owltools.gaf
Class GeneAnnotation

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

public class GeneAnnotation
extends Object

Author:
Shahid Manzoor

Field Summary
protected  String actsOnTaxonId
           
protected  AnnotationSource annotationSource
           
protected  String assignedBy
           
protected  String bioentity
           
protected  Bioentity bioentityObject
           
protected  String cls
           
protected  String compositeQualifier
           
protected  Collection<CompositeQualifier> compositeQualifierList
           
protected  String evidenceCls
           
protected  String extensionExpression
           
protected  Collection<ExtensionExpression> extensionExpressionList
           
protected  String gafDocument
           
protected  GafDocument gafDocumentObject
           
protected  String geneProductForm
           
protected  boolean isChanged
          If value of this variable is true then toString is re-calculated
protected  boolean isContributesTo
           
protected  boolean isIntegralTo
           
protected  String lastUpdateDate
           
protected  String referenceId
           
protected  String relation
           
protected  String toString
           
protected  String withExpression
           
protected  Collection<WithInfo> withInfoList
           
 
Constructor Summary
GeneAnnotation()
           
GeneAnnotation(String bioentity, boolean isContributesTo, boolean isIntegralTo, String compositeQualifier, String cls, String referenceId, String evidenceCls, String withExpression, String actsOnTaxonId, String lastUpdateDate, String assignedBy, String extensionExpression, String geneProductForm, String gafDocument)
           
 
Method Summary
protected  void buildRow()
          this method generates/updates the tab separated row of a gene annotation.
 String getActsOnTaxonId()
           
 String getAssignedBy()
           
 String getBioentity()
           
 Bioentity getBioentityObject()
           
 String getCls()
           
 String getCompositeQualifier()
           
 Collection<CompositeQualifier> getCompositeQualifiers()
           
 String getEvidenceCls()
           
 String getExtensionExpression()
           
 Collection<ExtensionExpression> getExtensionExpressions()
           
 String getGafDocument()
           
 String getGeneProductForm()
           
 boolean getIsContributesTo()
           
 boolean getIsIntegralTo()
           
 String getLastUpdateDate()
           
 String getReferenceId()
           
 String getRelation()
           
 AnnotationSource getSource()
           
 String getWithExpression()
           
 Collection<WithInfo> getWithInfos()
           
 void setActsOnTaxonId(String actsOnTaxonId)
           
 void setAssignedBy(String assignedBy)
           
 void setBioentity(String bioentity)
           
 void setBioentityObject(Bioentity bioentityObject)
           
 void setCls(String cls)
           
 void setCompositeQualifier(String compositeQualifier)
           
 void setEvidenceCls(String evidenceCls)
           
 void setExtensionExpression(String extensionExpression)
           
 void setGafDocument(String gafDocument)
           
 void setGeneProductForm(String geneProductForm)
           
 void setIsContributesTo(boolean isContributesTo)
           
 void setIsIntegralTo(boolean isIntegralTo)
           
 void setLastUpdateDate(String lastUpdateDate)
           
 void setReferenceId(String referenceId)
           
 void setRelation(String relation)
           
 void setWithExpression(String withExpression)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

bioentity

protected String bioentity

bioentityObject

protected Bioentity bioentityObject

isContributesTo

protected boolean isContributesTo

isIntegralTo

protected boolean isIntegralTo

compositeQualifier

protected String compositeQualifier

relation

protected String relation

cls

protected String cls

referenceId

protected String referenceId

evidenceCls

protected String evidenceCls

withExpression

protected String withExpression

actsOnTaxonId

protected String actsOnTaxonId

lastUpdateDate

protected String lastUpdateDate

assignedBy

protected String assignedBy

extensionExpression

protected String extensionExpression

geneProductForm

protected String geneProductForm

gafDocument

protected String gafDocument

withInfoList

protected Collection<WithInfo> withInfoList

extensionExpressionList

protected Collection<ExtensionExpression> extensionExpressionList

compositeQualifierList

protected Collection<CompositeQualifier> compositeQualifierList

gafDocumentObject

protected transient GafDocument gafDocumentObject

annotationSource

protected transient AnnotationSource annotationSource

isChanged

protected boolean isChanged
If value of this variable is true then toString is re-calculated


toString

protected String toString
Constructor Detail

GeneAnnotation

public GeneAnnotation()

GeneAnnotation

public GeneAnnotation(String bioentity,
                      boolean isContributesTo,
                      boolean isIntegralTo,
                      String compositeQualifier,
                      String cls,
                      String referenceId,
                      String evidenceCls,
                      String withExpression,
                      String actsOnTaxonId,
                      String lastUpdateDate,
                      String assignedBy,
                      String extensionExpression,
                      String geneProductForm,
                      String gafDocument)
Method Detail

buildRow

protected void buildRow()
this method generates/updates the tab separated row of a gene annotation.


toString

public String toString()
Overrides:
toString in class Object

getBioentity

public String getBioentity()

setBioentity

public void setBioentity(String bioentity)

getRelation

public String getRelation()

setRelation

public void setRelation(String relation)

getCls

public String getCls()

setCls

public void setCls(String cls)

getReferenceId

public String getReferenceId()

setReferenceId

public void setReferenceId(String referenceId)

getEvidenceCls

public String getEvidenceCls()

setEvidenceCls

public void setEvidenceCls(String evidenceCls)

getWithExpression

public String getWithExpression()

setWithExpression

public void setWithExpression(String withExpression)

getActsOnTaxonId

public String getActsOnTaxonId()

setActsOnTaxonId

public void setActsOnTaxonId(String actsOnTaxonId)

getLastUpdateDate

public String getLastUpdateDate()

setLastUpdateDate

public void setLastUpdateDate(String lastUpdateDate)

getAssignedBy

public String getAssignedBy()

setAssignedBy

public void setAssignedBy(String assignedBy)

getExtensionExpression

public String getExtensionExpression()

setExtensionExpression

public void setExtensionExpression(String extensionExpression)

getGeneProductForm

public String getGeneProductForm()

setGeneProductForm

public void setGeneProductForm(String geneProductForm)

getCompositeQualifier

public String getCompositeQualifier()

setCompositeQualifier

public void setCompositeQualifier(String compositeQualifier)

getBioentityObject

public Bioentity getBioentityObject()

setBioentityObject

public void setBioentityObject(Bioentity bioentityObject)

getGafDocument

public String getGafDocument()

setGafDocument

public void setGafDocument(String gafDocument)

getIsContributesTo

public boolean getIsContributesTo()

setIsContributesTo

public void setIsContributesTo(boolean isContributesTo)

getIsIntegralTo

public boolean getIsIntegralTo()

setIsIntegralTo

public void setIsIntegralTo(boolean isIntegralTo)

getExtensionExpressions

public Collection<ExtensionExpression> getExtensionExpressions()

getWithInfos

public Collection<WithInfo> getWithInfos()

getCompositeQualifiers

public Collection<CompositeQualifier> getCompositeQualifiers()

getSource

public AnnotationSource getSource()


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