uk.ac.ebi.adfconverter.tools.checker.ontology
Class MGEDOntologyChecker

java.lang.Object
  uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker

public class MGEDOntologyChecker

extends java.lang.Object

Check if a term is in the MGED ontology using Ontology helper from MAGEstk (read daml file) From TestMOE of MAGESTK

Version:

1 TODO file is red each time/ optimize

Author:

Pierre MARGUERITE

Constructor Summary

MGEDOntologyChecker()
Creates a new instance of testMGEDOE

MGEDOntologyChecker(java.lang.String _OntologyFilePath)
Creates a new instance of MGEDOntologyChecker

MGEDOntologyChecker(java.lang.String _OntologyFilePath, java.io.File _ADFMGEDOntology, java.lang.String _descriptionFile, boolean _isOntologyCheckerEnable)
Creates a new instance of MGEDOntologyChecker

Method Summary

void	assignFirstValue(org.biomage.tools.helpers.MGEDOntologyEntry entry) Assign first value to current entry if assignable
boolean	checkOntologyEntry(ADFConverterLogger log, Extendable MAGEobj, OntologyEntry oentry, java.lang.String link) Check the ontology term in a an OntologyEntry
boolean	checkontologyTerm(ADFConverterLogger log, java.lang.String type, DataBuffer value) Check if a term belong to the MGED ontology
OntologyEntry	createOntologyEntry(java.lang.String type, java.lang.String value) Creates an ontology entry object
void	setIdentifierRule(java.lang.String databaseRule) Set the database identifier generation rule.
void	testAssigningValues(java.util.Vector mgedOntClassEntries) Tests if Ontoloy class entries are correct
java.util.Vector	testInitOfMGEDOE(java.util.Vector mgedOntClassNames)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MGEDOntologyChecker

public MGEDOntologyChecker()

Creates a new instance of testMGEDOE

MGEDOntologyChecker

public MGEDOntologyChecker(java.lang.String _OntologyFilePath)
                    throws java.lang.Exception

Creates a new instance of MGEDOntologyChecker

Parameters:

_OntologyFilePath - The path to the ontology daml file

Throws:

java.lang.Exception - if error during ontology file reading

MGEDOntologyChecker

public MGEDOntologyChecker(java.lang.String _OntologyFilePath,
                           java.io.File _ADFMGEDOntology,
                           java.lang.String _descriptionFile,
                           boolean _isOntologyCheckerEnable)
                    throws java.lang.Exception

Creates a new instance of MGEDOntologyChecker

Parameters:

_OntologyFilePath - The path to the ontology daml file

_ADFMGEDOntology - the path to the ADF MGEDOntology link file

_descriptionFile - the path to the file describing the file structure

Throws:

java.lang.Exception - if error during ontology file reading

Method Detail

assignFirstValue

public void assignFirstValue(org.biomage.tools.helpers.MGEDOntologyEntry entry)

Assign first value to current entry if assignable

Parameters:

entry -

checkOntologyEntry

public boolean checkOntologyEntry(ADFConverterLogger log,
                                  Extendable MAGEobj,
                                  OntologyEntry oentry,
                                  java.lang.String link)

Check the ontology term in a an OntologyEntry

Parameters:

log - the log for text output

MAGEobj - The MAGE Object associated to the Ontology entry

oentry - The ontology entry itself

link - the link for MAGE and MGED classes

Returns:

true, if the ontology entry value is correct for the given MAGEObj and link. false,othewise

checkontologyTerm

public boolean checkontologyTerm(ADFConverterLogger log,
                                 java.lang.String type,
                                 DataBuffer value)

Check if a term belong to the MGED ontology

Parameters:

log - the logger to report information

type - the ontology type

value - the ontlogy value

Returns:

true, if the term is correct, false otherwise

createOntologyEntry

public OntologyEntry createOntologyEntry(java.lang.String type,
                                         java.lang.String value)

Creates an ontology entry object

Parameters:

type - the type of the ontology

value - the value of the ontology

Returns:

the corresponding ontology entry

setIdentifierRule

public void setIdentifierRule(java.lang.String databaseRule)
                       throws java.lang.Exception

Set the database identifier generation rule.

Parameters:

databaseRule - the database identifier rule

Throws:

java.lang.Exception - if an error occurs during ontology manager initialisation

testAssigningValues

public void testAssigningValues(java.util.Vector mgedOntClassEntries)

Tests if Ontoloy class entries are correct

Parameters:

mgedOntClassEntries - Vector of Entries to test

testInitOfMGEDOE

public java.util.Vector testInitOfMGEDOE(java.util.Vector mgedOntClassNames)