owltools.gaf.godb
Class GoMySQLDatabaseDumper

java.lang.Object
  extended by owltools.gaf.godb.Dumper
      extended by owltools.gaf.godb.DatabaseDumper
          extended by owltools.gaf.godb.GoMySQLDatabaseDumper

public class GoMySQLDatabaseDumper
extends DatabaseDumper

implements DatabaseDumper for GO MySQL db

Author:
cjm

Nested Class Summary
protected static class GoMySQLDatabaseDumper.GOMySQLTable
           
 
Field Summary
 
Fields inherited from class owltools.gaf.godb.DatabaseDumper
incrementallyLoadedTables, isStrict, objLastIdMap, tableObjIdMap
 
Fields inherited from class owltools.gaf.godb.Dumper
gafdocs, graph, problems, targetDirectory
 
Constructor Summary
GoMySQLDatabaseDumper(OWLGraphWrapper g)
           
 
Method Summary
 void dump()
          dumps all tables
 void dumpAssociationModule()
           
 void dumpAssociationRowsForGaf(PrintStream s, GafDocument gafdoc)
           
 void dumpAssociationTable()
           
 void dumpDbxrefTable()
           
 void dumpGeneProductRowsForGaf(PrintStream s, GafDocument gafdoc)
           
 void dumpGraphModule()
           
 void dumpGraphPathTable()
           
 void dumpMetaModule()
           
 void dumpOptModule()
           
 void dumpSpeciesRow(PrintStream s, String taxId)
           
 void dumpSpeciesTable()
           
 void dumpTerm2TermTable()
           
 void dumpTermSubsetTable()
           
 void dumpTermTable()
           
 
Methods inherited from class owltools.gaf.godb.DatabaseDumper
cleanup, closeAllPrintStreams, closePrintStream, dumpRow, getId, getId, getPrintStream, getPrintStream, showStats
 
Methods inherited from class owltools.gaf.godb.Dumper
addGafDocument, addProblem, getGafdocs, getTargetDirectory, reportProblems, setGafdocs, setTargetDirectory
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GoMySQLDatabaseDumper

public GoMySQLDatabaseDumper(OWLGraphWrapper g)
Parameters:
g -
Method Detail

dump

public void dump()
          throws IOException,
                 ReferentialIntegrityException
dumps all tables

Specified by:
dump in class Dumper
Throws:
IOException
ReferentialIntegrityException

dumpGraphModule

public void dumpGraphModule()
                     throws IOException,
                            ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpTermTable

public void dumpTermTable()
                   throws IOException,
                          ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpTermSubsetTable

public void dumpTermSubsetTable()
                         throws IOException,
                                ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpTerm2TermTable

public void dumpTerm2TermTable()
                        throws IOException,
                               ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpMetaModule

public void dumpMetaModule()
                    throws IOException,
                           ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpDbxrefTable

public void dumpDbxrefTable()
                     throws IOException,
                            ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpOptModule

public void dumpOptModule()
                   throws IOException,
                          ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpGraphPathTable

public void dumpGraphPathTable()
                        throws IOException,
                               ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpAssociationModule

public void dumpAssociationModule()
                           throws IOException,
                                  ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpSpeciesTable

public void dumpSpeciesTable()
                      throws IOException,
                             ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpSpeciesRow

public void dumpSpeciesRow(PrintStream s,
                           String taxId)
                    throws IOException,
                           ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpAssociationTable

public void dumpAssociationTable()
                          throws IOException,
                                 ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpAssociationRowsForGaf

public void dumpAssociationRowsForGaf(PrintStream s,
                                      GafDocument gafdoc)
                               throws IOException,
                                      ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException

dumpGeneProductRowsForGaf

public void dumpGeneProductRowsForGaf(PrintStream s,
                                      GafDocument gafdoc)
                               throws IOException,
                                      ReferentialIntegrityException
Throws:
IOException
ReferentialIntegrityException


Copyright © 2010-2014. All Rights Reserved.