owltools.gaf
Class GafDocument

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

public class GafDocument
extends Object


Field Summary
protected  List<GeneAnnotation> annotations
           
protected  Hashtable<String,Bioentity> bioentities
           
protected  Hashtable<String,List<CompositeQualifier>> compositeQualifiers
           
protected  String documentPath
           
protected  Hashtable<String,List<ExtensionExpression>> extensionExpressions
           
protected  String id
           
protected  Hashtable<String,List<WithInfo>> withInfos
           
 
Constructor Summary
GafDocument()
           
GafDocument(String id, String documentPath)
           
 
Method Summary
 void addBioentity(Bioentity bioentity)
           
 void addCompositeQualifier(CompositeQualifier compositeQualifier)
           
 void addExtensionExpression(ExtensionExpression extensionExpression)
           
 void addGeneAnnotation(GeneAnnotation ga)
           
 void addWithInfo(WithInfo withInfo)
           
 Collection<Bioentity> getBioentities()
           
 Bioentity getBioentity(String id)
           
 List<CompositeQualifier> getCompositeQualifiers(String id)
           
 Set<String> getCompositeQualifiersIds()
           
 String getDocumentPath()
           
 List<ExtensionExpression> getExpressions(String id)
           
 Set<String> getExtensionExpressionIds()
           
 List<GeneAnnotation> getGeneAnnotations()
           
 Set<GeneAnnotation> getGeneAnnotations(String bioentity)
           
 Set<GeneAnnotation> getGeneAnnotationsByGoCls(String cls)
           
 String getId()
           
 List<WithInfo> getWithInfos(String id)
           
 Set<String> getWithInfosIds()
           
 void index()
           
 void setDocumentPath(String documentPath)
           
 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 Hashtable<String,Bioentity> bioentities

withInfos

protected transient Hashtable<String,List<WithInfo>> withInfos

extensionExpressions

protected transient Hashtable<String,List<ExtensionExpression>> extensionExpressions

compositeQualifiers

protected transient Hashtable<String,List<CompositeQualifier>> compositeQualifiers

annotations

protected transient List<GeneAnnotation> annotations
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)

getGeneAnnotationsByGoCls

public Set<GeneAnnotation> getGeneAnnotationsByGoCls(String cls)

addBioentity

public void addBioentity(Bioentity bioentity)

addCompositeQualifier

public void addCompositeQualifier(CompositeQualifier compositeQualifier)

getCompositeQualifiersIds

public Set<String> getCompositeQualifiersIds()

getCompositeQualifiers

public List<CompositeQualifier> getCompositeQualifiers(String id)

addWithInfo

public void addWithInfo(WithInfo withInfo)

getWithInfosIds

public Set<String> getWithInfosIds()

getWithInfos

public List<WithInfo> getWithInfos(String id)

getExpressions

public List<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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