apollo.dataadapter.chado.jdbc
Class PostgresChadoAdapter

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

public class PostgresChadoAdapter
extends JdbcChadoAdapter

A subclass of JdbcChadoAdapter specific to Postgres installations of Chado. This should just be a has-a not an is-a with JdbcChadoAdapter

Field Summary

protected static org.apache.log4j.Logger

logger

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

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

Constructor Summary

PostgresChadoAdapter()

Method Summary

protected java.lang.Object	getBooleanValue(boolean val)
protected java.lang.String	getClobLengthFunction()
long	getNextPrimaryKeyId(java.lang.String tableName) Run a SELECT(MAX()) + 1 query to get the next available primary key value for a chado table.

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, getAnalysisFeatureIdentityField, 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, getNewConnection, 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

Constructor Detail

PostgresChadoAdapter

public PostgresChadoAdapter()

Method Detail

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.

getNextPrimaryKeyId

public long getNextPrimaryKeyId(java.lang.String tableName)

Description copied from class: JdbcChadoAdapter

Run a SELECT(MAX()) + 1 query to get the next available primary key value for a chado table. Note that this is the preferred method to obtain new ids in Sybase (since the primary key columns are not defined as Sybase IDENTITY types, at least in the current TIGR implementation).

Overrides:

getNextPrimaryKeyId in class JdbcChadoAdapter