apollo.dataadapter.chado.jdbc
Class SybaseChadoAdapter

java.lang.Object
  apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
      apollo.dataadapter.chado.jdbc.SybaseChadoAdapter

public class SybaseChadoAdapter
extends JdbcChadoAdapter

A subclass of JdbcChadoAdapter specific to Sybase installations of Chado. (And, furthermore, probably specific to the TIGR Chado instances.)

Version:

$Revision: 1.34 $ $Date: 2007-02-07 21:14:14 $ $Author: jcrabtree $

Author:

Jonathan Crabtree

Field Summary

protected static java.lang.Integer	FALSEVAL
protected static org.apache.log4j.Logger	logger
protected static java.lang.Integer	TRUEVAL

Fields inherited from class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

chadoDb, chadoVersion, fkcMap, jdbcUrl, organismLike, password, pkcMap, sqlLogPath, transactionConnection, txnLogPath, username

Constructor Summary

SybaseChadoAdapter()

Method Summary

protected java.lang.String	getAnalysisFeatureIdentityField() analysisfeature.identity was renamed to pidentity in the TIGR/Sybase port of Chado, since identity is a reserved word in Sybase.
protected java.lang.Object	getBooleanValue(boolean val)
protected java.lang.String	getClobLengthFunction()
protected java.sql.Connection	getNewConnection() Opens and return a new Connection to the database specified in the arguments to init.
protected boolean	setForcePlan(java.sql.Statement stmt, boolean on) Run 'set forceplan on' or 'set forceplan off'; this is a Sybase option that forces the Sybase query optimizer to access the tables in the order that they are named in the FROM clause of the SQL query.

Methods inherited from class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

_addExonsToTranscript, _addFeatures, _addFeaturesToFeatureSet, _addTranscriptsToGene, _makeExon, _makeFeatureSet, _makeNewTranscript, _makeSeqFeature, _makeSeqFeature, addGenePredictionResults, addGenePredictionResults, addGenePredictionResults, addOneLevelAnnotations, addPrimaryKeyColumnValue, addProteinAlignments, addSearchHits, beginTransaction, chadoFeatureExists, chadoFeatureExists, commitChanges, commitTransaction, computeMD5Checksum, copyAnnotatedGenesIntoResultTier, decrementGeneTranscriptRanks, decrementTranscriptExonRanks, deleteFeatureDbXrefRow, deleteFeaturepropRow, deleteFeatureRelationshipRow, deleteFeatureSynonymRow, deleteReferencingRows, deleteRow, deleteSynonymRowIfNoLongerNeeded, deleteUnreferencedRow, executeLoggedSelectQuery, executeLoggedSelectQuery, executeLoggedUpdate, getAllChadoSequencesByType, getCDSFeatures, getCDSFeatures, getCDSFeatures, getCdsPolypeptideIds, getChadoInstance, getChadoProgramWhereClause, getChadoVersion, getConnection, getConnectionUsedForLastTransaction, getConnectionWithException, getCurationSet, getCurationSetInRange, getDbId, getDbXrefId, getExonRank, getFeatNamesByType, getFeatureDbXrefId, getFeatureId, getFeatureId, getFeatureIdBySynonym, getFeatureRelationshipId, getFeatureType, getForeignKeyConstraints, getForeignKeyReferenceMapping, getGeneTranscriptIds, getNextPrimaryKeyId, getNullCVTermId, getPrimaryKeyColumn, getPrimaryKeyColumnMapping, getReferencingRowIds, getRelatedFeatureIds, getRelatedFeatureRank, getRelationshipCVTermId, getSeqLengthForFeatureId, getSequence, getSequence, getSynonymId, getTranscriptCdsIds, getTranscriptExonIds, getTranscriptPolypeptideIds, getTranscriptRank, hasOpenTransaction, incrementGeneTranscriptRanks, incrementTranscriptExonRanks, init, initWithException, insertDbRowIfNeeded, insertDbXrefRowIfNeeded, insertFeatureDbXrefRow, insertFeaturelocRow, insertFeaturepropPubRow, insertFeaturepropRow, insertFeaturepropRow, insertFeatureRelationshipRow, insertFeatureRow, insertFeatureSynonymRow, insertPubRowIfNeeded, insertRow, insertSynonymRowIfNeeded, integersTheSame, isSharedExon, loadClass, longsTheSame, rollbackTransaction, setChadoInstance, setPropertyScheme, stringsTheSame, updateFeatureDbXrefRow, updateFeaturelocRow, updateFeaturepropRow, updateFeatureRelationshipRanks, updateFeatureRow, updateRow, validateConnectionAndSequence, validateConnectionAndSequence, zeroPad

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected static final org.apache.log4j.Logger logger

TRUEVAL

protected static final java.lang.Integer TRUEVAL

FALSEVAL

protected static final java.lang.Integer FALSEVAL

Constructor Detail

SybaseChadoAdapter

public SybaseChadoAdapter()

Method Detail

setForcePlan

protected boolean setForcePlan(java.sql.Statement stmt,
                               boolean on)

Run 'set forceplan on' or 'set forceplan off'; this is a Sybase option that forces the Sybase query optimizer to access the tables in the order that they are named in the FROM clause of the SQL query. It is the equivalent of the Oracle optimizer hint "ORDERED".

Parameters:

stmt - JDBC Statement used to execute the set forceplan command.

on - Whether to set this Sybase option on (true) or off (false).

Returns:

The JDBC result value from the executeUpdate command.

getNewConnection

protected java.sql.Connection getNewConnection()
                                        throws java.sql.SQLException

Description copied from class: JdbcChadoAdapter

Opens and return a new Connection to the database specified in the arguments to init.

Overrides:

getNewConnection in class JdbcChadoAdapter

Throws:

java.sql.SQLException

getAnalysisFeatureIdentityField

protected java.lang.String getAnalysisFeatureIdentityField()

analysisfeature.identity was renamed to pidentity in the TIGR/Sybase port of Chado, since identity is a reserved word in Sybase.

Overrides:

getAnalysisFeatureIdentityField in class JdbcChadoAdapter

getBooleanValue

protected java.lang.Object getBooleanValue(boolean val)

Specified by:

getBooleanValue in class JdbcChadoAdapter

Returns:

The Java object that represents the "true" or "false" value for chado columns of type boolean.

getClobLengthFunction

protected java.lang.String getClobLengthFunction()

Specified by:

getClobLengthFunction in class JdbcChadoAdapter

Returns:

The name of a function that can be used to compute the length (in characters) of a CLOB (Character Large OBject) or TEXT value.