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

Class SourceOboLoader

java.lang.Object

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

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

psidev.psi.mi.jami.bridges.obo.SourceOboLoader

All Implemented Interfaces:

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

public class SourceOboLoader
extends AbstractOboLoader<Source>

Implementation of Obo loader for sources

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
SourceOboLoader(String databaseName)	Constructor for SourceOboLoader.
SourceOboLoader(CvTerm database)	Constructor for SourceOboLoader.

Method Summary

Modifier and Type	Method	Description
protected void	createDefinitionFor(String def, Source term)	createDefinitionFor.
protected Source	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

SourceOboLoader

public SourceOboLoader(CvTerm database)

Constructor for SourceOboLoader.

Parameters:

database - a CvTerm object.

SourceOboLoader

public SourceOboLoader(String databaseName)

Constructor for SourceOboLoader.

Parameters:

databaseName - a String object.

Method Detail

instantiateNewTerm

protected Source instantiateNewTerm(String name,
                                    Xref identity)

instantiateNewTerm.

Specified by:

instantiateNewTerm in class AbstractOboLoader<Source>

Parameters:

name - a String object.

identity - a Xref object.

Returns:

a T object.

createDefinitionFor

protected void createDefinitionFor(String def,
                                   Source term)

createDefinitionFor.

Specified by:

createDefinitionFor in class AbstractOboLoader<Source>

Parameters:

def - a String object.

term - a T object.