apollo.dataadapter.chado.jdbc
Class JdbcChadoWriter

java.lang.Object
  apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
      apollo.dataadapter.chado.jdbc.JdbcChadoWriter

public class JdbcChadoWriter
extends PureJDBCTransactionWriter

This class handles writing back to a Chado instance. It primarily uses the PureJDBCTransactionWriter implementation, but instead of writing based on transactions (which have been revamped to support undo) it writes based on a diff system.

Field Summary

protected static org.apache.log4j.Logger

logger

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

adapter, copyOnWrite, jdbcAdapter, logApolloTransactions, logSql, noCommit, useCDS

Constructor Summary

JdbcChadoWriter(ChadoAdapter adapter, JdbcChadoAdapter jdbcAdapter, boolean copyOnWrite, boolean noCommit, boolean useCDS, ChadoInstance chadoInstance)
Constructor

Method Summary

protected java.lang.Long	addExon(SeqFeatureI exon, java.lang.String author, java.util.Date date, java.lang.Long transId, int exonNum, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature, boolean checkExons) Add an exon to the database.
protected java.lang.Long	addSequenceEdit(SequenceEdit seqEdit, java.lang.String author, java.util.Date date) Add a sequence edit to the database.
protected java.lang.Long	addTopLevelAnnot(SeqFeatureI annot, java.lang.String author, java.util.Date date, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature) Add a top level annotation to the database.
protected java.lang.Long	addTranscript(Transcript transcript, java.lang.String author, java.util.Date date, java.lang.Long geneId, long transcriptRank, apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature, boolean checkExons) Add a transcript to the database.
protected java.lang.String	getChadoCdsName(ApolloNameAdapterI nameAdapter, java.lang.String name) The the Chado name for a CDS.
protected java.lang.String	getChadoPeptideName(ApolloNameAdapterI nameAdapter, java.lang.String name, SeqFeatureI pfeat) Get the Chado name for a peptide.
java.lang.String	getGFFSource()
void	setGFFSource(java.lang.String gffSource)
void	write(CurationSet cs) Write the data to the database

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

addComment, addComment, addComments, addDbXref, addDbXref, addDbxrefs, addGene, addSynonym, addSynonym, addSynonyms, commitAddTransaction, commitDeleteTransaction, commitTransaction, commitTransactions, commitUpdateParentTransaction, commitUpdateTransaction, deleteCDS, deleteComment, deleteDbXref, deleteExon, deleteExon, deleteGene, deletePolypeptide, deleteSynonym, deleteTranscript, deleteTranscript, fatalError, getCdsCoordinatesFromTranscript, getChadoFeatureId, getChadoIdForFeature, getChadoIsAnalysis, getChadoLocgroup, getChadoLocgroup, getChadoPrimaryDbxrefId, getChadoRelationshipCvTermId, getChadoResidues, getSeqEditRefFeature, logTransactionList, updateCdsFeatureLocation, updateFeatureLocation, updateFeatureName, updateFeatureType, updateOwner, updateStatus

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

JdbcChadoWriter

public JdbcChadoWriter(ChadoAdapter adapter,
                       JdbcChadoAdapter jdbcAdapter,
                       boolean copyOnWrite,
                       boolean noCommit,
                       boolean useCDS,
                       ChadoInstance chadoInstance)

Constructor

Parameters:

adapter - - ChadoAdapter to use for writing changes

jdbcAdapter - - JdbcChadoAdapter to use for writing changes

copyOnWrite - - Whether to keep a copy of the old object(s) when writing changes

noCommit - - Whether to run in 'no commit' mode

useCDS - - Whether to generate CDS features

chadoInstance - - ChadoInstance representing this Chado database`a

Method Detail

write

public void write(CurationSet cs)

Write the data to the database

Parameters:

cs - - CurationSet containing annotations to write

getGFFSource

public java.lang.String getGFFSource()

setGFFSource

public void setGFFSource(java.lang.String gffSource)

addTopLevelAnnot

protected java.lang.Long addTopLevelAnnot(SeqFeatureI annot,
                                          java.lang.String author,
                                          java.util.Date date,
                                          apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature)

Add a top level annotation to the database.

Overrides:

addTopLevelAnnot in class PureJDBCTransactionWriter

Parameters:

annot - - SeqFeatureI object for the top level annotation.

author - - Owner of this annotation.

date - - Date of edit.

srcFeature - - ChadoFeature object for the source of this feature.

Returns:

Primary key for the newly added feature.

addTranscript

protected java.lang.Long addTranscript(Transcript transcript,
                                       java.lang.String author,
                                       java.util.Date date,
                                       java.lang.Long geneId,
                                       long transcriptRank,
                                       apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature,
                                       boolean checkExons)

Add a transcript to the database.

Overrides:

addTranscript in class PureJDBCTransactionWriter

Parameters:

transcript - - Transcript object to be added to the database.

author - - Owner of this transcript.

date - - Date of edit.

geneId - - Primary key of the parent gene.

transcriptRank - - Rank of transcript in parent gene.

srcFeature - - ChadoFeature object for the source of the transcript.

checkExons - - Whether to check for shared exons (the convention for Chado is to have shared exons).

Returns:

Primary key of the newly added transcript.

addExon

protected java.lang.Long addExon(SeqFeatureI exon,
                                 java.lang.String author,
                                 java.util.Date date,
                                 java.lang.Long transId,
                                 int exonNum,
                                 apollo.dataadapter.chado.jdbc.ChadoFeature srcFeature,
                                 boolean checkExons)

Add an exon to the database.

Overrides:

addExon in class PureJDBCTransactionWriter

Parameters:

exon - - SeqFeatureI object for the exon to be added to the database.

author - - Owner of this exon.

date - - Date of edit.

transId - - Primary key of the parent transcript.

exonNum - - Rank of exon in parent transcript.

srcFeature - - ChadoFeature object for the source of the exon.

checkExons - - Whether to check for shared exons (the convention for Chado is to have shared exons).

Returns:

Primary key of the newly added exon.

addSequenceEdit

protected java.lang.Long addSequenceEdit(SequenceEdit seqEdit,
                                         java.lang.String author,
                                         java.util.Date date)

Add a sequence edit to the database.

Overrides:

addSequenceEdit in class PureJDBCTransactionWriter

Parameters:

seqEdit - - SequenceEdit object to be added.

author - - Owner of sequence edit.

date - - Date of edit.

Returns:

Primary key of newly added sequence edit.

getChadoPeptideName

protected java.lang.String getChadoPeptideName(ApolloNameAdapterI nameAdapter,
                                               java.lang.String name,
                                               SeqFeatureI pfeat)

Get the Chado name for a peptide.

Overrides:

getChadoPeptideName in class PureJDBCTransactionWriter

Parameters:

nameAdapter - - ApolloNameAdapterI object that defines what the name should be.

name - - Parent transcript name.

pfeat - - SeqFeatureI object for the peptide feature.

Returns:

Generated peptide name.

getChadoCdsName

protected java.lang.String getChadoCdsName(ApolloNameAdapterI nameAdapter,
                                           java.lang.String name)

The the Chado name for a CDS.

Overrides:

getChadoCdsName in class PureJDBCTransactionWriter

Parameters:

nameAdapter - - ApolloNameAdapterI object that defines what the name should be.

name - - Parent transcript name

Returns:

Generated CDS name.