gov.nih.nci.mageom.domain.Array.impl
Class ArrayGroupImpl

java.lang.Object
  extended by gov.nih.nci.mageom.domain.impl.MAGEOMObject
      extended by gov.nih.nci.mageom.domain.impl.ExtendableImpl
          extended by gov.nih.nci.mageom.domain.impl.DescribableImpl
              extended by gov.nih.nci.mageom.domain.impl.IdentifiableImpl
                  extended by gov.nih.nci.mageom.domain.Array.impl.ArrayGroupImpl
All Implemented Interfaces:
ArrayGroup, Describable, Extendable, Identifiable, java.io.Serializable

public class ArrayGroupImpl
extends IdentifiableImpl
implements ArrayGroup

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%
See Also:
Serialized Form

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected  Array[] arrays
          DOCUMENT ME
protected  int arraysCount
          The count of Array objects.
protected  java.lang.Float arraySpacingX
          If there exist more than one array on a slide or a chip, then the spacing between the arrays is so that scanning / feature extraction software can crop images representing 1 unique
protected  java.lang.Float arraySpacingY
          If there exist more than one array on a slide or a chip, then the spacing between the arrays is so that scanning / feature extraction software can crop images representing 1 unique
protected static java.util.Hashtable associationMethods
           
protected  java.lang.String barcode
          Identifier for the ArrayGroup.
protected  DistanceUnit distanceUnit
          DOCUMENT ME
protected  java.lang.Long distanceUnitId
          The internal ID of the associated distanceUnit object.
protected  Fiducial[] fiducials
          DOCUMENT ME
protected  int fiducialsCount
          The count of Fiducial objects.
protected  java.lang.Float length
          The length of the platform.
protected  java.lang.Integer numArrays
          This attribute defines the number of arrays on a chip or a slide.
protected  java.lang.String orientationMark
          For a human to determine where the top left side of the array is, such as a barcode or frosted side the glass, etc.
protected  java.lang.String orientationMarkPosition
          One of top, bottom, left or right.
protected  OntologyEntry substrateType
          DOCUMENT ME
protected  java.lang.Long substrateTypeId
          The internal ID of the associated substrateType object.
protected  java.lang.Float width
          The width of the platform
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
identifier, name
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
auditTrail, auditTrailCount, descriptions, descriptionsCount, security, securityId
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
ArrayGroupImpl()
          Default constructor
 
Method Summary
 Array[] getArrays()
          Returns the value of this ArrayGroup object's arrays attribute.
 int getArraysCount()
          Returns the count of all Array associated with this ArrayGroup object.
 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.
 int getFiducialsCount()
          Returns the count of all Fiducial associated with this ArrayGroup object.
 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.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 ArrayGroup[] searchArrayGroups(ArrayGroupSearchCriteria criteria)
          Returns an array of ArrayGroup objects that satisfy the given ArrayGroupSearchCriteria.
 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.
 java.lang.String toString()
          Returns a String representation of this object suitable for console display.
 org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc, java.util.ArrayList fillOutValues)
          Returns an XML representation of the object.
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
getIdentifier, getName, searchIdentifiables, setIdentifier, setName
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
getAuditTrail, getAuditTrailCount, getDescriptions, getDescriptionsCount, getSecurity, searchDescribables, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
getPropertySets, getPropertySetsCount, getSecuredElementId, searchExtendables, setPropertySets, setSecuredElementId
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.MAGEOMObject
getId, getIsEditable, setId
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
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
 

Field Detail

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

barcode

protected java.lang.String barcode
Identifier for the ArrayGroup.


arraySpacingX

protected java.lang.Float arraySpacingX
If there exist more than one array on a slide or a chip, then the spacing between the arrays is so that scanning / feature extraction software can crop images representing 1 unique


arraySpacingY

protected java.lang.Float arraySpacingY
If there exist more than one array on a slide or a chip, then the spacing between the arrays is so that scanning / feature extraction software can crop images representing 1 unique


numArrays

protected java.lang.Integer numArrays
This attribute defines the number of arrays on a chip or a slide.


orientationMark

protected java.lang.String orientationMark
For a human to determine where the top left side of the array is, such as a barcode or frosted side the glass, etc.


orientationMarkPosition

protected java.lang.String orientationMarkPosition
One of top, bottom, left or right.


width

protected java.lang.Float width
The width of the platform


length

protected java.lang.Float length
The length of the platform.


arraysCount

protected int arraysCount
The count of Array objects.


arrays

protected Array[] arrays
DOCUMENT ME


fiducialsCount

protected int fiducialsCount
The count of Fiducial objects.


fiducials

protected Fiducial[] fiducials
DOCUMENT ME


distanceUnit

protected DistanceUnit distanceUnit
DOCUMENT ME


distanceUnitId

protected java.lang.Long distanceUnitId
The internal ID of the associated distanceUnit object.


substrateType

protected OntologyEntry substrateType
DOCUMENT ME


substrateTypeId

protected java.lang.Long substrateTypeId
The internal ID of the associated substrateType object.

Constructor Detail

ArrayGroupImpl

public ArrayGroupImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchArrayGroups

public ArrayGroup[] searchArrayGroups(ArrayGroupSearchCriteria criteria)
                               throws gov.nih.nci.common.search.SearchException
Returns an array of ArrayGroup objects that satisfy the given ArrayGroupSearchCriteria.

Parameters:
criteria - The ArrayGroupSearchCriteria which represents a query for ArrayGroup objects.
Returns:
An array of ArrayGroup objects.
Throws:
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchException

setBarcode

public 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.

Specified by:
setBarcode in interface ArrayGroup
Parameters:
p_barcode - The new value for barcode.
See Also:
ArrayGroup.getBarcode()

getBarcode

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

Specified by:
getBarcode in interface ArrayGroup
Returns:
String The value of barcode.
See Also:
ArrayGroup.getBarcode()

setArraySpacingX

public 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.

Specified by:
setArraySpacingX in interface ArrayGroup
Parameters:
p_arraySpacingX - The new value for arraySpacingX.
See Also:
ArrayGroup.getArraySpacingX()

getArraySpacingX

public java.lang.Float getArraySpacingX()
Description copied from interface: ArrayGroup
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.

Specified by:
getArraySpacingX in interface ArrayGroup
Returns:
float The value of arraySpacingX.
See Also:
ArrayGroup.getArraySpacingX()

setArraySpacingY

public 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.

Specified by:
setArraySpacingY in interface ArrayGroup
Parameters:
p_arraySpacingY - The new value for arraySpacingY.
See Also:
ArrayGroup.getArraySpacingY()

getArraySpacingY

public java.lang.Float getArraySpacingY()
Description copied from interface: ArrayGroup
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.

Specified by:
getArraySpacingY in interface ArrayGroup
Returns:
float The value of arraySpacingY.
See Also:
ArrayGroup.getArraySpacingY()

setNumArrays

public 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.

Specified by:
setNumArrays in interface ArrayGroup
Parameters:
p_numArrays - The new value for numArrays.
See Also:
ArrayGroup.getNumArrays()

getNumArrays

public java.lang.Integer getNumArrays()
Description copied from interface: ArrayGroup
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.

Specified by:
getNumArrays in interface ArrayGroup
Returns:
int The value of numArrays.
See Also:
ArrayGroup.getNumArrays()

setOrientationMark

public 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.

Specified by:
setOrientationMark in interface ArrayGroup
Parameters:
p_orientationMark - The new value for orientationMark.
See Also:
ArrayGroup.getOrientationMark()

getOrientationMark

public java.lang.String getOrientationMark()
Description copied from interface: ArrayGroup
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.

Specified by:
getOrientationMark in interface ArrayGroup
Returns:
String The value of orientationMark.
See Also:
ArrayGroup.getOrientationMark()

setOrientationMarkPosition

public 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.

Specified by:
setOrientationMarkPosition in interface ArrayGroup
Parameters:
p_orientationMarkPosition - The new value for orientationMarkPosition.
See Also:
ArrayGroup.getOrientationMarkPosition()

getOrientationMarkPosition

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

Specified by:
getOrientationMarkPosition in interface ArrayGroup
Returns:
enum {top,bottom,left,right} The value of orientationMarkPosition.
See Also:
ArrayGroup.getOrientationMarkPosition()

setWidth

public 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.

Specified by:
setWidth in interface ArrayGroup
Parameters:
p_width - The new value for width.
See Also:
ArrayGroup.getWidth()

getWidth

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

Specified by:
getWidth in interface ArrayGroup
Returns:
float The value of width.
See Also:
ArrayGroup.getWidth()

setLength

public 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.

Specified by:
setLength in interface ArrayGroup
Parameters:
p_length - The new value for length.
See Also:
ArrayGroup.getLength()

getLength

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

Specified by:
getLength in interface ArrayGroup
Returns:
float The value of length.
See Also:
ArrayGroup.getLength()

setArrays

public 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.

Specified by:
setArrays in interface ArrayGroup
Parameters:
p_arrays - The new value for arrays.
See Also:
ArrayGroup.getArrays()

getArrays

public Array[] getArrays()
Description copied from interface: ArrayGroup
Returns the value of this ArrayGroup object's arrays attribute.

Specified by:
getArrays in interface ArrayGroup
Returns:
gov.nih.nci.mageom.bean.Array.Array[] The value of arrays.
See Also:
ArrayGroup.getArrays()

setFiducials

public 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.

Specified by:
setFiducials in interface ArrayGroup
Parameters:
p_fiducials - The new value for fiducials.
See Also:
ArrayGroup.getFiducials()

getFiducials

public Fiducial[] getFiducials()
Description copied from interface: ArrayGroup
Returns the value of this ArrayGroup object's fiducials attribute.

Specified by:
getFiducials in interface ArrayGroup
Returns:
gov.nih.nci.mageom.bean.Array.Fiducial[] The value of fiducials.
See Also:
ArrayGroup.getFiducials()

setDistanceUnit

public 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.

Specified by:
setDistanceUnit in interface ArrayGroup
Parameters:
p_distanceUnit - The new value for distanceUnit.
See Also:
ArrayGroup.getDistanceUnit()

getDistanceUnit

public DistanceUnit getDistanceUnit()
Description copied from interface: ArrayGroup
Returns the value of this ArrayGroup object's distanceUnit attribute.

Specified by:
getDistanceUnit in interface ArrayGroup
Returns:
gov.nih.nci.mageom.bean.Measurement.DistanceUnit The value of distanceUnit.
See Also:
ArrayGroup.getDistanceUnit()

setSubstrateType

public 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.

Specified by:
setSubstrateType in interface ArrayGroup
Parameters:
p_substrateType - The new value for substrateType.
See Also:
ArrayGroup.getSubstrateType()

getSubstrateType

public OntologyEntry getSubstrateType()
Description copied from interface: ArrayGroup
Returns the value of this ArrayGroup object's substrateType attribute.

Specified by:
getSubstrateType in interface ArrayGroup
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of substrateType.
See Also:
ArrayGroup.getSubstrateType()

getArraysCount

public int getArraysCount()
Returns the count of all Array associated with this ArrayGroup object.

Returns:
the count
See Also:
ArrayGroup.getArrays()

getFiducialsCount

public int getFiducialsCount()
Returns the count of all Fiducial associated with this ArrayGroup object.

Returns:
the count
See Also:
ArrayGroup.getFiducials()

toXML

public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
Overrides:
toXML in class IdentifiableImpl

toXMLDoc

public org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
Overrides:
toXMLDoc in class IdentifiableImpl

toXMLProcessor

public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
                                          java.util.ArrayList fillOutValues)
Returns an XML representation of the object. The document is not modified.

Overrides:
toXMLProcessor in class IdentifiableImpl
Parameters:
doc - the working document
fillOutValues - a list of attribute names that should have full XML for their values.
Returns:
org.w3c.dom.Element an XML representation

getXMLMethodDescriptors

public java.util.Hashtable getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.

Overrides:
getXMLMethodDescriptors in class IdentifiableImpl
Returns:
Hashtable The Hashtable of descriptors.

toString

public java.lang.String toString()
Returns a String representation of this object suitable for console display.

Overrides:
toString in class IdentifiableImpl
Returns:
the String representation.