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java.lang.Objectowltools.gaf.bioentities.ProteinTools
public class ProteinTools
Constructor Summary | |
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ProteinTools()
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Method Summary | |
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static void |
createProteinClassesFromQuestForOrthologs(org.semanticweb.owlapi.model.OWLOntology ontology,
InputStream inputStream,
org.semanticweb.owlapi.model.OWLClass proRoot)
Add a named class for each protein extracted from the InputStream . |
static org.semanticweb.owlapi.model.OWLOntology |
createProteinLabelOntology(org.semanticweb.owlapi.model.OWLOntologyManager manager,
org.semanticweb.owlapi.model.IRI ontologyId,
File file)
Create a new ontology (with the given ID) for all proteins in the given Quest for Orthlogs seq XML file. |
static void |
createProteinOntologies(Set<String> ids,
String inputFolder,
String outputFolder,
String catalogXML)
Create protein ontologies from the qfo files. |
static org.semanticweb.owlapi.model.IRI |
createProteinOntologyIRI(String name)
Create an protein ontology IRI for the given subset name. |
static Map<String,String> |
getDefaultDbToTaxon()
Retrieve the default mapping from db name to the numeric part of the NCBI taxon id. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinTools()
Method Detail |
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public static Map<String,String> getDefaultDbToTaxon()
public static void createProteinOntologies(Set<String> ids, String inputFolder, String outputFolder, String catalogXML) throws Exception
ids
- set of taxon idsinputFolder
- the folder for the input qfo seq xml fileoutputFolder
- folder for the owl filescatalogXML
-
Exception
public static org.semanticweb.owlapi.model.IRI createProteinOntologyIRI(String name)
name
- subset
public static org.semanticweb.owlapi.model.OWLOntology createProteinLabelOntology(org.semanticweb.owlapi.model.OWLOntologyManager manager, org.semanticweb.owlapi.model.IRI ontologyId, File file) throws IOException, XMLStreamException, org.semanticweb.owlapi.model.OWLOntologyCreationException
manager
- ontologyId
- ontology idfile
- qfo file
IOException
XMLStreamException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public static void createProteinClassesFromQuestForOrthologs(org.semanticweb.owlapi.model.OWLOntology ontology, InputStream inputStream, org.semanticweb.owlapi.model.OWLClass proRoot) throws XMLStreamException
InputStream
.
Expects to stream to be an seqXML from Quest for Orthologs.
ontology
- inputStream
- proRoot
-
XMLStreamException
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