com.inscoper.nbo.Channel

Represents the XML element Channel. More...

Inherits from com.inscoper.nbo.NBOBaseClass

Public Functions

	Name
synchronized void	delete()
	Channel()
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(ChannelID_Type value) Sets the value of the ID attribute.
ChannelID_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	setIlluminationType(ImagingMethodList_Type value) Sets the value of the IlluminationType attribute.
ImagingMethodList_Type	getIlluminationType() Returns the value of the IlluminationType attribute.
void	resetIlluminationType() Resets the IlluminationType attribute to an unset state.
boolean	hasIlluminationType() Checks whether the optional IlluminationType attribute is present.
void	setIlluminationTypeTermAcession(String value) Sets the value of the IlluminationTypeTermAcession attribute.
String	getIlluminationTypeTermAcession() Returns the value of the IlluminationTypeTermAcession attribute.
void	resetIlluminationTypeTermAcession() Resets the IlluminationTypeTermAcession attribute to an unset state.
boolean	hasIlluminationTypeTermAcession() Checks whether the optional IlluminationTypeTermAcession attribute is present.
void	setContrastMethod(ChannelContrastMethod_Type value) Sets the value of the ContrastMethod attribute.
ChannelContrastMethod_Type	getContrastMethod() Returns the value of the ContrastMethod attribute.
void	resetContrastMethod() Resets the ContrastMethod attribute to an unset state.
boolean	hasContrastMethod() Checks whether the optional ContrastMethod attribute is present.
void	setColor(Color_Type value) Sets the value of the Color attribute.
Color_Type	getColor() Returns the value of the Color attribute.
void	resetColor() Resets the Color attribute to an unset state.
boolean	hasColor() Checks whether the optional Color attribute is present.
void	setSamplesPerPixel(PositiveInt_Type value) Sets the value of the SamplesPerPixel attribute.
PositiveInt_Type	getSamplesPerPixel() Returns the value of the SamplesPerPixel attribute.
void	resetSamplesPerPixel() Resets the SamplesPerPixel attribute to an unset state.
boolean	hasSamplesPerPixel() Checks whether the optional SamplesPerPixel attribute is present.
void	setFluorophore_List(FluorophoreVector value) Sets the list of Fluorophore elements.
FluorophoreVector	getFluorophore_List() Returns the list of Fluorophore elements.
void	addToFluorophore_List(Fluorophore value) Adds a new Fluorophore element to this object.
void	clearFluorophore_List() Clear the list of Fluorophore.
void	setLightPath(LightPath value) Sets the value of the LightPath element.
LightPath	getLightPath() Returns the value of the LightPath element.
void	resetLightPath() Resets the LightPath element to an unset state.
boolean	hasLightPath() Checks whether the optional LightPath element is present.
void	setExcitationCalibration_List(ExcitationCalibrationVector value) Sets the list of ExcitationCalibration elements.
ExcitationCalibrationVector	getExcitationCalibration_List() Returns the list of ExcitationCalibration elements.
void	addToExcitationCalibration_List(ExcitationCalibration value) Adds a new ExcitationCalibration element to this object.
void	clearExcitationCalibration_List() Clear the list of ExcitationCalibration.
void	setAnnotationRef(AnnotationRef value) Sets the value of the AnnotationRef element.
AnnotationRef	getAnnotationRef() Returns the value of the AnnotationRef element.
void	resetAnnotationRef() Resets the AnnotationRef element to an unset state.
boolean	hasAnnotationRef() Checks whether the optional AnnotationRef element is present.
Channel	__internal_create(long cPtr, boolean own)

Protected Functions

	Name
	Channel(long cPtr, boolean cMemoryOwn)
void	swigSetCMemOwn(boolean own)
void	finalize()
long	getCPtr(Channel 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.Channel;

Represents the XML element Channel.

Each Image has to have at least one Plane and one Channel. The Channel element stores information about how the each Image Channel was acquired. The total number of Channel elements for a given Image must equal to SizeC.

Public Functions Documentation

function delete

public synchronized void delete()

Reimplements: com.inscoper.nbo.NBOBaseClass.delete

function Channel

public Channel()

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(
    ChannelID_Type value
)

Sets the value of the ID attribute.

Parameters:

value The value to set

A unique identifier for this Channel.

function getID

public ChannelID_Type getID()

Returns the value of the ID attribute.

Return: The value of the attribute

A unique identifier for this Channel.

function resetID

public void resetID()

Resets the ID attribute to an unset state.

A unique identifier for this Channel.

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 Channel.

function setName

public void setName(
    Denomination_Type value
)

Sets the value of the Name attribute.

Parameters:

value The value to set

A Name for this Channel that is suitable for presentation to the user.

function getName

public Denomination_Type getName()

Returns the value of the Name attribute.

Return: The value of the attribute

A Name for this Channel that is suitable for presentation to the user.

function resetName

public void resetName()

Resets the Name attribute to an unset state.

A Name for this Channel that is suitable for presentation to the user.

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 Name for this Channel that is suitable for presentation to the user.

function setIlluminationType

public void setIlluminationType(
    ImagingMethodList_Type value
)

Sets the value of the IlluminationType attribute.

Parameters:

value The value to set

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

function getIlluminationType

public ImagingMethodList_Type getIlluminationType()

Returns the value of the IlluminationType attribute.

Return: The value of the attribute

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

function resetIlluminationType

public void resetIlluminationType()

Resets the IlluminationType attribute to an unset state.

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

function hasIlluminationType

public boolean hasIlluminationType()

Checks whether the optional IlluminationType attribute is present.

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

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

function setIlluminationTypeTermAcession

public void setIlluminationTypeTermAcession(
    String value
)

Sets the value of the IlluminationTypeTermAcession attribute.

Parameters:

value The value to set

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

function getIlluminationTypeTermAcession

public String getIlluminationTypeTermAcession()

Returns the value of the IlluminationTypeTermAcession attribute.

Return: The value of the attribute

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

function resetIlluminationTypeTermAcession

public void resetIlluminationTypeTermAcession()

Resets the IlluminationTypeTermAcession attribute to an unset state.

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

function hasIlluminationTypeTermAcession

public boolean hasIlluminationTypeTermAcession()

Checks whether the optional IlluminationTypeTermAcession 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 Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

function setContrastMethod

public void setContrastMethod(
    ChannelContrastMethod_Type value
)

Sets the value of the ContrastMethod attribute.

Parameters:

value The value to set

This field describes the technique used to achieve contrast for this Channel.

function getContrastMethod

public ChannelContrastMethod_Type getContrastMethod()

Returns the value of the ContrastMethod attribute.

Return: The value of the attribute

This field describes the technique used to achieve contrast for this Channel.

function resetContrastMethod

public void resetContrastMethod()

Resets the ContrastMethod attribute to an unset state.

This field describes the technique used to achieve contrast for this Channel.

function hasContrastMethod

public boolean hasContrastMethod()

Checks whether the optional ContrastMethod attribute is present.

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

This field describes the technique used to achieve contrast for this Channel.

function setColor

public void setColor(
    Color_Type value
)

Sets the value of the Color attribute.

Parameters:

value The value to set

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

function getColor

public Color_Type getColor()

Returns the value of the Color attribute.

Return: The value of the attribute

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

function resetColor

public void resetColor()

Resets the Color attribute to an unset state.

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

function hasColor

public boolean hasColor()

Checks whether the optional Color attribute is present.

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

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

function setSamplesPerPixel

public void setSamplesPerPixel(
    PositiveInt_Type value
)

Sets the value of the SamplesPerPixel attribute.

Parameters:

value The value to set

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

function getSamplesPerPixel

public PositiveInt_Type getSamplesPerPixel()

Returns the value of the SamplesPerPixel attribute.

Return: The value of the attribute

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

function resetSamplesPerPixel

public void resetSamplesPerPixel()

Resets the SamplesPerPixel attribute to an unset state.

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

function hasSamplesPerPixel

public boolean hasSamplesPerPixel()

Checks whether the optional SamplesPerPixel attribute is present.

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

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

function setFluorophore_List

public void setFluorophore_List(
    FluorophoreVector value
)

Sets the list of Fluorophore elements.

Parameters:

value The new list of Fluorophore elements