Package psidev.psi.mi.jami.bridges.obo

Class CvOboLoader

java.lang.Object

uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

psidev.psi.mi.jami.bridges.obo.AbstractOboLoader<CvTerm>

psidev.psi.mi.jami.bridges.obo.CvOboLoader

All Implemented Interfaces:

uk.ac.ebi.ols.loader.interfaces.Loader

public class CvOboLoader
extends AbstractOboLoader<CvTerm>

Basic implementation of Obo loader

Since:

17/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.bridges.obo.AbstractOboLoader

ALIAS_IDENTIFIER, COMMENT_KEY, EXACT_KEY, GO, GO_MI_REF, HTTP_DEF, LINE_BREAK, log, META_XREF_SEPARATOR, METHOD_REFERENCE, METHOD_REFERENCE_MI_REF, MOD_ALIAS_IDENTIFIER, MOD_SHORTLABEL_IDENTIFIER, PMID, PMID_APPLICATION, QUOTE, RESID, RESID_IDENTIFIER, RESID_MI_REF, RESID_MISNOMER_IDENTIFIER, RESID_NAME_IDENTIFIER, RESID_SYSTEMATIC_IDENTIFIER, SEARCH_URL, SEARCH_URL_MI_REF, SHORTLABEL_IDENTIFIER, SO, SO_MI_REF, UNIPROT_FEATURE_IDENTIFIER, XREF_TYPE, XREF_VALIDATION_REGEXP, XREF_VALIDATION_REGEXP_MI_REF

Fields inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

ALT_ID, BATCH_MODE, BROAD, DEV_FROM_SET, DEVELOPS_FROM, EXACT, FULL_NAME, IS_A, IS_A_SET, logger, NARROW, ontBean, ONTOLOGY_DEFINITION, ontologyTerms, parser, PART_OF, PART_OF_SET, QUERY_URL, RELATED, SHORT_NAME, SOURCE_URL, SYNONYM, useGreedy

Fields inherited from interface uk.ac.ebi.ols.loader.interfaces.Loader

RELATION_TYPE, SYNONYM_TYPE

Constructor Summary

Constructors

Constructor	Description
CvOboLoader(String databaseName)	Constructor for CvOboLoader.
CvOboLoader(CvTerm database)	Constructor for CvOboLoader.

Method Summary

Modifier and Type	Method	Description
protected void	createDefinitionFor(String def, CvTerm term)	createDefinitionFor.
protected CvTerm	instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.

Methods inherited from class psidev.psi.mi.jami.bridges.obo.AbstractOboLoader

buildOntology, configure, createNewTerm, getOntologyDatabase, parseOboFile, processAnnotations, processDefinition, processDefinition, processInfoInDescription, processShortLabel, processSynonyms, processXref, processXrefDefinition, processXrefs

Methods inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

dumpOntology, dumpOntologyStats, dumpTerm, getOntology, getRootTerms, getUnknownRelationTermBean, initializeCommonObjects, initializeTermBean, load, process, processTerm, safeTrim, safeTrim, setParser, setUseGreedy, unload

Methods inherited from class java.lang.Object

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

Constructor Detail

CvOboLoader

public CvOboLoader(CvTerm database)

Constructor for CvOboLoader.

Parameters:

database - a CvTerm object.

CvOboLoader

public CvOboLoader(String databaseName)

Constructor for CvOboLoader.

Parameters:

databaseName - a String object.

Method Detail

instantiateNewTerm

protected CvTerm instantiateNewTerm(String name,
                                    Xref identity)

instantiateNewTerm.

Specified by:

instantiateNewTerm in class AbstractOboLoader<CvTerm>

Parameters:

name - a String object.

identity - a Xref object.

Returns:

a T object.

createDefinitionFor

protected void createDefinitionFor(String def,
                                   CvTerm term)

createDefinitionFor.

Specified by:

createDefinitionFor in class AbstractOboLoader<CvTerm>

Parameters:

def - a String object.

term - a T object.