owltools.gaf.parser

Class GpadGpiObjectsBuilder

java.lang.Object

owltools.gaf.parser.GpadGpiObjectsBuilder

public class GpadGpiObjectsBuilder
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	GpadGpiObjectsBuilder.AspectProvider

Constructor Summary

Constructors

Constructor and Description
GpadGpiObjectsBuilder(SimpleEcoMapper ecoMapper)

Method Summary

Methods

Modifier and Type	Method and Description
void	addGpadFilter(LineFilter<GpadParser> filter)
void	addGpiFilter(LineFilter<GpiParser> filter)
void	addIssueListener(IssueListener listener)
boolean	isGpadIncludeUnknowBioentities()
boolean	isGpadIncludeUnmappedECO()
org.apache.commons.lang3.tuple.Pair<BioentityDocument,GafDocument>	loadGpadGpi(File gpad, File gpi)
protected void	reportEvidenceIssue(String eco, String msg, boolean fatal)
protected void	reportUnknowBioentityId(String fullId, boolean fatal)
void	setAspectProvider(GpadGpiObjectsBuilder.AspectProvider aspectProvider)
void	setGpadIncludeUnknowBioentities(boolean gpadIncludeUnknowBioentities)
void	setGpadIncludeUnmappedECO(boolean gpadIncludeUnmappedECO)

Methods inherited from class java.lang.Object

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

Constructor Detail

GpadGpiObjectsBuilder

public GpadGpiObjectsBuilder(SimpleEcoMapper ecoMapper)

Method Detail

addGpadFilter

public void addGpadFilter(LineFilter<GpadParser> filter)

addGpiFilter

public void addGpiFilter(LineFilter<GpiParser> filter)

addIssueListener

public void addIssueListener(IssueListener listener)

isGpadIncludeUnknowBioentities

public boolean isGpadIncludeUnknowBioentities()

setGpadIncludeUnknowBioentities

public void setGpadIncludeUnknowBioentities(boolean gpadIncludeUnknowBioentities)

isGpadIncludeUnmappedECO

public boolean isGpadIncludeUnmappedECO()

setGpadIncludeUnmappedECO

public void setGpadIncludeUnmappedECO(boolean gpadIncludeUnmappedECO)

loadGpadGpi

public org.apache.commons.lang3.tuple.Pair<BioentityDocument,GafDocument> loadGpadGpi(File gpad,
                                                                             File gpi)
                                                                               throws IOException

Throws:

IOException

setAspectProvider

public void setAspectProvider(GpadGpiObjectsBuilder.AspectProvider aspectProvider)

reportUnknowBioentityId

protected void reportUnknowBioentityId(String fullId,
                           boolean fatal)

reportEvidenceIssue

protected void reportEvidenceIssue(String eco,
                       String msg,
                       boolean fatal)