m_BFP_production.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.PRODUCT);
// Production of gRNA_b from the gRNA_b gene
Interaction gRNA_b_production = CRPb_circuit.createInteraction("gRNA_b_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
gRNA_b_production.createParticipation("gRNA_b_gene", "gRNA_b_gene", SystemsBiologyOntology.PROMOTER);
gRNA_b_production.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.PRODUCT);
// Activation of EYFP production by GAL4VP16
Interaction EYFP_Activation = CRPb_circuit.createInteraction("EYFP_Activation", SystemsBiologyOntology.STIMULATION);
EYFP_Activation.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.STIMULATOR);
EYFP_Activation.createParticipation("EYFP_gene", "EYFP_gene", SystemsBiologyOntology.PROMOTER);
// Degradation of mKate
Interaction mKate_deg = CRPb_circuit.createInteraction("mKate_deg", SystemsBiologyOntology.DEGRADATION);
mKate_deg.createParticipation("mKate", "mKate", SystemsBiologyOntology.REACTANT);
// Degradation of GAL4VP16
Interaction GAL4VP16_deg = CRPb_circuit.createInteraction("Gal4VP16_deg", SystemsBiologyOntology.DEGRADATION);
GAL4VP16_deg.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.REACTANT);
// Degradation of cas9m_BFP
Interaction cas9m_BFP_deg = CRPb_circuit.createInteraction("cas9m_BFP_deg", SystemsBiologyOntology.DEGRADATION);
cas9m_BFP_deg.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.REACTANT);
// Degradation of gRNA_b
Interaction gRNA_b_deg = CRPb_circuit.createInteraction("gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
gRNA_b_deg.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.REACTANT);
// Degradation of EYFP
Interaction EYFP_deg = CRPb_circuit.createInteraction("EYFP_deg", SystemsBiologyOntology.DEGRADATION);
EYFP_deg.createParticipation("EYFP", "EYFP", SystemsBiologyOntology.REACTANT);
// Degradation of cas9m_BFP_gRNA_b
Interaction cas9m_BFP_gRNA_b_deg = CRPb_circuit.createInteraction("cas9m_BFP_gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
cas9m_BFP_gRNA_b_deg.createParticipation("cas9m_BFP_gRNA_b", "cas9m_BFP_gRNA_b", SystemsBiologyOntology.REACTANT);
// Create Template Module
Module Template_Module = CRPb_circuit.createModule("CRISPR_Template", "CRISPR_Template", version);
// Add MapsTos to Template Module
Template_Module.createMapsTo("cas9m_BFP_map", RefinementType.USELOCAL, "cas9m_BFP", "cas9_generic");
Template_Module.createMapsTo("gRNA_b_map", RefinementType.USELOCAL, "gRNA_b", "gRNA_generic");
Template_Module.createMapsTo("cas9m_BFP_gRNA_map", RefinementType.USELOCAL, "cas9m_BFP_gRNA_b", "cas9_gRNA_complex");
Template_Module.createMapsTo("EYFP_map", RefinementType.USELOCAL, "EYFP", "target");
Template_Module.createMapsTo("EYFP_gene_map", RefinementType.USELOCAL, "EYFP_gene", "target_gene");
// try {
// SBOLWriter.write(doc, "/Users/myers/RepressionModel.rdf");
// }
// catch (XMLStreamException | FactoryConfigurationError | CoreIoException e) {
// e.printStackTrace();
// }
// catch (IOException e) {
// e.printStackTrace();
// }
// END of Repression Model construction. Code below uses trivial manipulations to show other major methods in the library.
ComponentDefinition cas9_generic1 = doc.getComponentDefinition("cas9_generic", version);
ComponentDefinition cas9_generic2 = doc.getComponentDefinition("cas9_generic", null);
if (cas9_generic1.equals(cas9_generic2)) {
System.out.println("Two Cas9 generic protein objects are equal.");
}
gRNA_b_gene.getSequenceConstraint("gRNA_b_gene_constraint1");
CRISPR_Template.setName("C~R*I!S@P#R-based Repression Template");
if (CRISPR_Template.isSetName()) {
CRISPR_Template.unsetName();
CRISPR_Template.setName("CRISPR-based Repression Template");
}
CRISPR_Template.setDescription("Authors: S. Kiani, J. Beal, M. Ebrahimkhani, J. Huh, R. Hall, Z. Xie, Y. Li, and R. Weiss" + "Titel: Crispr transcriptional repression devices and layered circuits in mammalian cells" + "Journal: Nature Methods, vol. 11, no. 7, pp. 723–726, 2014.");
URI gRNA_b_gene_role2 = URI.create("http://identifiers.org/so/SO:0000613");
gRNA_b_gene.addRole(gRNA_b_gene_role2);
if (gRNA_b_gene.containsRole(gRNA_b_gene_role2)) {
gRNA_b_gene.removeRole(gRNA_b_gene_role2);
}
gRNA_b_gene.clearRoles();
if (!gRNA_b_gene.getRoles().isEmpty()) {
System.out.println("gRNA_b_gene set is not empty.");
}
gRNA_b_gene.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
CRP_b.clearSequences();
CRP_b.addSequence("CRP_b_seq");
// CRP_b.addSequence(
// URI.create("http://partsregistry.org/seq/partseq_154")
// );
String prURI = "http://partsregistry.org/";
String prPrefix = "pr";
doc.addNamespace(URI.create(prURI), prPrefix);
ComponentDefinition pConst = doc.getComponentDefinition("pConst", version);
pConst.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/Part:BBa_J23119:Experience"));
String myersLabURI = "http://www.async.ece.utah.edu/";
String myersLabPrefix = "myersLab";
doc.addNamespace(URI.create(myersLabURI), myersLabPrefix);
GenericTopLevel datasheet = doc.createGenericTopLevel("datasheet", "1.1", new QName(myersLabURI, "datasheet", myersLabPrefix));
datasheet.setName("Datasheet for Custom Parameters");
datasheet.createAnnotation(new QName(myersLabURI, "characterizationData", myersLabPrefix), URI.create(myersLabURI + "/measurement/BBa_J23119"));
datasheet.createAnnotation(new QName(myersLabURI, "transcriptionRate", myersLabPrefix), 0.75);
pConst.createAnnotation(new QName(myersLabURI, "datasheet", myersLabPrefix), datasheet.getIdentity());
ComponentDefinition pConst_alt = (ComponentDefinition) doc.createCopy(pConst, "pConst_alt");
// pConst_alt.createAnnotation(
// new QName(prURI, "", prPrefix),
// URI.create("http://parts.igem.org/Part:BBa_J23100"));
Sequence pConst_alt_seq = doc.createSequence("pConst_alt_seq", version, "ttgacggctagctcagtcctaggtacagtgctagc", Sequence.IUPAC_DNA);
pConst_alt.addSequence(pConst_alt_seq);
SBOLValidate.validateSBOL(doc, true, true, true);
if (SBOLValidate.getNumErrors() > 0) {
for (String error : SBOLValidate.getErrors()) {
System.out.println(error);
}
return;
}
SBOLWriter.write(doc, (System.out));
SBOLWriter.write(doc, "RepressionModel.rdf");
}
Also used :
SequenceOntology(org.sbolstandard.core2.SequenceOntology)
ModuleDefinition(org.sbolstandard.core2.ModuleDefinition)
Interaction(org.sbolstandard.core2.Interaction)
QName(javax.xml.namespace.QName)
SBOLDocument(org.sbolstandard.core2.SBOLDocument)
GenericTopLevel(org.sbolstandard.core2.GenericTopLevel)
Sequence(org.sbolstandard.core2.Sequence)
Module(org.sbolstandard.core2.Module)
URI(java.net.URI)
ComponentDefinition(org.sbolstandard.core2.ComponentDefinition)
Example 2 with SBOLConversionException
use of org.sbolstandard.core2.SBOLConversionException in project libSBOLj by SynBioDex.
the class CollectionOutput method main.
/**
* @param args
* @throws SBOLValidationException see SBOL validation rule violation at {@link Collection#addMember(URI)}
* @throws SBOLConversionException
*/
public static void main(String[] args) throws SBOLValidationException, SBOLConversionException {
SBOLDocument document = new SBOLDocument();
document.setDefaultURIprefix("http://parts.igem.org/Promoters/Catalog");
document.setTypesInURIs(false);
Collection col = document.createCollection("Anderson", "");
col.setName("Anderson promoters");
col.setDescription("The Anderson promoter collection");
col.addMember(URI.create("http://partsregistry.org/Part:BBa_J23119"));
col.addMember(URI.create("http://partsregistry.org/Part:BBa_J23118"));
SBOLWriter.write(document, (System.out));
}
Also used :
SBOLDocument(org.sbolstandard.core2.SBOLDocument)
Collection(org.sbolstandard.core2.Collection)
Example 3 with SBOLConversionException
use of org.sbolstandard.core2.SBOLConversionException 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);
}
Also used :
QName(javax.xml.namespace.QName)
SBOLDocument(org.sbolstandard.core2.SBOLDocument)
GenericTopLevel(org.sbolstandard.core2.GenericTopLevel)
Sequence(org.sbolstandard.core2.Sequence)
URI(java.net.URI)
HashSet(java.util.HashSet)
ComponentDefinition(org.sbolstandard.core2.ComponentDefinition)
Example 4 with SBOLConversionException
use of org.sbolstandard.core2.SBOLConversionException in project libSBOLj by SynBioDex.
the class SBOLReader method parseSequenceAnnotationV1.
/**
* @param SBOLDoc
* @param sequenceAnnotation
* @param precedePairs
* @param parentURI
* @param sa_num
* @param instantiatedComponents
* @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)}, </li>
* <li>{@link #parseDnaComponentV1(SBOLDocument, IdentifiableDocument)}, </li>
* <li>{@link Range#Range(URI, int, int)}, </li>
* <li>{@link Range#setDisplayId(String)}, </li>
* <li>{@link Range#setVersion(String)}, </li>
* <li>{@link GenericLocation#GenericLocation(URI)}, </li>
* <li>{@link SequenceAnnotation#SequenceAnnotation(URI, Set)}, </li>
* <li>{@link SequenceAnnotation#setDisplayId(String)}, </li>
* <li>{@link SequenceAnnotation#setVersion(String)}, </li>
* <li>{@link SequenceAnnotation#setWasDerivedFrom(URI)}, </li>
* <li>{@link SequenceAnnotation#setComponent(URI)}, or </li>
* <li>{@link SequenceAnnotation#setAnnotations(List)}; or</li>
* </ul>
* </li>
* <li>the following SBOL validation rule was violated: 11002.</li>
* </ul>
* @throws SBOLConversionException
*/
private static SequenceAnnotation parseSequenceAnnotationV1(SBOLDocument SBOLDoc, NestedDocument<QName> sequenceAnnotation, List<SBOLPair> precedePairs, String parentURI, int sa_num, Set<String> instantiatedComponents) throws SBOLValidationException, SBOLConversionException {
Integer start = null;
Integer end = null;
String strand = null;
URI componentURI = null;
URI identity = sequenceAnnotation.getIdentity();
String persIdentity = sequenceAnnotation.getIdentity().toString();
List<Annotation> annotations = new ArrayList<>();
if (URIPrefix != null) {
persIdentity = createCompliantURI(parentURI, "annotation" + sa_num, "").toString();
identity = createCompliantURI(parentURI, "annotation" + sa_num, version);
}
if (!sequenceAnnotation.getType().equals(Sbol1Terms.SequenceAnnotations.SequenceAnnotation)) {
throw new SBOLConversionException("QName has to be" + Sbol1Terms.SequenceAnnotations.SequenceAnnotation.toString());
}
for (NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.bioStart)) {
if (!(namedProperty.getValue() instanceof Literal) || start != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-11102", sequenceAnnotation.getIdentity());
}
String temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
start = Integer.parseInt(temp);
} else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.bioEnd)) {
if (!(namedProperty.getValue() instanceof Literal) || end != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-11103", sequenceAnnotation.getIdentity());
}
String temp2 = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
end = Integer.parseInt(temp2);
} else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.strand)) {
if (!(namedProperty.getValue() instanceof Literal) || strand != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-11002", sequenceAnnotation.getIdentity());
}
strand = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.subComponent)) {
if (componentURI != null) {
throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
}
if (namedProperty.getValue() instanceof NestedDocument) {
componentURI = parseDnaComponentV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity();
} else {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
}
componentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
}
} else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.precedes)) {
URI left = sequenceAnnotation.getIdentity();
URI right = null;
if (namedProperty.getValue() instanceof NestedDocument) {
// TODO: need to check if ++sa_num here okay
right = parseSequenceAnnotationV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue(), precedePairs, parentURI, ++sa_num, instantiatedComponents).getIdentity();
} else {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-11404", sequenceAnnotation.getIdentity());
}
right = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
}
SBOLPair pair = new SBOLPair(left, right);
precedePairs.add(pair);
} else {
annotations.add(new Annotation(namedProperty));
}
}
String componentDisplayId = URIcompliance.extractDisplayId(componentURI);
String displayId = "annotation" + sa_num;
if (compliant && componentDisplayId != null && !instantiatedComponents.contains(componentDisplayId)) {
identity = createCompliantURI(parentURI, componentDisplayId + "_annotation", version);
persIdentity = createCompliantURI(parentURI, componentDisplayId + "_annotation", "").toString();
displayId = componentDisplayId + "_annotation";
}
// Note: Do not create a seqAnnotation if Location is empty
Location location = null;
if (// create SequenceAnnotation & Component
start != null && end != null) {
URI range_identity = createCompliantURI(persIdentity, "range", version);
location = new Range(range_identity, start, end);
if (!persIdentity.equals("")) {
location.setPersistentIdentity(createCompliantURI(persIdentity, "range", ""));
location.setDisplayId("range");
location.setVersion(version);
}
if (strand != null) {
if (strand.equals("+")) {
location.setOrientation(OrientationType.INLINE);
} else if (strand.equals("-")) {
location.setOrientation(OrientationType.REVERSECOMPLEMENT);
}
}
} else {
URI dummyGenericLoc_id = createCompliantURI(persIdentity, "genericLocation", version);
location = new GenericLocation(dummyGenericLoc_id);
if (!persIdentity.equals("")) {
location.setPersistentIdentity(createCompliantURI(persIdentity, "genericLocation", ""));
location.setDisplayId("genericLocation");
location.setVersion(version);
}
if (strand != null) {
if (strand.equals("+")) {
location.setOrientation(OrientationType.INLINE);
} else if (strand.equals("-")) {
location.setOrientation(OrientationType.REVERSECOMPLEMENT);
}
}
}
Set<Location> locations = new HashSet<>();
locations.add(location);
SequenceAnnotation s = new SequenceAnnotation(identity, locations);
if (!persIdentity.equals("")) {
s.setPersistentIdentity(URI.create(persIdentity));
s.setDisplayId(displayId);
s.setVersion(version);
}
if (identity != sequenceAnnotation.getIdentity())
s.addWasDerivedFrom(sequenceAnnotation.getIdentity());
if (componentURI != null)
s.setComponent(componentURI);
if (!annotations.isEmpty())
s.setAnnotations(annotations);
return s;
}
Also used :
StringifyQName(org.sbolstandard.core.io.json.StringifyQName)
QName(javax.xml.namespace.QName)
ArrayList(java.util.ArrayList)
URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)
URI(java.net.URI)
NestedDocument(org.sbolstandard.core.datatree.NestedDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
Example 5 with SBOLConversionException
use of org.sbolstandard.core2.SBOLConversionException in project libSBOLj by SynBioDex.
the class SBOLReader method parseDnaComponentV1.
/**
* @param SBOLDoc
* @param componentDef
* @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 #parseSequenceAnnotationV1(SBOLDocument, NestedDocument, List, String, int, Set)},</li>
* <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
* <li>{@link Component#Component(URI, AccessType, URI)},</li>
* <li>{@link Component#setDisplayId(String)}, </li>
* <li>{@link Component#setVersion(String)}</li>
* <li>{@link SequenceAnnotation#setComponent(URI)}, </li>
* <li>{@link #parseDnaSequenceV1(SBOLDocument, IdentifiableDocument)}</li>
* <li>{@link RestrictionType#convertToURI(RestrictionType)},</li>
* <li>{@link SequenceConstraint#SequenceConstraint(URI, URI, URI, URI)},</li>
* <li>{@link SequenceConstraint#setDisplayId(String)},</li>
* <li>{@link SequenceConstraint#setVersion(String)},</li>
* <li>{@link ComponentDefinition#ComponentDefinition(URI, Set)},</li>
* <li>{@link ComponentDefinition#setVersion(String)},</li>
* <li>{@link ComponentDefinition#setWasDerivedFrom(URI)}, </li>
* <li>{@link Identified#setAnnotations(List)},</li>
* <li>{@link ComponentDefinition#setComponents(Set)}</li>
* <li>{@link ComponentDefinition#setSequenceConstraints(Set)}</li>
* <li>{@link ComponentDefinition#addSequence(URI)}</li>
* <li>{@link ComponentDefinition#addSequenceAnnotation(SequenceAnnotation)},</li>
* <li>{@link SBOLDocument#addComponentDefinition(ComponentDefinition)}, or</li>
* <li>{@link ComponentDefinition#copy(String, String, String)}; or</li>
* </ul>
* </li>
* <li>the following SBOL validation rule was violated: 10202.</li>
* </ul>
* @throws SBOLConversionException
*/
private static ComponentDefinition parseDnaComponentV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> componentDef) throws SBOLValidationException, SBOLConversionException {
String displayId = null;
String name = null;
String description = null;
URI seq_identity = null;
Set<URI> roles = new HashSet<>();
URI identity = componentDef.getIdentity();
String persIdentity = componentDef.getIdentity().toString();
List<Annotation> annotations = new ArrayList<>();
List<SequenceAnnotation> sequenceAnnotations = new ArrayList<>();
Set<String> instantiatedComponents = new HashSet<>();
Set<Component> components = new HashSet<>();
Set<SequenceConstraint> sequenceConstraints = new HashSet<>();
List<SBOLPair> precedePairs = new ArrayList<>();
Map<URI, URI> componentDefMap = new HashMap<>();
Set<URI> type = new HashSet<>();
type.add(ComponentDefinition.DNA);
type.add(SequenceOntology.LINEAR);
int component_num = 0;
int sa_num = 0;
if (URIPrefix != null) {
displayId = URIcompliance.findDisplayId(componentDef.getIdentity().toString());
identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
}
for (NamedProperty<QName> namedProperty : componentDef.getProperties()) {
if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.displayId)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10204", componentDef.getIdentity());
}
displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
displayId = URIcompliance.fixDisplayId(displayId);
if (URIPrefix != null) {
persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
}
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.name)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10212", componentDef.getIdentity());
}
name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.description)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
throw new SBOLValidationException("sbol-10213", componentDef.getIdentity());
}
description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.type)) {
if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
throw new SBOLValidationException("sbol-10507", componentDef.getIdentity());
}
URI convertedSO = SequenceOntology.convertSeqOntologyV1(((Literal<QName>) namedProperty.getValue()).getValue().toString());
roles.add(convertedSO);
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.annotations)) {
if (namedProperty.getValue() instanceof IdentifiableDocument) {
SequenceAnnotation sa = parseSequenceAnnotationV1(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), precedePairs, persIdentity, ++sa_num, instantiatedComponents);
sequenceAnnotations.add(sa);
URI component_identity = createCompliantURI(persIdentity, "component" + component_num, version);
URI component_persIdentity = createCompliantURI(persIdentity, "component" + component_num, "");
String component_displayId = "component" + component_num;
AccessType access = AccessType.PUBLIC;
URI instantiatedComponent = sa.getComponentURI();
ComponentDefinition instantiatedDef = SBOLDoc.getComponentDefinition(instantiatedComponent);
if (compliant && instantiatedDef != null && instantiatedDef.isSetDisplayId() && !instantiatedComponents.contains(instantiatedDef.getDisplayId())) {
component_identity = createCompliantURI(persIdentity, instantiatedDef.getDisplayId(), version);
component_persIdentity = createCompliantURI(persIdentity, instantiatedDef.getDisplayId(), "");
component_displayId = instantiatedDef.getDisplayId();
instantiatedComponents.add(instantiatedDef.getDisplayId());
} else {
component_num++;
}
Component component = new Component(component_identity, access, instantiatedComponent);
if (!persIdentity.equals("")) {
component.setPersistentIdentity(component_persIdentity);
component.setDisplayId(component_displayId);
component.setVersion(version);
}
components.add(component);
URI originalURI = ((NestedDocument<QName>) namedProperty.getValue()).getIdentity();
componentDefMap.put(originalURI, component_identity);
sa.setComponent(component_identity);
} else {
throw new SBOLConversionException("SequenceAnnotation must be nested in SBOL1.");
}
} else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.dnaSequence)) {
if (seq_identity != null) {
throw new SBOLValidationException("sbol-10512", componentDef.getIdentity());
}
if (namedProperty.getValue() instanceof Literal) {
if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
throw new SBOLValidationException("sbol-10512", componentDef.getIdentity());
}
seq_identity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
} else {
seq_identity = parseDnaSequenceV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity();
}
} else {
annotations.add(new Annotation(namedProperty));
}
}
if (roles.isEmpty())
roles.add(SequenceOntology.ENGINEERED_REGION);
int sc_number = 0;
for (SBOLPair pair : precedePairs) {
URI sc_identity = createCompliantURI(persIdentity, "sequenceConstraint" + ++sc_number, version);
URI restrictionURI = RestrictionType.convertToURI(RestrictionType.PRECEDES);
// RestrictionType restriction = RestrictionType.convertToRestrictionType(restrictionURI);
URI subject = null;
URI object = null;
for (URI key : componentDefMap.keySet()) {
if (pair.getLeft().equals(key)) {
subject = componentDefMap.get(key);
} else if (pair.getRight().equals(key)) {
object = componentDefMap.get(key);
}
}
SequenceConstraint sc = null;
if (compliant && !persIdentity.equals("")) {
String subjectId = URIcompliance.extractDisplayId(subject);
String objectId = URIcompliance.extractDisplayId(object);
sc_identity = createCompliantURI(persIdentity, subjectId + "_cons_" + objectId, version);
sc = new SequenceConstraint(sc_identity, restrictionURI, subject, object);
sc.setPersistentIdentity(createCompliantURI(persIdentity, subjectId + "_cons_" + objectId, ""));
sc.setDisplayId(subjectId + "_cons_" + objectId);
sc.setVersion(version);
} else {
sc = new SequenceConstraint(sc_identity, restrictionURI, subject, object);
}
sequenceConstraints.add(sc);
}
ComponentDefinition c = new ComponentDefinition(identity, type);
if (!persIdentity.equals("")) {
c.setPersistentIdentity(URI.create(persIdentity));
c.setVersion(version);
}
if (roles != null)
c.setRoles(roles);
if (identity != componentDef.getIdentity())
c.addWasDerivedFrom(componentDef.getIdentity());
if (displayId != null)
c.setDisplayId(displayId);
if (name != null && !name.isEmpty())
c.setName(name);
if (description != null && !description.isEmpty())
c.setDescription(description);
if (seq_identity != null)
c.addSequence(seq_identity);
if (!annotations.isEmpty())
c.setAnnotations(annotations);
if (!components.isEmpty())
c.setComponents(components);
if (!sequenceAnnotations.isEmpty()) {
for (SequenceAnnotation sa : sequenceAnnotations) {
if (!dropObjectsWithDuplicateURIs || c.getSequenceAnnotation(sa.getIdentity()) == null) {
c.addSequenceAnnotation(sa);
}
}
}
if (!sequenceConstraints.isEmpty())
c.setSequenceConstraints(sequenceConstraints);
ComponentDefinition oldC = SBOLDoc.getComponentDefinition(identity);
if (oldC == null) {
SBOLDoc.addComponentDefinition(c);
} else if (c.getWasDerivedFroms().size() > 0 && oldC.getWasDerivedFroms().size() > 0 && !c.getWasDerivedFroms().equals(oldC.getWasDerivedFroms())) {
URI wasDerivedFrom = (URI) c.getWasDerivedFroms().toArray()[0];
Set<TopLevel> topLevels = SBOLDoc.getByWasDerivedFrom(wasDerivedFrom);
for (TopLevel topLevel : topLevels) {
if (topLevel instanceof ComponentDefinition) {
return (ComponentDefinition) topLevel;
}
}
do {
displayId = displayId + "_";
identity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, version, typesInURI);
persIdentity = createCompliantURI(URIPrefix, TopLevel.COMPONENT_DEFINITION, displayId, "", typesInURI).toString();
} while (SBOLDoc.getComponentDefinition(identity) != null);
c = c.copy(URIPrefix, displayId, version);
if (identity != componentDef.getIdentity()) {
c.clearWasDerivedFroms();
c.addWasDerivedFrom(componentDef.getIdentity());
}
SBOLDoc.addComponentDefinition(c);
} else if (dropObjectsWithDuplicateURIs) {
return oldC;
} else {
if (!c.equals(oldC)) {
throw new SBOLValidationException("sbol-10202", c);
}
}
return c;
}
Also used :
HashSet(java.util.HashSet)
Set(java.util.Set)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)
URI(java.net.URI)
NestedDocument(org.sbolstandard.core.datatree.NestedDocument)
Literal(org.sbolstandard.core.datatree.Literal)
HashSet(java.util.HashSet)
StringifyQName(org.sbolstandard.core.io.json.StringifyQName)
QName(javax.xml.namespace.QName)
IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument)
Aggregations
SBOLDocument (org.sbolstandard.core2.SBOLDocument)6
URI (java.net.URI)5
QName (javax.xml.namespace.QName)5
ArrayList (java.util.ArrayList)4
HashSet (java.util.HashSet)4
Literal (org.sbolstandard.core.datatree.Literal)3
NestedDocument (org.sbolstandard.core.datatree.NestedDocument)3
StringifyQName (org.sbolstandard.core.io.json.StringifyQName)3
URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)3
ComponentDefinition (org.sbolstandard.core2.ComponentDefinition)2
GenericTopLevel (org.sbolstandard.core2.GenericTopLevel)2
ModuleDefinition (org.sbolstandard.core2.ModuleDefinition)2
Sequence (org.sbolstandard.core2.Sequence)2
IOException (java.io.IOException)1
InputStream (java.io.InputStream)1
URISyntaxException (java.net.URISyntaxException)1
HashMap (java.util.HashMap)1
Set (java.util.Set)1
Test (org.junit.Test)1
IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)1
