owltools.gaf
Class GafDocument

java.lang.Object
  extended by owltools.gaf.GafDocument

public class GafDocument
extends Object


Field Summary
protected  List<GeneAnnotation> annotations
           
protected  Map<String,Bioentity> bioentities
           
protected  List<String> comments
           
protected  Map<String,Set<CompositeQualifier>> compositeQualifiers
           
protected  String documentPath
           
protected  Map<String,Set<ExtensionExpression>> extensionExpressions
           
protected  String id
           
protected  Map<String,Set<WithInfo>> withInfos
           
 
Constructor Summary
GafDocument()
           
GafDocument(String id, String documentPath)
           
 
Method Summary
 void addBioentity(Bioentity bioentity)
           
 void addComment(String c)
           
 void addCompositeQualifier(CompositeQualifier compositeQualifier)
           
 void addExtensionExpression(ExtensionExpression extensionExpression)
           
 void addGeneAnnotation(GeneAnnotation ga)
           
 void addWithInfo(WithInfo withInfo)
           
 Collection<Bioentity> getBioentities()
           
 Bioentity getBioentity(String id)
           
 List<String> getComments()
           
 Collection<CompositeQualifier> getCompositeQualifiers(String id)
           
 Set<String> getCompositeQualifiersIds()
           
 String getDocumentPath()
           
 Collection<ExtensionExpression> getExpressions(String id)
           
 Set<String> getExtensionExpressionIds()
           
 List<GeneAnnotation> getGeneAnnotations()
           
 Set<GeneAnnotation> getGeneAnnotations(String bioentity)
           
 List<GeneAnnotation> getGeneAnnotationsByDirectGoCls(String cls)
           
 String getId()
           
 Collection<WithInfo> getWithInfos(String id)
           
 Set<String> getWithInfosIds()
           
 void index()
           
 void setComments(List<String> comments)
           
 void setDocumentPath(String documentPath)
           
 void setGeneAnnotations(List<GeneAnnotation> newAnns)
           
 void setId(String id)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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

comments

protected transient List<String> comments
Constructor Detail

GafDocument

public GafDocument()

GafDocument

public GafDocument(String id,
                   String documentPath)
Method Detail

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)

setGeneAnnotations

public void setGeneAnnotations(List<GeneAnnotation> newAnns)

getComments

public List<String> getComments()

setComments

public void setComments(List<String> comments)

addComment

public void addComment(String c)


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