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) Populates this object from a JSON file.
void	fromJsonString(String json_string) Populates this object from a JSON string.
void	fromXmlFile(String path) Populates this object from a XML file.
void	fromXmlString(String xml_string) Populates this object from a XML string.
void	toXmlFile(String filename) Serializes this object to an XML file.
String	toXmlString() Serializes this object to an XML string.
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) 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) Sets the value of the BiologicalOrigin attribute.
boolean	getBiologicalOrigin() Returns the value of the BiologicalOrigin 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) Sets the value of the LiveSample attribute.
boolean	getLiveSample() Returns the value of the LiveSample attribute.
void	setOrganism(String value) Sets the value of the Organism attribute.
String	getOrganism() Returns the value of the Organism 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 optional OrganismTermAccession attribute is present.
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 optional OrganismPart attribute is present.
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 optional OrganismPartTermAccession attribute is present.
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 optional SamplePreparationMethod attribute is present.
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 optional SamplePreparationMethodTermAccession attribute is present.
void	setMetrologySample(boolean value) Sets the value of the MetrologySample attribute.
boolean	getMetrologySample() Returns the value of the MetrologySample 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) Sets the list of MountingMedium elements.
MountingMediumVector	getMountingMedium_List() Returns the list of MountingMedium elements.
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) Sets the list of CoverGlass elements.
CoverGlassVector	getCoverGlass_List() Returns the list of CoverGlass elements.
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) Sets the list of SampleHolder elements.
SampleHolderVector	getSampleHolder_List() Returns the list of SampleHolder elements.
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) 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) Sets the list of AnnotationRef elements.
AnnotationRefVector	getAnnotationRef_List() Returns the list of AnnotationRef elements.
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)

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

public synchronized void delete()

Reimplements: com.inscoper.nbo.NBOBaseClass.delete

function Sample

public Sample()

function getTypeName

public String getTypeName()

Returns the class type name.

Return: The class type name

Reimplements: com.inscoper.nbo.NBOBaseClass.getTypeName

function getXMLName

public String getXMLName()

Returns the XML element name corresponding to this class.

Return: The XML element name

Reimplements: com.inscoper.nbo.NBOBaseClass.getXMLName

function getNBOType

public ENBOType getNBOType()

Returns the NBO Type corresponding to this class.

Return: The NBO Type value

Reimplements: com.inscoper.nbo.NBOBaseClass.getNBOType

function getChildren

public NBOBaseClassVector getChildren()

Returns a list of all classes derived from this class.

Return: The list of derived classes

Reimplements: com.inscoper.nbo.NBOBaseClass.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
)

Populates this object from a JSON file.

Parameters:

path The path to the JSON file

function fromJsonString

public void fromJsonString(
    String json_string
)

Populates this object from a JSON string.

Parameters:

json_string The JSON content as a string

function fromXmlFile

public void fromXmlFile(
    String path
)

Populates this object from a XML file.

Parameters:

path The path to the XML file

function fromXmlString

public void fromXmlString(
    String xml_string
)

Populates this object from a XML string.

Parameters:

xml_string The XML content as a string

function toXmlFile

public void toXmlFile(
    String filename
)

Serializes this object to an XML file.

Parameters:

filename The path to the output XML file

function toXmlString

public String toXmlString()

Serializes this object to an XML string.

Return: A string containing the XML representation of this object

function setID

public void setID(
    LSID_Type value
)

Sets the value of the ID attribute.

Parameters:

value The value to set

A unique identifier for this Sample.

function getID

public LSID_Type getID()

Returns the value of the ID attribute.

Return: The value of the attribute

A unique identifier for this Sample.

function resetID

public void resetID()

Resets the ID attribute to an unset state.

A unique identifier for this Sample.

function hasID

public boolean hasID()

Checks whether the optional ID attribute is present.

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

A unique identifier for this Sample.

function setName

public void setName(
    Denomination_Type value
)

Sets the value of the Name attribute.

Parameters:

value The value to set

A user assigned Name for this Sample.

function getName

public Denomination_Type getName()

Returns the value of the Name attribute.

Return: The value of the attribute

A user assigned Name for this Sample.

function resetName

public void resetName()

Resets the Name attribute to an unset state.

A user assigned Name for this Sample.

function hasName

public boolean hasName()

Checks whether the optional Name attribute is present.

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

A user assigned Name for this Sample.

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 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

public void resetSampleType()

Resets the SampleType attribute to an unset state.

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

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
)

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 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 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 optional OrganismTermAccession attribute is present.

Return: true if the optional 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
)

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 optional OrganismPart attribute is present.

Return: true if the optional 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
)

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 optional OrganismPartTermAccession attribute is present.

Return: true if the optional 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
)

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 optional SamplePreparationMethod attribute is present.

Return: true if the optional 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
)

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 optional SamplePreparationMethodTermAccession attribute is present.

Return: true if the optional 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
)

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 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
)

Sets the list of MountingMedium elements.

Parameters:

value The new list of MountingMedium elements