gov.nih.nci.mageom.domain.Array
Interface ArrayGroup

All Superinterfaces:
Describable, Extendable, Identifiable
All Known Implementing Classes:
ArrayGroupImpl

public interface ArrayGroup
extends Identifiable

An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays. The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes.

Version:
%I%, %G%

Method Summary
 Array[] getArrays()
          Returns the value of this ArrayGroup object's arrays attribute.
 java.lang.Float getArraySpacingX()
          Returns the value of this ArrayGroup object's arraySpacingX attribute.
 java.lang.Float getArraySpacingY()
          Returns the value of this ArrayGroup object's arraySpacingY attribute.
 java.lang.String getBarcode()
          Returns the value of this ArrayGroup object's barcode attribute.
 DistanceUnit getDistanceUnit()
          Returns the value of this ArrayGroup object's distanceUnit attribute.
 Fiducial[] getFiducials()
          Returns the value of this ArrayGroup object's fiducials attribute.
 java.lang.Float getLength()
          Returns the value of this ArrayGroup object's length attribute.
 java.lang.Integer getNumArrays()
          Returns the value of this ArrayGroup object's numArrays attribute.
 java.lang.String getOrientationMark()
          Returns the value of this ArrayGroup object's orientationMark attribute.
 java.lang.String getOrientationMarkPosition()
          Returns the value of this ArrayGroup object's orientationMarkPosition attribute.
 OntologyEntry getSubstrateType()
          Returns the value of this ArrayGroup object's substrateType attribute.
 java.lang.Float getWidth()
          Returns the value of this ArrayGroup object's width attribute.
 void setArrays(Array[] p_arrays)
          Sets the arrays attribute.
 void setArraySpacingX(java.lang.Float p_arraySpacingX)
          Sets the arraySpacingX attribute.
 void setArraySpacingY(java.lang.Float p_arraySpacingY)
          Sets the arraySpacingY attribute.
 void setBarcode(java.lang.String p_barcode)
          Sets the barcode attribute.
 void setDistanceUnit(DistanceUnit p_distanceUnit)
          Sets the distanceUnit attribute.
 void setFiducials(Fiducial[] p_fiducials)
          Sets the fiducials attribute.
 void setLength(java.lang.Float p_length)
          Sets the length attribute.
 void setNumArrays(java.lang.Integer p_numArrays)
          Sets the numArrays attribute.
 void setOrientationMark(java.lang.String p_orientationMark)
          Sets the orientationMark attribute.
 void setOrientationMarkPosition(java.lang.String p_orientationMarkPosition)
          Sets the orientationMarkPosition attribute.
 void setSubstrateType(OntologyEntry p_substrateType)
          Sets the substrateType attribute.
 void setWidth(java.lang.Float p_width)
          Sets the width attribute.
 
Methods inherited from interface gov.nih.nci.mageom.domain.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from interface gov.nih.nci.mageom.domain.Describable
getAuditTrail, getDescriptions, getSecurity, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from interface gov.nih.nci.mageom.domain.Extendable
getPropertySets, setPropertySets
 

Method Detail

setBarcode

void setBarcode(java.lang.String p_barcode)
Sets the barcode attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_barcode - The new value for barcode.
See Also:
getBarcode()

getBarcode

java.lang.String getBarcode()
Returns the value of this ArrayGroup object's barcode attribute. Description of barcode: Identifier for the ArrayGroup.

Returns:
String The value of barcode.

setArraySpacingX

void setArraySpacingX(java.lang.Float p_arraySpacingX)
Sets the arraySpacingX attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_arraySpacingX - The new value for arraySpacingX.
See Also:
getArraySpacingX()

getArraySpacingX

java.lang.Float getArraySpacingX()
Returns the value of this ArrayGroup object's arraySpacingX attribute. Description of arraySpacingX: If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

Returns:
float The value of arraySpacingX.

setArraySpacingY

void setArraySpacingY(java.lang.Float p_arraySpacingY)
Sets the arraySpacingY attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_arraySpacingY - The new value for arraySpacingY.
See Also:
getArraySpacingY()

getArraySpacingY

java.lang.Float getArraySpacingY()
Returns the value of this ArrayGroup object's arraySpacingY attribute. Description of arraySpacingY: If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

Returns:
float The value of arraySpacingY.

setNumArrays

void setNumArrays(java.lang.Integer p_numArrays)
Sets the numArrays attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_numArrays - The new value for numArrays.
See Also:
getNumArrays()

getNumArrays

java.lang.Integer getNumArrays()
Returns the value of this ArrayGroup object's numArrays attribute. Description of numArrays: This attribute defines the number of arrays on a chip or a slide.

Returns:
int The value of numArrays.

setOrientationMark

void setOrientationMark(java.lang.String p_orientationMark)
Sets the orientationMark attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_orientationMark - The new value for orientationMark.
See Also:
getOrientationMark()

getOrientationMark

java.lang.String getOrientationMark()
Returns the value of this ArrayGroup object's orientationMark attribute. Description of orientationMark: For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.

Returns:
String The value of orientationMark.

setOrientationMarkPosition

void setOrientationMarkPosition(java.lang.String p_orientationMarkPosition)
Sets the orientationMarkPosition attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_orientationMarkPosition - The new value for orientationMarkPosition.
See Also:
getOrientationMarkPosition()

getOrientationMarkPosition

java.lang.String getOrientationMarkPosition()
Returns the value of this ArrayGroup object's orientationMarkPosition attribute. Description of orientationMarkPosition: One of top, bottom, left or right.

Returns:
enum {top,bottom,left,right} The value of orientationMarkPosition.

setWidth

void setWidth(java.lang.Float p_width)
Sets the width attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_width - The new value for width.
See Also:
getWidth()

getWidth

java.lang.Float getWidth()
Returns the value of this ArrayGroup object's width attribute. Description of width: The width of the platform

Returns:
float The value of width.

setLength

void setLength(java.lang.Float p_length)
Sets the length attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_length - The new value for length.
See Also:
getLength()

getLength

java.lang.Float getLength()
Returns the value of this ArrayGroup object's length attribute. Description of length: The length of the platform.

Returns:
float The value of length.

setArrays

void setArrays(Array[] p_arrays)
Sets the arrays attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_arrays - The new value for arrays.
See Also:
getArrays()

getArrays

Array[] getArrays()
Returns the value of this ArrayGroup object's arrays attribute.

Returns:
gov.nih.nci.mageom.bean.Array.Array[] The value of arrays.
See Also:
Array

setFiducials

void setFiducials(Fiducial[] p_fiducials)
Sets the fiducials attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_fiducials - The new value for fiducials.
See Also:
getFiducials()

getFiducials

Fiducial[] getFiducials()
Returns the value of this ArrayGroup object's fiducials attribute.

Returns:
gov.nih.nci.mageom.bean.Array.Fiducial[] The value of fiducials.
See Also:
Fiducial

setDistanceUnit

void setDistanceUnit(DistanceUnit p_distanceUnit)
Sets the distanceUnit attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_distanceUnit - The new value for distanceUnit.
See Also:
getDistanceUnit()

getDistanceUnit

DistanceUnit getDistanceUnit()
Returns the value of this ArrayGroup object's distanceUnit attribute.

Returns:
gov.nih.nci.mageom.bean.Measurement.DistanceUnit The value of distanceUnit.
See Also:
DistanceUnit

setSubstrateType

void setSubstrateType(OntologyEntry p_substrateType)
Sets the substrateType attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayGroup object.

Parameters:
p_substrateType - The new value for substrateType.
See Also:
getSubstrateType()

getSubstrateType

OntologyEntry getSubstrateType()
Returns the value of this ArrayGroup object's substrateType attribute.

Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of substrateType.
See Also:
OntologyEntry