public interface Cache
Modifier and Type | Method and Description |
---|---|
java.util.Collection<Alignment> |
alignments() |
java.util.Collection<Alignment> |
alignments(java.net.URI u1,
java.net.URI u2) |
void |
close() |
void |
eraseAlignment(java.lang.String uri,
boolean eraseFromDB)
Non publicised class
|
void |
eraseOntologyNetwork(java.lang.String uri,
boolean eraseFromDB) |
void |
flushCache()
The equivalent primitives to both getAlignments()
within a network of ontologies are available from the network itself
|
java.lang.String |
generateAlignmentUri() |
java.lang.String |
generateOntologyNetworkUri() |
Alignment |
getAlignment(java.lang.String uri)
retrieve full alignment from id (and cache it)
|
java.util.Set<Alignment> |
getAlignmentByURI(java.lang.String uri)
retrieve full alignment from URI or description
|
java.util.Set<Alignment> |
getAlignments(java.net.URI uri) |
java.util.Set<Alignment> |
getAlignments(java.net.URI uri1,
java.net.URI uri2)
returns the alignments between two ontologies
if one of the ontologies is null, then return them all
|
java.util.Set<Alignment> |
getAlignmentsByDescription(java.lang.String desc) |
Alignment |
getMetadata(java.lang.String uri)
retrieve alignment metadata from id
This is more difficult because we return the alignment we have
disreagarding if it is complete o only metadata
|
OntologyNetwork |
getOntologyNetwork(java.lang.String uri)
retrieve network of ontologies from id
|
void |
init(java.util.Properties p,
java.lang.String prefix)
loads the alignment descriptions from the database and put them in the
alignmentTable hashtable
|
boolean |
isAlignmentStored(Alignment alignment) |
boolean |
isNetworkStored(OntologyNetwork network) |
java.util.Collection<java.net.URI> |
ontologies() |
java.util.Collection<OntologyNetwork> |
ontologyNetworks() |
java.lang.String |
recordNewAlignment(Alignment alignment,
boolean force)
records newly created alignment and returns its idenfifier
|
java.lang.String |
recordNewAlignment(java.lang.String uri,
Alignment al,
boolean force)
records alignment identified by id and returns its idenfifier
|
java.lang.String |
recordNewNetwork(OntologyNetwork network,
boolean force)
records newly created network and returns its idenfifier
|
java.lang.String |
recordNewNetwork(java.lang.String uri,
OntologyNetwork network,
boolean force)
records network identified by id and returns its idenfifier
|
void |
reset() |
void |
storeAlignment(java.lang.String uri) |
void |
storeOntologyNetwork(java.lang.String uri) |
void init(java.util.Properties p, java.lang.String prefix) throws AlignmentException
p:
- the initialisation parametersprefix:
- the URI prefix of the current serverAlignmentException
- when something goes wrong (cannot access database, but format)void reset() throws AlignmentException
AlignmentException
void close() throws AlignmentException
AlignmentException
java.util.Collection<Alignment> alignments()
java.util.Collection<java.net.URI> ontologies()
java.util.Collection<OntologyNetwork> ontologyNetworks()
java.util.Collection<Alignment> alignments(java.net.URI u1, java.net.URI u2)
java.lang.String generateAlignmentUri()
java.lang.String generateOntologyNetworkUri()
Alignment getMetadata(java.lang.String uri) throws AlignmentException
uri:
- the URI of the alignment whose metadata to retrieveAlignmentException
- when something goes wrong (cannot resolve URI)Alignment getAlignment(java.lang.String uri) throws AlignmentException
uri:
- the URI of the alignment to retrieveAlignmentException
- when something goes wrong (cannot resolve URI)java.util.Set<Alignment> getAlignmentByURI(java.lang.String uri) throws AlignmentException
uri:
- the URI of the alignments to retrieveAlignmentException
- when something goes wrong (cannot resolve URI)java.util.Set<Alignment> getAlignmentsByDescription(java.lang.String desc) throws AlignmentException
AlignmentException
OntologyNetwork getOntologyNetwork(java.lang.String uri) throws AlignmentException
uri:
- the URI of the network to retrieveAlignmentException
- when something goes wrong (cannot resolve URI)java.util.Set<Alignment> getAlignments(java.net.URI uri)
java.util.Set<Alignment> getAlignments(java.net.URI uri1, java.net.URI uri2)
uri1
- anduri2:
- the URIs two ontologies from which retrieving alignmentsvoid flushCache()
java.lang.String recordNewAlignment(Alignment alignment, boolean force)
alignment:
- the alignment to recordforce:
- true if the alignment is too be recorded even if it was recordedjava.lang.String recordNewAlignment(java.lang.String uri, Alignment al, boolean force) throws AlignmentException
uri:
- the URI of the alignment to recordal:
- the alignment to recordforce:
- true if the alignment is too be recorded even if it was recordedAlignmentException
- when something goes wrong (cannot resolve URI)java.lang.String recordNewNetwork(OntologyNetwork network, boolean force)
network:
- the network of ontologies to recordforce:
- true if the network is too be recorded even if it was recordedjava.lang.String recordNewNetwork(java.lang.String uri, OntologyNetwork network, boolean force) throws AlignmentException
uri:
- the URI of the network to recordnetwork:
- the network of ontologies to recordforce:
- true if the network is too be recorded even if it was recordedAlignmentException
- when something goes wrong (cannot resolve URI)boolean isAlignmentStored(Alignment alignment)
boolean isNetworkStored(OntologyNetwork network)
void eraseAlignment(java.lang.String uri, boolean eraseFromDB) throws AlignmentException
uri:
- the URI of the alignment to eraseeraseFromDB:
- true if the alignment is erased from the database cacheAlignmentException
- when something goes wrong (cannot resolve URI)void eraseOntologyNetwork(java.lang.String uri, boolean eraseFromDB) throws AlignmentException
AlignmentException
void storeAlignment(java.lang.String uri) throws AlignmentException
AlignmentException
void storeOntologyNetwork(java.lang.String uri) throws AlignmentException
AlignmentException
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