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SUMMARY: JavaDoc of org.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter JAVADOC | Sourc code of org.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter SOURCE | Download org.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

org.bdgp.apps.dagedit.dataadapter
Class JDBCDataAdapter  view JDBCDataAdapter download JDBCDataAdapter.java

java.lang.Object
  extended byAbstractDataAdapter
      extended byorg.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter
All Implemented Interfaces:
DEDataAdapterI
public class JDBCDataAdapter
extends AbstractDataAdapter
implements DEDataAdapterI

Nested Class Summary
 class JDBCDataAdapter.ConflictException
           
private  class JDBCDataAdapter.OperationWrapper
           
 
Field Summary
private  java.util.Hashtable allterms_hash
           
private  java.util.Hashtable catHash
           
private  java.util.Vector catList
           
private  java.util.Hashtable databaseIDHash
           
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType DEVELOPS_FROM
           
private  java.lang.String driver
           
private  boolean driverLoaded
           
private  DEDataAdapterI idAdapter
           
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType ISA_TYPE
           
(package private)  java.lang.String lastComment
           
(package private)  java.util.Date lastModified
           
(package private)  java.lang.String lastUser
           
(package private)  java.lang.String lastVersion
           
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType PARTOF_TYPE
           
private  java.lang.String password
           
private static int PERCENT_INC
           
private  java.util.Hashtable relTypeHash
           
private  java.util.Vector relTypeList
           
(package private)  boolean repopulate
           
private  org.bdgp.apps.dagedit.datamodel.Term root_term
           
private  java.lang.String saveComment
           
private  java.lang.String url
           
private  java.lang.String username
           
 
Fields inherited from interface org.bdgp.apps.dagedit.dataadapter.DEDataAdapterI
CONFIGURE, EXPORT_TERMS, FIND_PRODUCTS, GET_HISTORY, GET_ID, IMPORT_TERMS, READ_TERMS, WRITE_TERMS
 
Constructor Summary
JDBCDataAdapter()
           
 
Method Summary
protected  void addDbxref(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target, org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit, int operation_id)
           
private  void buildCatList(java.sql.Statement stmt)
           
private  java.util.Hashtable buildIDHash(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term root)
           
private  void buildImpliedDeletes(org.bdgp.apps.dagedit.datamodel.Term term, java.util.Vector deleted, java.util.Vector impliedDeletes)
           
private  void buildRelTypeList(java.sql.Statement stmt)
           
protected  void checkConflicts(org.bdgp.apps.dagedit.datamodel.DEEditHistory history, org.bdgp.apps.dagedit.datamodel.Term currentRoot)
          Checks to see if two GO trees are in conflict
protected  void checkSameRelationships(org.bdgp.apps.dagedit.datamodel.Term oldTerm, org.bdgp.apps.dagedit.datamodel.Term newTerm)
           
protected  void clearDatabase(java.sql.Statement stmt)
           
 void delegateToIDAdapter(DEDataAdapterI idAdapter)
           
protected  void deleteDbxref(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target, org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit, int operation_id)
           
protected  java.lang.String formatString(java.lang.String in)
           
 java.util.Vector getAllTerms()
           
protected  java.util.Hashtable getCategoryIndex(java.sql.Statement stmt)
           
 java.sql.Connection getConnection()
           
protected  int getDatabaseIDForTerm(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term term)
           
 java.util.Vector getHistories()
           
private  org.bdgp.apps.dagedit.datamodel.HistoryItem getHistoryItem(JDBCDataAdapter.OperationWrapper ow)
           
 java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root, org.bdgp.apps.dagedit.datamodel.Term term, java.lang.String prefix, int length, int count)
           
 java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root, org.bdgp.apps.dagedit.datamodel.Term term, java.lang.String prefix, int min, int max, int length, int count)
           
protected  int getIntForType(org.bdgp.apps.dagedit.datamodel.TermRelationshipType type)
           
 java.lang.String getName()
           
private  java.lang.String getPrettyTermName(org.bdgp.apps.dagedit.datamodel.Term term)
           
 java.util.Vector getRelationshipTypes()
           
protected  java.util.Hashtable getRelTypeIndex(java.sql.Statement stmt)
           
 org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot()
           
 org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot(boolean showProgress)
           
 java.util.Properties getStateInformation()
           
 IOOperation[] getSupportedOperations()
           
 java.util.Vector getTermCategories()
           
 java.lang.String getType()
           
protected  org.bdgp.apps.dagedit.datamodel.TermRelationshipType getTypeForInt(int type_id)
           
 DataAdapterUI getUI(IOOperation op)
           
 void init()
           
 void init(java.lang.String driver, java.lang.String url)
           
 void init(java.lang.String driver, java.lang.String url, java.lang.String username, java.lang.String password)
           
 void readTerms()
           
 void readTerms(boolean showProgress)
           
 void setRepopulate(boolean repopulate)
           
 void setSaveComment(java.lang.String saveComment)
           
 void setStateInformation(java.util.Properties props)
           
 org.bdgp.apps.dagedit.datamodel.DEEditHistory write(org.bdgp.apps.dagedit.datamodel.DEEditHistory history)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermAddHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermCommitAndObsoleteHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermCopyHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermDeleteHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermMergeHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermMoveHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermRelationshipHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermSplitHistoryItem item)
           
 void write(java.sql.Statement stmt, int session_id, org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem item)
           
protected  void writeCategories(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target, org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.CategoryEdit edit, int operation_id, java.util.Hashtable catIndex)
           
protected  void writeComment(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target)
           
protected  void writeDbxrefs(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target, org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit, int operation_id)
           
protected  void writeDefinition(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target)
           
protected  void writeRelationships(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term term)
           
protected  int writeSubtree(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term term, boolean fireProgressEvents)
           
protected  void writeSynonyms(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target, org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.SynonymEdit edit, int operation_id)
           
protected  int writeTerm(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term term)
           
protected  int writeTermAndRelationships(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term term)
           
protected  void writeTermText(java.sql.Statement stmt, org.bdgp.apps.dagedit.datamodel.Term target)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

PERCENT_INC

private static int PERCENT_INC

driver

private java.lang.String driver

url

private java.lang.String url

username

private java.lang.String username

password

private java.lang.String password

driverLoaded

private boolean driverLoaded

saveComment

private java.lang.String saveComment

root_term

private org.bdgp.apps.dagedit.datamodel.Term root_term

allterms_hash

private java.util.Hashtable allterms_hash

databaseIDHash

private java.util.Hashtable databaseIDHash

idAdapter

private DEDataAdapterI idAdapter

repopulate

boolean repopulate

ISA_TYPE

protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType ISA_TYPE

PARTOF_TYPE

protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType PARTOF_TYPE

DEVELOPS_FROM

protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType DEVELOPS_FROM

catHash

private java.util.Hashtable catHash

catList

private java.util.Vector catList

relTypeHash

private java.util.Hashtable relTypeHash

relTypeList

private java.util.Vector relTypeList

lastModified

java.util.Date lastModified

lastUser

java.lang.String lastUser

lastComment

java.lang.String lastComment

lastVersion

java.lang.String lastVersion
Constructor Detail

JDBCDataAdapter

public JDBCDataAdapter()
Method Detail

getRelationshipTypes

public java.util.Vector getRelationshipTypes()
                                      throws DataAdapterException
Specified by:
getRelationshipTypes in interface DEDataAdapterI

setRepopulate

public void setRepopulate(boolean repopulate)

getName

public java.lang.String getName()

getType

public java.lang.String getType()

getIDs

public java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
                                 org.bdgp.apps.dagedit.datamodel.Term term,
                                 java.lang.String prefix,
                                 int length,
                                 int count)
                          throws DataAdapterException
Specified by:
getIDs in interface DEDataAdapterI

getIDs

public java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
                                 org.bdgp.apps.dagedit.datamodel.Term term,
                                 java.lang.String prefix,
                                 int min,
                                 int max,
                                 int length,
                                 int count)
                          throws DataAdapterException
Specified by:
getIDs in interface DEDataAdapterI

buildIDHash

private java.util.Hashtable buildIDHash(java.sql.Statement stmt,
                                        org.bdgp.apps.dagedit.datamodel.Term root)
                                 throws java.sql.SQLException

clearDatabase

protected void clearDatabase(java.sql.Statement stmt)
                      throws java.sql.SQLException

checkConflicts

protected void checkConflicts(org.bdgp.apps.dagedit.datamodel.DEEditHistory history,
                              org.bdgp.apps.dagedit.datamodel.Term currentRoot)
                       throws JDBCDataAdapter.ConflictException
Checks to see if two GO trees are in conflict

getPrettyTermName

private java.lang.String getPrettyTermName(org.bdgp.apps.dagedit.datamodel.Term term)

checkSameRelationships

protected void checkSameRelationships(org.bdgp.apps.dagedit.datamodel.Term oldTerm,
                                      org.bdgp.apps.dagedit.datamodel.Term newTerm)
                               throws JDBCDataAdapter.ConflictException

getHistoryItem

private org.bdgp.apps.dagedit.datamodel.HistoryItem getHistoryItem(JDBCDataAdapter.OperationWrapper ow)

getTypeForInt

protected org.bdgp.apps.dagedit.datamodel.TermRelationshipType getTypeForInt(int type_id)

getIntForType

protected int getIntForType(org.bdgp.apps.dagedit.datamodel.TermRelationshipType type)

getHistories

public java.util.Vector getHistories()
                              throws DataAdapterException
Specified by:
getHistories in interface DEDataAdapterI

write

public org.bdgp.apps.dagedit.datamodel.DEEditHistory write(org.bdgp.apps.dagedit.datamodel.DEEditHistory history)
                                                    throws DataAdapterException
Specified by:
write in interface DEDataAdapterI

delegateToIDAdapter

public void delegateToIDAdapter(DEDataAdapterI idAdapter)
Specified by:
delegateToIDAdapter in interface DEDataAdapterI

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermMergeHistoryItem item)
           throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermCommitAndObsoleteHistoryItem item)
           throws java.sql.SQLException

writeRelationships

protected void writeRelationships(java.sql.Statement stmt,
                                  org.bdgp.apps.dagedit.datamodel.Term term)
                           throws java.sql.SQLException

writeSubtree

protected int writeSubtree(java.sql.Statement stmt,
                           org.bdgp.apps.dagedit.datamodel.Term term,
                           boolean fireProgressEvents)
                    throws java.sql.SQLException

writeTermAndRelationships

protected int writeTermAndRelationships(java.sql.Statement stmt,
                                        org.bdgp.apps.dagedit.datamodel.Term term)
                                 throws java.sql.SQLException

writeTerm

protected int writeTerm(java.sql.Statement stmt,
                        org.bdgp.apps.dagedit.datamodel.Term term)
                 throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermSplitHistoryItem item)
           throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermCopyHistoryItem item)
           throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermMoveHistoryItem item)
           throws java.sql.SQLException

buildImpliedDeletes

private void buildImpliedDeletes(org.bdgp.apps.dagedit.datamodel.Term term,
                                 java.util.Vector deleted,
                                 java.util.Vector impliedDeletes)

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermRelationshipHistoryItem item)
           throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermDeleteHistoryItem item)
           throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermAddHistoryItem item)
           throws java.sql.SQLException

getDatabaseIDForTerm

protected int getDatabaseIDForTerm(java.sql.Statement stmt,
                                   org.bdgp.apps.dagedit.datamodel.Term term)
                            throws java.sql.SQLException

write

public void write(java.sql.Statement stmt,
                  int session_id,
                  org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem item)
           throws java.sql.SQLException

addDbxref

protected void addDbxref(java.sql.Statement stmt,
                         org.bdgp.apps.dagedit.datamodel.Term target,
                         org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
                         int operation_id)
                  throws java.sql.SQLException

deleteDbxref

protected void deleteDbxref(java.sql.Statement stmt,
                            org.bdgp.apps.dagedit.datamodel.Term target,
                            org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
                            int operation_id)
                     throws java.sql.SQLException

writeDbxrefs

protected void writeDbxrefs(java.sql.Statement stmt,
                            org.bdgp.apps.dagedit.datamodel.Term target,
                            org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.DbxrefEdit edit,
                            int operation_id)
                     throws java.sql.SQLException

writeSynonyms

protected void writeSynonyms(java.sql.Statement stmt,
                             org.bdgp.apps.dagedit.datamodel.Term target,
                             org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.SynonymEdit edit,
                             int operation_id)
                      throws java.sql.SQLException

getTermCategories

public java.util.Vector getTermCategories()
                                   throws DataAdapterException
Specified by:
getTermCategories in interface DEDataAdapterI

buildRelTypeList

private void buildRelTypeList(java.sql.Statement stmt)
                       throws java.sql.SQLException

getRelTypeIndex

protected java.util.Hashtable getRelTypeIndex(java.sql.Statement stmt)
                                       throws java.sql.SQLException

buildCatList

private void buildCatList(java.sql.Statement stmt)
                   throws java.sql.SQLException

getCategoryIndex

protected java.util.Hashtable getCategoryIndex(java.sql.Statement stmt)
                                        throws java.sql.SQLException

writeCategories

protected void writeCategories(java.sql.Statement stmt,
                               org.bdgp.apps.dagedit.datamodel.Term target,
                               org.bdgp.apps.dagedit.datamodel.TermTextHistoryItem.CategoryEdit edit,
                               int operation_id,
                               java.util.Hashtable catIndex)
                        throws java.sql.SQLException

writeDefinition

protected void writeDefinition(java.sql.Statement stmt,
                               org.bdgp.apps.dagedit.datamodel.Term target)
                        throws java.sql.SQLException

writeComment

protected void writeComment(java.sql.Statement stmt,
                            org.bdgp.apps.dagedit.datamodel.Term target)
                     throws java.sql.SQLException

writeTermText

protected void writeTermText(java.sql.Statement stmt,
                             org.bdgp.apps.dagedit.datamodel.Term target)
                      throws java.sql.SQLException

formatString

protected java.lang.String formatString(java.lang.String in)

getSupportedOperations

public IOOperation[] getSupportedOperations()

getUI

public DataAdapterUI getUI(IOOperation op)

getConnection

public java.sql.Connection getConnection()
                                  throws java.sql.SQLException,
                                         java.lang.ClassNotFoundException

init

public void init()

init

public void init(java.lang.String driver,
                 java.lang.String url)

init

public void init(java.lang.String driver,
                 java.lang.String url,
                 java.lang.String username,
                 java.lang.String password)

setSaveComment

public void setSaveComment(java.lang.String saveComment)

readTerms

public void readTerms()
               throws java.sql.SQLException,
                      java.lang.ClassNotFoundException

readTerms

public void readTerms(boolean showProgress)
               throws java.sql.SQLException,
                      java.lang.ClassNotFoundException

getRoot

public org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot()
                                                      throws DataAdapterException
Specified by:
getRoot in interface DEDataAdapterI

getRoot

public org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot(boolean showProgress)
                                                      throws DataAdapterException

getAllTerms

public java.util.Vector getAllTerms()

getStateInformation

public java.util.Properties getStateInformation()
Specified by:
getStateInformation in interface DEDataAdapterI

setStateInformation

public void setStateInformation(java.util.Properties props)
Specified by:
setStateInformation in interface DEDataAdapterI
Overview  Package   Class  Use  Deprecated  Index 
Home >> All >> org >> bdgp >> apps >> dagedit >> [ dataadapter overview ]  PREV CLASS  NEXT CLASS
SUMMARY: JavaDoc of org.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter JAVADOC | Sourc code of org.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter SOURCE | Download org.bdgp.apps.dagedit.dataadapter.JDBCDataAdapter DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD