| Package | Description |
|---|---|
| org.sbolstandard.core2 | |
| org.synbiohub.frontend |
| Modifier and Type | Method and Description |
|---|---|
SBOLDocument |
SBOLDocument.changeURIPrefixVersion(String URIPrefix,
String version,
String defaultVersion)
Copy all objects to an a new SBOL Document and change the URI prefix/version
of each object
|
SBOLDocument |
SBOLDocument.createRecursiveCopy(TopLevel topLevel)
Creates an identical copy of the given top-level and returns it in a new
SBOLDocument.
|
static SBOLDocument |
SnapGene.detectFeatures(String sequence,
String uriPrefix,
String displayId,
String version,
String pngFileName,
String name)
Detect features in a sequence using a SnapGene Server
|
static SBOLDocument |
SnapGene.detectFeatures(String sequence,
String uriPrefix,
String displayId,
String version,
String pngFileName,
String name,
boolean circular)
Detect features in a sequence using a SnapGene Server
|
static SBOLDocument |
SBOLReader.read(File file)
Parses the given RDF file and stores its contents in an SBOLDocument object.
|
static SBOLDocument |
SBOLReader.read(InputStream in)
Takes in a given RDF InputStream and converts the file to an SBOLDocument.
|
static SBOLDocument |
SBOLReader.read(String fileName)
Takes in the given RDF filename and converts the file to an SBOLDocument.
|
static SBOLDocument |
SBOLValidate.validate(PrintStream outputStream,
PrintStream errorStream,
String fileName,
String URIPrefix,
boolean complete,
boolean compliant,
boolean bestPractice,
boolean typesInURI,
String version,
boolean keepGoing,
String compareFile,
String compareFileName,
String mainFileName,
String topLevelURIStr,
boolean genBankOut,
boolean sbolV1out,
boolean fastaOut,
boolean snapGeneOut,
String outputFile,
boolean showDetail,
boolean noOutput,
boolean changeURIPrefix)
Deprecated.
|
static SBOLDocument |
SBOLValidate.validate(PrintStream outputStream,
PrintStream errorStream,
String fileName,
String URIPrefix,
boolean complete,
boolean compliant,
boolean bestPractice,
boolean typesInURI,
String version,
boolean keepGoing,
String compareFile,
String compareFileName,
String mainFileName,
String topLevelURIStr,
boolean genBankOut,
boolean sbolV1out,
boolean fastaOut,
String outputFile,
boolean showDetail,
boolean noOutput,
boolean changeURIPrefix)
Deprecated.
|
static SBOLDocument |
SBOLValidate.validate(PrintStream outputStream,
PrintStream errorStream,
String fileName,
String URIPrefix,
String defaultDisplayId,
boolean complete,
boolean compliant,
boolean bestPractice,
boolean typesInURI,
String version,
boolean keepGoing,
String compareFile,
String compareFileName,
String mainFileName,
String topLevelURIStr,
boolean genBankOut,
boolean sbolV1out,
boolean fastaOut,
boolean snapGeneOut,
String outputFile,
boolean showDetail,
boolean noOutput,
boolean changeURIPrefix)
The validate function will: - perform validation on the given input SBOL file
- perform comparison between 2 SBOL files - perform interconversion between
SBOL1 and SBOL2 - convert from SBOL to GenBank - convert from SBOL to FASTA
|
| Modifier and Type | Method and Description |
|---|---|
static void |
SBOLValidate.compareDocuments(String file1,
SBOLDocument doc1,
String file2,
SBOLDocument doc2)
Compares the given two SBOL documents and outputs the difference into the
list of errors.
|
void |
SBOLDocument.createCopy(SBOLDocument document)
Creates an identical copy of each top-level element of a document, and then
adds the created top-level to the corresponding list of top-levels in this
SBOL document.
|
void |
SBOLDocument.createRecursiveCopy(SBOLDocument document,
TopLevel topLevel) |
static void |
SBOLValidate.validateSBOL(SBOLDocument sbolDocument,
boolean complete,
boolean compliant,
boolean bestPractice)
Validates the given SBOL document.
|
void |
IdentifiedVisitor.visitDocument(SBOLDocument sbolDocument)
Visits all identified objects within an SBOL document
|
static void |
SBOLWriter.write(SBOLDocument doc,
File file)
Outputs the given SBOL document's data from the RDF/XML serialization to the given file.
|
static void |
SBOLWriter.write(SBOLDocument doc,
File file,
String fileType)
Outputs this SBOL document's data from the serialization in the given serialization format
to the given file.
|
static void |
SBOLWriter.write(SBOLDocument doc,
OutputStream out)
Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.
|
static void |
SBOLWriter.write(SBOLDocument doc,
OutputStream out,
String fileType)
Serializes a given SBOLDocument and outputs the data from the serialization to the given output stream
in the specified fileType format.
|
static void |
SBOLWriter.write(SBOLDocument doc,
String filename)
Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.
|
static void |
SBOLWriter.write(SBOLDocument doc,
String filename,
String fileType)
Outputs this SBOL document's data from serialization in the given serialization format
to a new file with the given file name.
|
| Modifier and Type | Method and Description |
|---|---|
SBOLDocument |
SynBioHubFrontend.getSBOL(URI topLevelUri)
Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
|
SBOLDocument |
SynBioHubFrontend.getSBOL(URI topLevelUri,
boolean recursive)
Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
|
| Modifier and Type | Method and Description |
|---|---|
void |
SynBioHubFrontend.addToCollection(URI collectionUri,
boolean overwrite,
SBOLDocument document)
Add SBOL document to an existing private collection on SynBioHub
|
void |
SynBioHubFrontend.createCollection(String id,
String version,
String name,
String description,
String citations,
boolean overwrite,
SBOLDocument document)
Create a new private collection on SynBioHub and add the contents of the
SBOL document to this collection
|
void |
SynBioHubFrontend.removeRegistryParts(SBOLDocument document)
Remove all parts from this registry from a given SBOL document
|