owltools.gaf
Class GafDocument
java.lang.Object
owltools.gaf.GafDocument
public class GafDocument
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
id
protected String id
documentPath
protected String documentPath
bioentities
protected transient Map<String,Bioentity> bioentities
withInfos
protected transient Map<String,Set<WithInfo>> withInfos
extensionExpressions
protected transient Map<String,Set<ExtensionExpression>> extensionExpressions
compositeQualifiers
protected transient Map<String,Set<CompositeQualifier>> compositeQualifiers
annotations
protected transient List<GeneAnnotation> annotations
GafDocument
public GafDocument()
GafDocument
public GafDocument(String id,
String documentPath)
index
public void index()
getId
public String getId()
setId
public void setId(String id)
getDocumentPath
public String getDocumentPath()
setDocumentPath
public void setDocumentPath(String documentPath)
getBioentity
public Bioentity getBioentity(String id)
getBioentities
public Collection<Bioentity> getBioentities()
getGeneAnnotations
public List<GeneAnnotation> getGeneAnnotations()
getGeneAnnotations
public Set<GeneAnnotation> getGeneAnnotations(String bioentity)
getGeneAnnotationsByDirectGoCls
public List<GeneAnnotation> getGeneAnnotationsByDirectGoCls(String cls)
addBioentity
public void addBioentity(Bioentity bioentity)
addCompositeQualifier
public void addCompositeQualifier(CompositeQualifier compositeQualifier)
getCompositeQualifiersIds
public Set<String> getCompositeQualifiersIds()
getCompositeQualifiers
public Collection<CompositeQualifier> getCompositeQualifiers(String id)
addWithInfo
public void addWithInfo(WithInfo withInfo)
getWithInfosIds
public Set<String> getWithInfosIds()
getWithInfos
public Collection<WithInfo> getWithInfos(String id)
getExpressions
public Collection<ExtensionExpression> getExpressions(String id)
getExtensionExpressionIds
public Set<String> getExtensionExpressionIds()
addExtensionExpression
public void addExtensionExpression(ExtensionExpression extensionExpression)
addGeneAnnotation
public void addGeneAnnotation(GeneAnnotation ga)
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