com.inscoper.nbo.Sample¶

Represents the XML element Sample. More...

Inherits from com.inscoper.nbo.NBOBaseClass

Public Functions¶

	Name
synchronized void	delete()
	Sample()
String	getTypeName() Returns the class type name.
String	getXMLName() Returns the XML element name corresponding to this class.
ENBOType	getNBOType() Returns the NBO Type corresponding to this class.
NBOBaseClassVector	getChildren() Returns a list of all classes derived from this class.
NBOBaseClassVector	getSubElements() Returns a list of all child elements contained in this class.
void	fromJsonFile(String path, boolean validate) Populates this object from a JSON file.
void	fromJsonFile(String path) Populates this object from a JSON file.
void	fromJsonString(String json_string, boolean validate) Populates this object from a JSON string.
void	fromJsonString(String json_string) Populates this object from a JSON string.
void	fromXmlFile(String path, boolean validate) Populates this object from a XML file.
void	fromXmlFile(String path) Populates this object from a XML file.
void	fromXmlString(String xml_string, boolean validate) Populates this object from a XML string.
void	fromXmlString(String xml_string) Populates this object from a XML string.
void	toXmlFile(String filename, boolean validate) Serializes this object to an XML file.
void	toXmlFile(String filename) Serializes this object to an XML file.
String	toXmlString(boolean validate) Serializes this object to an XML string.
String	toXmlString() Serializes this object to an XML string.
void	setID(LSID_Type value, boolean validate) Sets the value of the ID attribute.
void	setID(LSID_Type value) Sets the value of the ID attribute.
LSID_Type	getID() Returns the value of the ID attribute.
void	resetID() Resets the ID attribute to an unset state.
boolean	hasID() Checks whether the optional ID attribute is present.
void	setName(Denomination_Type value, boolean validate) Sets the value of the Name attribute.
void	setName(Denomination_Type value) Sets the value of the Name attribute.
Denomination_Type	getName() Returns the value of the Name attribute.
void	resetName() Resets the Name attribute to an unset state.
boolean	hasName() Checks whether the optional Name attribute is present.
void	setBiologicalOrigin(boolean value, boolean validate) Sets the value of the BiologicalOrigin attribute.
void	setBiologicalOrigin(boolean value) Sets the value of the BiologicalOrigin attribute.
boolean	getBiologicalOrigin() Returns the value of the BiologicalOrigin attribute.
void	resetBiologicalOrigin() Resets the BiologicalOrigin attribute to an unset state.
boolean	hasBiologicalOrigin() Checks whether the BiologicalOrigin attribute is present.
void	setSampleType(SampleType_Type value, boolean validate) Sets the value of the SampleType attribute.
void	setSampleType(SampleType_Type value) Sets the value of the SampleType attribute.
SampleType_Type	getSampleType() Returns the value of the SampleType attribute.
void	resetSampleType() Resets the SampleType attribute to an unset state.
boolean	hasSampleType() Checks whether the optional SampleType attribute is present.
void	setLiveSample(boolean value, boolean validate) Sets the value of the LiveSample attribute.
void	setLiveSample(boolean value) Sets the value of the LiveSample attribute.
boolean	getLiveSample() Returns the value of the LiveSample attribute.
void	resetLiveSample() Resets the LiveSample attribute to an unset state.
boolean	hasLiveSample() Checks whether the LiveSample attribute is present.
void	setOrganism(String value, boolean validate) Sets the value of the Organism attribute.
void	setOrganism(String value) Sets the value of the Organism attribute.
String	getOrganism() Returns the value of the Organism attribute.
void	resetOrganism() Resets the Organism attribute to an unset state.
boolean	hasOrganism() Checks whether the Organism attribute is present.
void	setOrganismTermAccession(String value, boolean validate) Sets the value of the OrganismTermAccession attribute.
void	setOrganismTermAccession(String value) Sets the value of the OrganismTermAccession attribute.
String	getOrganismTermAccession() Returns the value of the OrganismTermAccession attribute.
void	resetOrganismTermAccession() Resets the OrganismTermAccession attribute to an unset state.
boolean	hasOrganismTermAccession() Checks whether the OrganismTermAccession attribute is present.
void	setOrganismPart(String value, boolean validate) Sets the value of the OrganismPart attribute.
void	setOrganismPart(String value) Sets the value of the OrganismPart attribute.
String	getOrganismPart() Returns the value of the OrganismPart attribute.
void	resetOrganismPart() Resets the OrganismPart attribute to an unset state.
boolean	hasOrganismPart() Checks whether the OrganismPart attribute is present.
void	setOrganismPartTermAccession(String value, boolean validate) Sets the value of the OrganismPartTermAccession attribute.
void	setOrganismPartTermAccession(String value) Sets the value of the OrganismPartTermAccession attribute.
String	getOrganismPartTermAccession() Returns the value of the OrganismPartTermAccession attribute.
void	resetOrganismPartTermAccession() Resets the OrganismPartTermAccession attribute to an unset state.
boolean	hasOrganismPartTermAccession() Checks whether the OrganismPartTermAccession attribute is present.
void	setSamplePreparationMethod(String value, boolean validate) Sets the value of the SamplePreparationMethod attribute.
void	setSamplePreparationMethod(String value) Sets the value of the SamplePreparationMethod attribute.
String	getSamplePreparationMethod() Returns the value of the SamplePreparationMethod attribute.
void	resetSamplePreparationMethod() Resets the SamplePreparationMethod attribute to an unset state.
boolean	hasSamplePreparationMethod() Checks whether the SamplePreparationMethod attribute is present.
void	setSamplePreparationMethodTermAccession(String value, boolean validate) Sets the value of the SamplePreparationMethodTermAccession attribute.
void	setSamplePreparationMethodTermAccession(String value) Sets the value of the SamplePreparationMethodTermAccession attribute.
String	getSamplePreparationMethodTermAccession() Returns the value of the SamplePreparationMethodTermAccession attribute.
void	resetSamplePreparationMethodTermAccession() Resets the SamplePreparationMethodTermAccession attribute to an unset state.
boolean	hasSamplePreparationMethodTermAccession() Checks whether the SamplePreparationMethodTermAccession attribute is present.
void	setMetrologySample(boolean value, boolean validate) Sets the value of the MetrologySample attribute.
void	setMetrologySample(boolean value) Sets the value of the MetrologySample attribute.
boolean	getMetrologySample() Returns the value of the MetrologySample attribute.
void	resetMetrologySample() Resets the MetrologySample attribute to an unset state.
boolean	hasMetrologySample() Checks whether the MetrologySample attribute is present.
void	setFacingTheObjective(FacingTheObjectiveChoice_Type value, boolean validate) Sets the value of the FacingTheObjective attribute.
void	setFacingTheObjective(FacingTheObjectiveChoice_Type value) Sets the value of the FacingTheObjective attribute.
FacingTheObjectiveChoice_Type	getFacingTheObjective() Returns the value of the FacingTheObjective attribute.
void	resetFacingTheObjective() Resets the FacingTheObjective attribute to an unset state.
boolean	hasFacingTheObjective() Checks whether the optional FacingTheObjective attribute is present.
void	setMountingMedium_List(MountingMediumVector value, boolean validate) Sets the list of MountingMedium elements.
void	setMountingMedium_List(MountingMediumVector value) Sets the list of MountingMedium elements.
MountingMediumVector	getMountingMedium_List() Returns the list of MountingMedium elements.
void	addToMountingMedium_List(MountingMedium value, boolean validate) Adds a new MountingMedium element to this object.
void	addToMountingMedium_List(MountingMedium value) Adds a new MountingMedium element to this object.
void	clearMountingMedium_List() Clear the list of MountingMedium.
void	setCoverGlass_List(CoverGlassVector value, boolean validate) Sets the list of CoverGlass elements.
void	setCoverGlass_List(CoverGlassVector value) Sets the list of CoverGlass elements.
CoverGlassVector	getCoverGlass_List() Returns the list of CoverGlass elements.
void	addToCoverGlass_List(CoverGlass value, boolean validate) Adds a new CoverGlass element to this object.
void	addToCoverGlass_List(CoverGlass value) Adds a new CoverGlass element to this object.
void	clearCoverGlass_List() Clear the list of CoverGlass.
void	setSampleHolder_List(SampleHolderVector value, boolean validate) Sets the list of SampleHolder elements.
void	setSampleHolder_List(SampleHolderVector value) Sets the list of SampleHolder elements.
SampleHolderVector	getSampleHolder_List() Returns the list of SampleHolder elements.
void	addToSampleHolder_List(SampleHolder value, boolean validate) Adds a new SampleHolder element to this object.
void	addToSampleHolder_List(SampleHolder value) Adds a new SampleHolder element to this object.
void	clearSampleHolder_List() Clear the list of SampleHolder.
void	setDescription(Description value, boolean validate) Sets the value of the Description element.
void	setDescription(Description value) Sets the value of the Description element.
Description	getDescription() Returns the value of the Description element.
void	resetDescription() Resets the Description element to an unset state.
boolean	hasDescription() Checks whether the optional Description element is present.
void	setAnnotationRef_List(AnnotationRefVector value, boolean validate) Sets the list of AnnotationRef elements.
void	setAnnotationRef_List(AnnotationRefVector value) Sets the list of AnnotationRef elements.
AnnotationRefVector	getAnnotationRef_List() Returns the list of AnnotationRef elements.
void	addToAnnotationRef_List(AnnotationRef value, boolean validate) Adds a new AnnotationRef element to this object.
void	addToAnnotationRef_List(AnnotationRef value) Adds a new AnnotationRef element to this object.
void	clearAnnotationRef_List() Clear the list of AnnotationRef.
Sample	__internal_create(long cPtr, boolean own)
Sample	fromBase(NBOBaseClass base) Cast a NBOBaseClass to a Sample.
StringSet	getOrganismAllowedValues() Returns the allowed values for this attribut.
StringSet	getOrganismTermAccessionAllowedValues() Returns the allowed values for this attribut.
StringSet	getOrganismPartAllowedValues() Returns the allowed values for this attribut.
StringSet	getOrganismPartTermAccessionAllowedValues() Returns the allowed values for this attribut.
StringSet	getSamplePreparationMethodAllowedValues() Returns the allowed values for this attribut.
StringSet	getSamplePreparationMethodTermAccessionAllowedValues() Returns the allowed values for this attribut.

Protected Functions¶

	Name
	Sample(long cPtr, boolean cMemoryOwn)
void	swigSetCMemOwn(boolean own)
void	finalize()
long	getCPtr(Sample obj)

Additional inherited members¶

Protected Functions inherited from com.inscoper.nbo.NBOBaseClass

	Name
	NBOBaseClass(long cPtr, boolean cMemoryOwn)

Detailed Description¶

public class com.inscoper.nbo.Sample;

Represents the XML element Sample.

This field captures a description of the sample that was imaged in this experiment.

Public Functions Documentation¶

function delete¶

function Sample¶

function getTypeName¶

function getXMLName¶

function getNBOType¶

function getChildren¶

function getSubElements¶

public NBOBaseClassVector getSubElements()

Returns a list of all child elements contained in this class.

Return: The list of child classes

Reimplements: com.inscoper.nbo.NBOBaseClass.getSubElements

function fromJsonFile¶

public void fromJsonFile(
    String path,
    boolean validate
)

Populates this object from a JSON file.

Parameters:

path The path to the JSON file
validate If true, validates constraints on value. Default is true.

function fromJsonFile¶

function fromJsonString¶

public void fromJsonString(
    String json_string,
    boolean validate
)

Populates this object from a JSON string.

Parameters:

json_string The JSON content as a string
validate If true, validates constraints on value. Default is true.

function fromJsonString¶

function fromXmlFile¶

public void fromXmlFile(
    String path,
    boolean validate
)

Populates this object from a XML file.

Parameters:

path The path to the XML file
validate If true, validates constraints on value. Default is true.

function fromXmlFile¶

function fromXmlString¶

public void fromXmlString(
    String xml_string,
    boolean validate
)

Populates this object from a XML string.

Parameters:

xml_string The XML content as a string
validate If true, validates constraints on value. Default is true.

function fromXmlString¶

function toXmlFile¶

public void toXmlFile(
    String filename,
    boolean validate
)

Serializes this object to an XML file.

Parameters:

filename The path to the output XML file
validate If true, validates constraints on value. Default is true.

function toXmlFile¶

function toXmlString¶

public String toXmlString(
    boolean validate
)

Serializes this object to an XML string.

Parameters:

validate If true, validates constraints on value. Default is true.

Return: A string containing the XML representation of this object

function toXmlString¶

function setID¶

public void setID(
    LSID_Type value,
    boolean validate
)

Sets the value of the ID attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

A unique identifier for this Sample.

function setID¶

function getID¶

function resetID¶

function hasID¶

function setName¶

public void setName(
    Denomination_Type value,
    boolean validate
)

Sets the value of the Name attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

A user assigned Name for this Sample.

function setName¶

function getName¶

function resetName¶

function hasName¶

function setBiologicalOrigin¶

public void setBiologicalOrigin(
    boolean value,
    boolean validate
)

Sets the value of the BiologicalOrigin attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field captures whether (True) or not (False) this Sample is of Biological Origin.

function setBiologicalOrigin¶

public void setBiologicalOrigin(
    boolean value
)

Sets the value of the BiologicalOrigin attribute.

Parameters:

value The value to set

This field captures whether (True) or not (False) this Sample is of Biological Origin.

function getBiologicalOrigin¶

public boolean getBiologicalOrigin()

Returns the value of the BiologicalOrigin attribute.

Return: The value of the attribute

This field captures whether (True) or not (False) this Sample is of Biological Origin.

function resetBiologicalOrigin¶

function hasBiologicalOrigin¶

public boolean hasBiologicalOrigin()

Checks whether the BiologicalOrigin attribute is present.

Return: true if the attribute has been set, false otherwise

This field captures whether (True) or not (False) this Sample is of Biological Origin.

function setSampleType¶

public void setSampleType(
    SampleType_Type value,
    boolean validate
)

Sets the value of the SampleType attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

If of Biological Origin, this field records a term that describes the general category of this Sample.

function setSampleType¶

public void setSampleType(
    SampleType_Type value
)

Sets the value of the SampleType attribute.

Parameters:

value The value to set

If of Biological Origin, this field records a term that describes the general category of this Sample.

function getSampleType¶

public SampleType_Type getSampleType()

Returns the value of the SampleType attribute.

Return: The value of the attribute

If of Biological Origin, this field records a term that describes the general category of this Sample.

function resetSampleType¶

function hasSampleType¶

public boolean hasSampleType()

Checks whether the optional SampleType attribute is present.

Return: true if the optional attribute has been set, false otherwise

If of Biological Origin, this field records a term that describes the general category of this Sample.

function setLiveSample¶

public void setLiveSample(
    boolean value,
    boolean validate
)

Sets the value of the LiveSample attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

function setLiveSample¶

public void setLiveSample(
    boolean value
)

Sets the value of the LiveSample attribute.

Parameters:

value The value to set

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

function getLiveSample¶

public boolean getLiveSample()

Returns the value of the LiveSample attribute.

Return: The value of the attribute

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

function resetLiveSample¶

function hasLiveSample¶

public boolean hasLiveSample()

Checks whether the LiveSample attribute is present.

Return: true if the attribute has been set, false otherwise

This field captures whether (True) or not (False) this Sample was living during Image Acquisition.

function setOrganism¶

public void setOrganism(
    String value,
    boolean validate
)

Sets the value of the Organism attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

function setOrganism¶

public void setOrganism(
    String value
)

Sets the value of the Organism attribute.

Parameters:

value The value to set

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

function getOrganism¶

public String getOrganism()

Returns the value of the Organism attribute.

Return: The value of the attribute

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

function resetOrganism¶

public void resetOrganism()

Resets the Organism attribute to an unset state.

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

function hasOrganism¶

public boolean hasOrganism()

Checks whether the Organism attribute is present.

Return: true if the attribute has been set, false otherwise

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

function setOrganismTermAccession¶

public void setOrganismTermAccession(
    String value,
    boolean validate
)

Sets the value of the OrganismTermAccession attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

function setOrganismTermAccession¶

public void setOrganismTermAccession(
    String value
)

Sets the value of the OrganismTermAccession attribute.

Parameters:

value The value to set

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

function getOrganismTermAccession¶

public String getOrganismTermAccession()

Returns the value of the OrganismTermAccession attribute.

Return: The value of the attribute

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

function resetOrganismTermAccession¶

public void resetOrganismTermAccession()

Resets the OrganismTermAccession attribute to an unset state.

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

function hasOrganismTermAccession¶

public boolean hasOrganismTermAccession()

Checks whether the OrganismTermAccession attribute is present.

Return: true if the attribute has been set, false otherwise

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

function setOrganismPart¶

public void setOrganismPart(
    String value,
    boolean validate
)

Sets the value of the OrganismPart attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function setOrganismPart¶

public void setOrganismPart(
    String value
)

Sets the value of the OrganismPart attribute.

Parameters:

value The value to set

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function getOrganismPart¶

public String getOrganismPart()

Returns the value of the OrganismPart attribute.

Return: The value of the attribute

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function resetOrganismPart¶

public void resetOrganismPart()

Resets the OrganismPart attribute to an unset state.

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function hasOrganismPart¶

public boolean hasOrganismPart()

Checks whether the OrganismPart attribute is present.

Return: true if the attribute has been set, false otherwise

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function setOrganismPartTermAccession¶

public void setOrganismPartTermAccession(
    String value,
    boolean validate
)

Sets the value of the OrganismPartTermAccession attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function setOrganismPartTermAccession¶

public void setOrganismPartTermAccession(
    String value
)

Sets the value of the OrganismPartTermAccession attribute.

Parameters:

value The value to set

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function getOrganismPartTermAccession¶

public String getOrganismPartTermAccession()

Returns the value of the OrganismPartTermAccession attribute.

Return: The value of the attribute

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function resetOrganismPartTermAccession¶

public void resetOrganismPartTermAccession()

Resets the OrganismPartTermAccession attribute to an unset state.

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function hasOrganismPartTermAccession¶

public boolean hasOrganismPartTermAccession()

Checks whether the OrganismPartTermAccession attribute is present.

Return: true if the attribute has been set, false otherwise

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function setSamplePreparationMethod¶

public void setSamplePreparationMethod(
    String value,
    boolean validate
)

Sets the value of the SamplePreparationMethod attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function setSamplePreparationMethod¶

public void setSamplePreparationMethod(
    String value
)

Sets the value of the SamplePreparationMethod attribute.

Parameters:

value The value to set

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function getSamplePreparationMethod¶

public String getSamplePreparationMethod()

Returns the value of the SamplePreparationMethod attribute.

Return: The value of the attribute

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function resetSamplePreparationMethod¶

public void resetSamplePreparationMethod()

Resets the SamplePreparationMethod attribute to an unset state.

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function hasSamplePreparationMethod¶

public boolean hasSamplePreparationMethod()

Checks whether the SamplePreparationMethod attribute is present.

Return: true if the attribute has been set, false otherwise

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function setSamplePreparationMethodTermAccession¶

public void setSamplePreparationMethodTermAccession(
    String value,
    boolean validate
)

Sets the value of the SamplePreparationMethodTermAccession attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function setSamplePreparationMethodTermAccession¶

public void setSamplePreparationMethodTermAccession(
    String value
)

Sets the value of the SamplePreparationMethodTermAccession attribute.

Parameters:

value The value to set

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function getSamplePreparationMethodTermAccession¶

public String getSamplePreparationMethodTermAccession()

Returns the value of the SamplePreparationMethodTermAccession attribute.

Return: The value of the attribute

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function resetSamplePreparationMethodTermAccession¶

public void resetSamplePreparationMethodTermAccession()

Resets the SamplePreparationMethodTermAccession attribute to an unset state.

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function hasSamplePreparationMethodTermAccession¶

public boolean hasSamplePreparationMethodTermAccession()

Checks whether the SamplePreparationMethodTermAccession attribute is present.

Return: true if the attribute has been set, false otherwise

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function setMetrologySample¶

public void setMetrologySample(
    boolean value,
    boolean validate
)

Sets the value of the MetrologySample attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

function setMetrologySample¶

public void setMetrologySample(
    boolean value
)

Sets the value of the MetrologySample attribute.

Parameters:

value The value to set

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

function getMetrologySample¶

public boolean getMetrologySample()

Returns the value of the MetrologySample attribute.

Return: The value of the attribute

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

function resetMetrologySample¶

public void resetMetrologySample()

Resets the MetrologySample attribute to an unset state.

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

function hasMetrologySample¶

public boolean hasMetrologySample()

Checks whether the MetrologySample attribute is present.

Return: true if the attribute has been set, false otherwise

This field captures whether (True) or not (False) this is a Metrology Sample (i.e., a Sample that is used specifcially to calibrate and assess the performance of the Instrument utilized for this experimental Image Acquisition.

function setFacingTheObjective¶

public void setFacingTheObjective(
    FacingTheObjectiveChoice_Type value,
    boolean validate
)

Sets the value of the FacingTheObjective attribute.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

function setFacingTheObjective¶

public void setFacingTheObjective(
    FacingTheObjectiveChoice_Type value
)

Sets the value of the FacingTheObjective attribute.

Parameters:

value The value to set

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

function getFacingTheObjective¶

public FacingTheObjectiveChoice_Type getFacingTheObjective()

Returns the value of the FacingTheObjective attribute.

Return: The value of the attribute

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

function resetFacingTheObjective¶

public void resetFacingTheObjective()

Resets the FacingTheObjective attribute to an unset state.

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

function hasFacingTheObjective¶

public boolean hasFacingTheObjective()

Checks whether the optional FacingTheObjective attribute is present.

Return: true if the optional attribute has been set, false otherwise

This field captures whether the CoverGlass, the SampleHolder, or neither (None), faced the Objective during Acquisition of this Image.

function setMountingMedium_List¶

public void setMountingMedium_List(
    MountingMediumVector value,
    boolean validate
)

Sets the list of MountingMedium elements.

Parameters:

value The new list of MountingMedium elements
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function setMountingMedium_List¶

public void setMountingMedium_List(
    MountingMediumVector value
)

Sets the list of MountingMedium elements.

Parameters:

value The new list of MountingMedium elements

No description available in the XSD standard.

function getMountingMedium_List¶

function addToMountingMedium_List¶

public void addToMountingMedium_List(
    MountingMedium value,
    boolean validate
)

Adds a new MountingMedium element to this object.

Parameters:

value The element to add
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function addToMountingMedium_List¶

public void addToMountingMedium_List(
    MountingMedium value
)

Adds a new MountingMedium element to this object.

Parameters:

value The element to add

No description available in the XSD standard.

function clearMountingMedium_List¶

function setCoverGlass_List¶

public void setCoverGlass_List(
    CoverGlassVector value,
    boolean validate
)

Sets the list of CoverGlass elements.

Parameters:

value The new list of CoverGlass elements
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function setCoverGlass_List¶

public void setCoverGlass_List(
    CoverGlassVector value
)

Sets the list of CoverGlass elements.

Parameters:

value The new list of CoverGlass elements

No description available in the XSD standard.

function getCoverGlass_List¶

function addToCoverGlass_List¶

public void addToCoverGlass_List(
    CoverGlass value,
    boolean validate
)

Adds a new CoverGlass element to this object.

Parameters:

value The element to add
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function addToCoverGlass_List¶

function clearCoverGlass_List¶

function setSampleHolder_List¶

public void setSampleHolder_List(
    SampleHolderVector value,
    boolean validate
)

Sets the list of SampleHolder elements.

Parameters:

value The new list of SampleHolder elements
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function setSampleHolder_List¶

public void setSampleHolder_List(
    SampleHolderVector value
)

Sets the list of SampleHolder elements.

Parameters:

value The new list of SampleHolder elements

No description available in the XSD standard.

function getSampleHolder_List¶

function addToSampleHolder_List¶

public void addToSampleHolder_List(
    SampleHolder value,
    boolean validate
)

Adds a new SampleHolder element to this object.

Parameters:

value The element to add
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function addToSampleHolder_List¶

function clearSampleHolder_List¶

function setDescription¶

public void setDescription(
    Description value,
    boolean validate
)

Sets the value of the Description element.

Parameters:

value The value to set
validate If true, validates constraints on value. Default is true.

No description available in the XSD standard.

function setDescription¶

function getDescription¶

function resetDescription¶

function hasDescription¶

public boolean hasDescription()

Checks whether the optional Description element is present.

Return: true if the optional attribute has been set, false otherwise

No description available in the XSD standard.

function setAnnotationRef_List¶

public void setAnnotationRef_List(
    AnnotationRefVector value,
    boolean validate
)

Sets the list of AnnotationRef elements.

Parameters:

value The new list of AnnotationRef elements
validate If true, validates constraints on value. Default is true.

This is a simple multi-line comment or annotation describing this component.

function setAnnotationRef_List¶

public void setAnnotationRef_List(
    AnnotationRefVector value
)

Sets the list of AnnotationRef elements.

Parameters:

value The new list of AnnotationRef elements

This is a simple multi-line comment or annotation describing this component.

function getAnnotationRef_List¶

public AnnotationRefVector getAnnotationRef_List()

Returns the list of AnnotationRef elements.

Return: The list of AnnotationRef elements

This is a simple multi-line comment or annotation describing this component.

function addToAnnotationRef_List¶

public void addToAnnotationRef_List(
    AnnotationRef value,
    boolean validate
)

Adds a new AnnotationRef element to this object.

Parameters:

value The element to add
validate If true, validates constraints on value. Default is true.

This is a simple multi-line comment or annotation describing this component.

function addToAnnotationRef_List¶

public void addToAnnotationRef_List(
    AnnotationRef value
)

Adds a new AnnotationRef element to this object.

Parameters:

value The element to add

This is a simple multi-line comment or annotation describing this component.

function clearAnnotationRef_List¶

function __internal_create¶

function fromBase¶

function getOrganismAllowedValues¶

public static StringSet getOrganismAllowedValues()

Returns the allowed values for this attribut.

Return: The list of allowed values

If this sample is of biological origin, this field records the biological organisn this sample derives from. A biological is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). The use terms from NCBITaxon (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended. Note: if the sample is not of biological origin please enter none.

function getOrganismTermAccessionAllowedValues¶

public static StringSet getOrganismTermAccessionAllowedValues()

Returns the allowed values for this attribut.

Return: The list of allowed values

This field records the Accession ID for the term used to describe the Organism. The use of the NCBITaxon ontology (http://purl.obolibrary.org/obo/NCBITaxon_1) is recommended.

function getOrganismPartAllowedValues¶

public static StringSet getOrganismPartAllowedValues()

Returns the allowed values for this attribut.

Return: The list of allowed values

If applicable, this field records the part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). The use of a sub-class of the 'Organism Part' (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function getOrganismPartTermAccessionAllowedValues¶

public static StringSet getOrganismPartTermAccessionAllowedValues()

Returns the allowed values for this attribut.

Return: The list of allowed values

This field records the Accession ID for the term used to describe the Organism. A sub-classe of the EFO:0000635 (http://www.ebi.ac.uk/efo/EFO_0000635) term from the Experimental Factor Ontology (EFO; http://www.ebi.ac.uk/efo/) is recommended.

function getSamplePreparationMethodAllowedValues¶

public static StringSet getSamplePreparationMethodAllowedValues()

Returns the allowed values for this attribut.

Return: The list of allowed values

This field records the method that was used to prepare this sample. The use of a sub-class of the 'Sample Preparation Method' (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.

function getSamplePreparationMethodTermAccessionAllowedValues¶

public static StringSet getSamplePreparationMethodTermAccessionAllowedValues()

Returns the allowed values for this attribut.

Return: The list of allowed values

This field records the the Accession ID for the term used to describe method that was used to prepare this sample. A subclass of the Fbbi:00000001 (http://purl.obolibrary.org/obo/FBbi_00000001) term from the Biological Imaging Methods Ontology (FBbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) is recommended.