apollo.dataadapter.chado
Class ChadoAdHocFlatFileWriter

java.lang.Object
  apollo.dataadapter.chado.ChadoAdHocFlatFileWriter

public class ChadoAdHocFlatFileWriter
extends java.lang.Object

Writes a curation set to an ad-hoc chado-based flat file format. Used primarily for chado roundtrip test suite; note that this class is not guaranteed to write *all* of Apollo's state to the file, but it should write at least as much as was read from the chado database by the JdbcChadoAdapter.

Author:

jcrabtree@sourceforge.net

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

ChadoAdHocFlatFileWriter()

Method Summary

boolean	write(java.lang.String filename, CurationSet cs)
protected void	writeCurationSet(java.io.PrintWriter pw, CurationSet cs)
protected void	writeCurationSets(java.io.PrintWriter pw, java.util.HashMap cs)
protected void	writeFeatureSet(java.io.PrintWriter pw, FeatureSetI fs)
protected void	writeSeqFeature(java.io.PrintWriter pw, SeqFeatureI sf)
protected void	writeSequence(java.io.PrintWriter pw, SequenceI seq)
protected void	writeSequences(java.io.PrintWriter pw, java.util.Vector seqs)
protected void	writeStrandedFeatureSet(java.io.PrintWriter pw, StrandedFeatureSetI sfs)
protected void	writeTransactions(java.io.PrintWriter pw, TransactionManager tm)

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

ChadoAdHocFlatFileWriter

public ChadoAdHocFlatFileWriter()

Method Detail

write

public boolean write(java.lang.String filename,
                     CurationSet cs)

Parameters:

filename - The name of the file to write to.

cs - The CurationSet whose data is to be written.

Returns:

whether the write succeeded

writeCurationSet

protected void writeCurationSet(java.io.PrintWriter pw,
                                CurationSet cs)

Parameters:

pw - Where to write the flat file output.

cs - The CurationSet to write.

writeStrandedFeatureSet

protected void writeStrandedFeatureSet(java.io.PrintWriter pw,
                                       StrandedFeatureSetI sfs)

Parameters:

pw - Where to write the flat file output.

sfs - The StrandedFeatureSetI to write.

writeFeatureSet

protected void writeFeatureSet(java.io.PrintWriter pw,
                               FeatureSetI fs)

Parameters:

pw - Where to write the flat file output.

fs - The FeatureSetI to write.

writeSeqFeature

protected void writeSeqFeature(java.io.PrintWriter pw,
                               SeqFeatureI sf)

Parameters:

pw - Where to write the flat file output.

sf - The SeqFeatureI to write.

writeSequences

protected void writeSequences(java.io.PrintWriter pw,
                              java.util.Vector seqs)

Parameters:

pw - Where to write the flat file output.

sfs - Vector of SequenceI

writeSequence

protected void writeSequence(java.io.PrintWriter pw,
                             SequenceI seq)

writeTransactions

protected void writeTransactions(java.io.PrintWriter pw,
                                 TransactionManager tm)

Parameters:

pw - Where to write the flat file output.

tm - TransactionManager.

writeCurationSets

protected void writeCurationSets(java.io.PrintWriter pw,
                                 java.util.HashMap cs)

Parameters:

pw - Where to write the flat file output.

cs - HashMap of child curation sets.