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Alignment API and Server 3.2 | |||||||||
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java.lang.Objectfr.inrialpes.exmo.align.service.CacheImpl
public class CacheImpl
This class caches the content of the alignment database. I.e., It loads the metadata in the hash table It stores the alignment when requested It
Field Summary | |
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(package private) Hashtable |
alignmentTable
|
static String |
CACHED
|
(package private) Connection |
conn
|
(package private) int |
CONNECTION_ERROR
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(package private) String |
host
|
(package private) int |
INIT_ERROR
|
(package private) Hashtable |
ontologyTable
|
static String |
OURI1
|
static String |
OURI2
|
(package private) String |
port
|
(package private) int |
rights
|
static String |
STORED
|
(package private) int |
SUCCESS
|
static String |
SVCNS
|
(package private) int |
VERSION
|
Constructor Summary | |
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CacheImpl(DBService service)
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Method Summary | |
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void |
cleanUpCache()
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void |
close()
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String |
generateAlignmentId()
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private String |
generateCellId(String alId)
|
Alignment |
getAlignment(String id)
retrieve full alignment from id (and cache it) |
Set |
getAlignments(URI uri)
|
Set<Alignment> |
getAlignments(URI uri1,
URI uri2)
|
Alignment |
getMetadata(String id)
retrieve alignment metadata from id This is more difficult because we return the alignment we have disreagarding if it is complete o only metadata |
void |
init(Parameters p)
loads the alignment descriptions from the database and put them in the alignmentTable hashtable |
void |
initDatabase()
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protected Enumeration |
listAlignments()
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private void |
loadAlignments(boolean force)
loads the alignment descriptions from the database and put them in the alignmentTable hashtable index them under the ontology URIs Beware, the Alignment API has two attributes: onto1 is the OWLOntology object uri1 is the URI object from which loading the ontologies In the database we store: owlontology1 the URI string of the ontology file1 the URI string from which loading the ontologies uri1 which should be the same as the last one... |
String |
quote(String s)
quote: Prepare a string to be used in SQL queries by preceeding occurences of "'", """, and "\" by a "\". |
private int |
randomNum()
|
String |
recordAlignment(String id,
Alignment alignment,
boolean force)
records alignment identified by id |
String |
recordNewAlignment(Alignment alignment,
boolean force)
records newly created alignment |
String |
recordNewAlignment(String id,
Alignment al,
boolean force)
records alignment identified by id |
void |
resetCacheStamp(Alignment result)
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void |
resetDatabase(boolean force)
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protected Alignment |
retrieveAlignment(String id,
Alignment alignment)
loads the full alignments from the database and put them in the alignmentTable hastable should be invoked when: ( result.getExtension(CACHED) == "" && result.getExtension(STORED) != "") { |
protected Alignment |
retrieveDescription(String id)
loads the description of alignments from the database and set them in an alignment object |
void |
storeAlignment(String id)
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void |
updateDatabase()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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Hashtable alignmentTable
Hashtable ontologyTable
String host
String port
int rights
final int VERSION
Connection conn
final int CONNECTION_ERROR
final int SUCCESS
final int INIT_ERROR
public static final String SVCNS
public static final String CACHED
public static final String STORED
public static final String OURI1
public static final String OURI2
Constructor Detail |
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public CacheImpl(DBService service)
Method Detail |
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public void init(Parameters p) throws SQLException, AlignmentException
SQLException
AlignmentException
public void close() throws SQLException
SQLException
private void loadAlignments(boolean force) throws SQLException
SQLException
protected Enumeration listAlignments()
protected Alignment retrieveDescription(String id)
protected Alignment retrieveAlignment(String id, Alignment alignment) throws SQLException, AlignmentException, URISyntaxException
SQLException
AlignmentException
URISyntaxException
public String generateAlignmentId()
private String generateCellId(String alId)
private int randomNum()
public Alignment getMetadata(String id) throws Exception
Exception
public Alignment getAlignment(String id) throws Exception
Exception
public Set getAlignments(URI uri)
public Set<Alignment> getAlignments(URI uri1, URI uri2)
public String recordNewAlignment(Alignment alignment, boolean force)
public String recordNewAlignment(String id, Alignment al, boolean force) throws AlignmentException
AlignmentException
public String recordAlignment(String id, Alignment alignment, boolean force)
public String quote(String s)
public void storeAlignment(String id) throws Exception
Exception
public void resetCacheStamp(Alignment result)
public void cleanUpCache()
public void initDatabase() throws SQLException
SQLException
public void resetDatabase(boolean force) throws SQLException, AlignmentException
SQLException
AlignmentException
public void updateDatabase() throws SQLException, AlignmentException
SQLException
AlignmentException
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Alignment API and Server 3.2 | |||||||||
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