owltools.gaf
Class GeneAnnotation
java.lang.Object
owltools.gaf.GeneAnnotation
public class GeneAnnotation
- extends Object
- Author:
- Shahid Manzoor
Constructor Summary |
GeneAnnotation()
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GeneAnnotation(GeneAnnotation ann)
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GeneAnnotation(String bioentity,
boolean isContributesTo,
boolean isIntegralTo,
String compositeQualifier,
String cls,
String referenceId,
String evidenceCls,
String withExpression,
String aspect,
String actsOnTaxonId,
String lastUpdateDate,
String assignedBy,
String extensionExpression,
String geneProductForm,
String gafDocument)
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GAF_Date_Format
public static final ThreadLocal<DateFormat> GAF_Date_Format
- Provide a thread-safe formatter for a GAF date.
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
aspect
protected String aspect
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
GeneAnnotation
public GeneAnnotation()
GeneAnnotation
public GeneAnnotation(String bioentity,
boolean isContributesTo,
boolean isIntegralTo,
String compositeQualifier,
String cls,
String referenceId,
String evidenceCls,
String withExpression,
String aspect,
String actsOnTaxonId,
String lastUpdateDate,
String assignedBy,
String extensionExpression,
String geneProductForm,
String gafDocument)
GeneAnnotation
public GeneAnnotation(GeneAnnotation ann)
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()
setAspect
public void setAspect(String inAspect)
getAspect
public String getAspect()
setActsOnTaxonId
public void setActsOnTaxonId(String actsOnTaxonId)
getLastUpdateDate
public String getLastUpdateDate()
setLastUpdateDate
public void setLastUpdateDate(Date date)
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)
setExtensionExpressionList
public void setExtensionExpressionList(Collection<ExtensionExpression> xs)
getExtensionExpressions
public Collection<ExtensionExpression> getExtensionExpressions()
getWithInfos
public Collection<WithInfo> getWithInfos()
getCompositeQualifiers
public Collection<CompositeQualifier> getCompositeQualifiers()
getSource
public AnnotationSource getSource()
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