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Types & classes568 in github.com/bio2rdf/bio2rdf-scripts

↓ 12 callersClassLiteral
toxkb/outdated_gems/rdfextraction/lib/literal.rb:10
↓ 2 callersClassGraph
toxkb/outdated_gems/rdfextraction/lib/graph.rb:9
↓ 1 callersClassDictItem
linkedSPLs/LinkedSPLs-activeMoiety/createActiveMoietySubInRDF.py:35
↓ 1 callersClassDictItem
linkedSPLs/LinkedSPLs-clinicalDrug/createClinicalDrugSubInRDF.py:31
ClassAbandonedConnectionCleanupThread
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/AbandonedConnectionCleanupThread.java:30
ClassAbsortCorrectionTypes
@author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/AbsortCorrectionTypes.java:29
ClassAbstractPdbXmlParser
@author Jose Cruz-Toledo @author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/AbstractPdbXmlParser.java:37
ClassAbstractPdbXmlParserTest
@author Alexander De Leon
pdb/pdb2rdf-parser/src/test/java/com/dumontierlab/pdb2rdf/parser/AbstractPdbXmlParserTest.java:34
ClassAffymetrixParser
* Affymetrix RDFizer * @version 1.0 * @author Michel Dumontier * @description http://www.affymetrix.com/support/technical/manual/taf_manual.affx *
affymetrix/affymetrix.php:30
EnumAnnotation
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/PdbOwlVocabulary.java:669
ClassAppCommand
toxkb/toxcast/toxcast2rdf.rb:60
ClassAppendingBatchVisitor
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/PreparedStatement.java:575
ClassArchival
toxkb/toxnet/archival2rdf.rb:13
ClassArray
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/fabric/xmlrpc/base/Array.java:26
ClassAssertionFailedException
Assertions for empty code paths that should never be executed.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/AssertionFailedException.java:29
ClassAtomSiteCategoryHandler
@author Jose Cruz-Toledo @author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/AtomSiteCategoryHandler.java:48
ClassAtomSiteCategoryHandlerTest
@author Alexander De Leon
pdb/pdb2rdf-parser/src/test/java/com/dumontierlab/pdb2rdf/parser/AtomSiteCategoryHandlerTest.java:39
ClassAuthTestPlugin
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/ConnectionRegressionTest.java:3710
ClassAuthenticatedXmlRpcMethodCaller
An XML-RPC method caller which wraps another caller with RFC-2617 authentication.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/fabric/proto/xmlrpc/AuthenticatedXmlRpcMethodCaller.java:35
InterfaceAuthenticationPlugin
Implementors of this interface can be installed via the "authenticationPlugins" configuration property. The driver will create one instance of a give
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/AuthenticationPlugin.java:35
InterfaceBalanceStrategy
Implement this interface to provide a new load balancing strategy for URLs of the form "jdbc:mysql:loadbalance://..", and provide the implementation c
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/BalanceStrategy.java:38
ClassBase64Decoder
This decoder implements standard Base64 decoding except it allows and silently ignores non-base64 input characters (spaces, line breaks etc) Note: Ja
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/util/Base64Decoder.java:31
ClassBaseBugReport
Base class to help file bug reports for Connector/J. <p> MySQL AB, 2008 Sun Microsystems, 2009 Oracle Corporation <ul> really </ul> appreciates repe
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/util/BaseBugReport.java:82
ClassBaseFabricTestCase
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/fabric/BaseFabricTestCase.java:30
ClassBasePerfTest
Base class for performance test cases. Handles statistics.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/perf/BasePerfTest.java:35
ClassBaseTestCase
Base class for all test cases. Creates connections, statements, etc. and closes them.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/BaseTestCase.java:57
ClassBatchParams
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/PreparedStatement.java:106
InterfaceBatchVisitor
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/PreparedStatement.java:565
ClassBatchedBindValues
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ServerPreparedStatement.java:80
ClassBestResponseTimeBalanceStrategy
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/BestResponseTimeBalanceStrategy.java:31
ClassBindValue
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ServerPreparedStatement.java:94
ClassBio2RDFApp
runparser.php:27
InterfaceBio2RdfPdbNamespace
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/uri/Bio2RdfPdbUriPattern.java:262
EnumBio2RdfPdbUriPattern
@author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/uri/Bio2RdfPdbUriPattern.java:26
ClassBiomodelsParser
biomodels/biomodels.php:33
ClassBioportalParser
bioportal/bioportal.php:33
ClassBlob
The representation (mapping) in the JavaTM programming language of an SQL BLOB value. An SQL BLOB is a built-in type that stores a Binary Large Object
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/Blob.java:40
ClassBlobFromLocator
The representation (mapping) in the JavaTM programming language of an SQL BLOB value. An SQL BLOB is a built-in type that stores a Binary Large Object
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/BlobFromLocator.java:42
ClassBlobRegressionTest
Tests fixes for BLOB handling.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/BlobRegressionTest.java:43
ClassBlobTest
Tests BLOB functionality in the driver.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/simple/BlobTest.java:40
ClassBooleanConnectionProperty
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionPropertiesImpl.java:50
ClassBuffer
Buffer contains code to read and write packets from/to the MySQL server.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/Buffer.java:33
ClassBufferRow
A RowHolder implementation that holds one row packet (which is re-used by the driver, and thus saves memory allocations), and tries when possible to a
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/BufferRow.java:49
ClassBug39426Interceptor
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/StatementRegressionTest.java:5376
ClassBug72712StatementInterceptor
Statement interceptor used to implement preceding test.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/ConnectionRegressionTest.java:6334
ClassBug73663StatementInterceptor
Statement interceptor used to implement preceding test.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/CharsetRegressionTest.java:71
ClassBusyThread
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/StressRegressionTest.java:183
ClassByteArrayRow
A RowHolder implementation that is for cached results (a-la mysql_store_result()).
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ByteArrayRow.java:41
ClassCTDParser
* Parser for CTD: The Comparative Toxicogenomics Database (http://ctd.mdibl.org/) * documentation: http://ctdbase.org/downloads * download pattern
ctd/ctd.php:31
InterfaceCacheAdapter
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CacheAdapter.java:28
InterfaceCacheAdapterFactory
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CacheAdapterFactory.java:29
ClassCachedResultSetMetaData
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CachedResultSetMetaData.java:28
ClassCachedRowsetTest
Regression test cases for the ResultSet class.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/CachedRowsetTest.java:36
ClassCallableStatement
Representation of stored procedures for JDBC
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CallableStatement.java:53
ClassCallableStatementParam
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CallableStatement.java:78
ClassCallableStatementParamInfo
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CallableStatement.java:127
ClassCallableStatementParamInfoJDBC3
Can't implement this directly, as then you can't use callable statements on JDK-1.3.1, which unfortunately isn't EOL'd yet, and still present quite a
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CallableStatement.java:363
ClassCallableStatementRegressionTest
Tests fixes for bugs in CallableStatement code.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/CallableStatementRegressionTest.java:47
ClassCallableStatementTest
Tests callable statement functionality.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/simple/CallableStatementTest.java:43
ClassCallableStatementWrapper
Wraps callable statements created by pooled connections.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/jdbc2/optional/CallableStatementWrapper.java:49
ClassCancelTask
Thread used to implement query timeouts...Eventually we could be more efficient and have one thread with timers, but this is a straightforward and sim
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/StatementImpl.java:69
ClassCancelTask
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/ConnectionRegressionTest.java:5413
ClassCcrisDatabase
toxkb/toxnet/ccris2rdf.rb:13
ClassCellCategoryHandler
@author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/CellCategoryHandler.java:37
ClassCharsetMapping
Mapping between MySQL charset names and Java charset names. I've investigated placing these in a .properties file, but unfortunately under most appser
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CharsetMapping.java:43
ClassCharsetRegressionTest
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/CharsetRegressionTest.java:35
ClassCharsetTest
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/simple/CharsetTest.java:48
ClassChemCompCategory
@author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/ChemCompCategory.java:42
ClassChemblParser
chembl/chembl.php:35
ClassCis
toxkb/toxnet/cis2rdf.rb:13
ClassCitationAuthorCategoryHandler
@author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/CitationAuthorCategoryHandler.java:41
ClassCitationCategoryHandler
@author Alexander De Leon
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/CitationCategoryHandler.java:43
EnumClass
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/PdbOwlVocabulary.java:46
EnumClass
pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/rna/vocabulary/RnaKbOwlVocabulary.java:40
ClassClient
XML-RPC client.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/fabric/xmlrpc/Client.java:49
ClassClient1_Fabric
Basic usage client. print out a bunch of information we can ask for from Fabric
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/demo/fabric/Client1_Fabric.java:31
ClassClinicalTrialsParser
clinicaltrials/clinicaltrials.php:32
ClassClob
Simplistic implementation of java.sql.Clob for MySQL Connector/J
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/Clob.java:37
ClassClusterController
@author Alexander De Leon
pdb/pdb2rdf-cluster/src/main/java/com/dumontierlab/pdb2rdf/cluster/servlet/ClusterController.java:41
ClassClusterIterator
@author Alexander De Leon
pdb/pdb2rdf-cli/src/main/java/com/dumontierlab/pdb2rdf/util/ClusterIterator.java:33
ClassClusterServer
@author Alexander De Leon
pdb/pdb2rdf-cluster/src/main/java/com/dumontierlab/pdb2rdf/cluster/ClusterServer.java:43
ClassCollation
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CharsetMapping.java:897
ClassCommunicationsException
An exception to represent communications errors with the database. Attempts to provide 'friendler' error messages to end-users, including last time a
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CommunicationsException.java:34
ClassCommunicationsException
An exception to represent communications errors with the database. Attempts to provide 'friendler' error messages to end-users, including last time a
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/exceptions/jdbc4/CommunicationsException.java:40
ClassComparableWrapper
Helper/wrapper class to provide means of sorting objects by using a sorting key.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/DatabaseMetaData.java:481
ClassCompoundCacheKey
Used as a key for caching callable statements which (may) depend on current catalog...In 5.0.x, they don't (currently), but stored procedure names soo
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionImpl.java:173
ClassCompressedInputStream
Used to de-compress packets from the MySQL server when protocol-level compression is turned on.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/CompressedInputStream.java:39
ClassConcept
toxkb/outdated_gems/rdfextraction/lib/concept.rb:10
InterfaceConnection
This interface contains methods that are considered the "vendor extension" to the JDBC API for MySQL's implementation of java.sql.Connection. For tho
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/Connection.java:39
ClassConnectionErrorFiringInvocationHandler
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/LoadBalancingConnectionProxy.java:83
ClassConnectionErrorFiringInvocationHandler
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/jdbc2/optional/WrapperBase.java:68
ClassConnectionFeatureNotAvailableException
Thrown when a client requests a connection-level feature that isn't available for this particular distribution of Connector/J (currently only used by
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionFeatureNotAvailableException.java:30
ClassConnectionGroup
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionGroup.java:35
ClassConnectionGroupManager
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionGroupManager.java:35
ClassConnectionImpl
A Connection represents a session with a specific database. Within the context of a Connection, SQL statements are executed and results are returned.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionImpl.java:78
InterfaceConnectionLifecycleInterceptor
Implementors of this interface can be installed via the "connectionLifecycleInterceptors" configuration property and receive events and alter behavior
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionLifecycleInterceptor.java:35
ClassConnectionListener
Listener for PooledConnection events.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/testsuite/regression/PooledConnectionRegressionTest.java:355
ClassConnectionPhantomReference
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/NonRegisteringDriver.java:885
InterfaceConnectionProperties
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionProperties.java:28
ClassConnectionPropertiesImpl
Represents configurable properties for Connections and DataSources. Can also expose properties as JDBC DriverPropertyInfo if required as well.
linkedSPLs/LinkedSPLs-update/lib/mysql-connector-java-5.1.33/src/com/mysql/jdbc/ConnectionPropertiesImpl.java:46
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