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java.lang.Objectgov.nih.nci.mageom.domain.impl.MAGEOMObject
gov.nih.nci.mageom.domain.impl.ExtendableImpl
gov.nih.nci.mageom.domain.impl.DescribableImpl
gov.nih.nci.mageom.domain.impl.IdentifiableImpl
gov.nih.nci.mageom.domain.Array.impl.ArrayGroupImpl
public class ArrayGroupImpl
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.
| 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 |
|---|
protected static java.util.ArrayList allAssociationMethods
protected static java.util.Hashtable associationMethods
protected java.lang.String barcode
protected java.lang.Float arraySpacingX
protected java.lang.Float arraySpacingY
protected java.lang.Integer numArrays
protected java.lang.String orientationMark
protected java.lang.String orientationMarkPosition
protected java.lang.Float width
protected java.lang.Float length
protected int arraysCount
protected Array[] arrays
protected int fiducialsCount
protected Fiducial[] fiducials
protected DistanceUnit distanceUnit
protected java.lang.Long distanceUnitId
protected OntologyEntry substrateType
protected java.lang.Long substrateTypeId
| Constructor Detail |
|---|
public ArrayGroupImpl()
| Method Detail |
|---|
protected void init()
init in class IdentifiableImpl
public ArrayGroup[] searchArrayGroups(ArrayGroupSearchCriteria criteria)
throws gov.nih.nci.common.search.SearchException
ArrayGroup objects that
satisfy the given ArrayGroupSearchCriteria.
criteria - The ArrayGroupSearchCriteria
which represents a query for ArrayGroup objects.
ArrayGroup objects.
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchExceptionpublic void setBarcode(java.lang.String p_barcode)
ArrayGroup object.
setBarcode in interface ArrayGroupp_barcode - The new value for barcode.ArrayGroup.getBarcode()public java.lang.String getBarcode()
ArrayGroupArrayGroup object's barcode attribute.
Description of barcode:
Identifier for the ArrayGroup.
getBarcode in interface ArrayGroupString The value of barcode.ArrayGroup.getBarcode()public void setArraySpacingX(java.lang.Float p_arraySpacingX)
ArrayGroup object.
setArraySpacingX in interface ArrayGroupp_arraySpacingX - The new value for arraySpacingX.ArrayGroup.getArraySpacingX()public java.lang.Float getArraySpacingX()
ArrayGroupArrayGroup 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.
getArraySpacingX in interface ArrayGroupfloat The value of arraySpacingX.ArrayGroup.getArraySpacingX()public void setArraySpacingY(java.lang.Float p_arraySpacingY)
ArrayGroup object.
setArraySpacingY in interface ArrayGroupp_arraySpacingY - The new value for arraySpacingY.ArrayGroup.getArraySpacingY()public java.lang.Float getArraySpacingY()
ArrayGroupArrayGroup 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.
getArraySpacingY in interface ArrayGroupfloat The value of arraySpacingY.ArrayGroup.getArraySpacingY()public void setNumArrays(java.lang.Integer p_numArrays)
ArrayGroup object.
setNumArrays in interface ArrayGroupp_numArrays - The new value for numArrays.ArrayGroup.getNumArrays()public java.lang.Integer getNumArrays()
ArrayGroupArrayGroup object's numArrays attribute.
Description of numArrays:
This attribute defines the number of arrays on a chip or a slide.
getNumArrays in interface ArrayGroupint The value of numArrays.ArrayGroup.getNumArrays()public void setOrientationMark(java.lang.String p_orientationMark)
ArrayGroup object.
setOrientationMark in interface ArrayGroupp_orientationMark - The new value for orientationMark.ArrayGroup.getOrientationMark()public java.lang.String getOrientationMark()
ArrayGroupArrayGroup 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.
getOrientationMark in interface ArrayGroupString The value of orientationMark.ArrayGroup.getOrientationMark()public void setOrientationMarkPosition(java.lang.String p_orientationMarkPosition)
ArrayGroup object.
setOrientationMarkPosition in interface ArrayGroupp_orientationMarkPosition - The new value for orientationMarkPosition.ArrayGroup.getOrientationMarkPosition()public java.lang.String getOrientationMarkPosition()
ArrayGroupArrayGroup object's orientationMarkPosition attribute.
Description of orientationMarkPosition:
One of top, bottom, left or right.
getOrientationMarkPosition in interface ArrayGroupenum {top,bottom,left,right} The value of orientationMarkPosition.ArrayGroup.getOrientationMarkPosition()public void setWidth(java.lang.Float p_width)
ArrayGroup object.
setWidth in interface ArrayGroupp_width - The new value for width.ArrayGroup.getWidth()public java.lang.Float getWidth()
ArrayGroupArrayGroup object's width attribute.
Description of width:
The width of the platform
getWidth in interface ArrayGroupfloat The value of width.ArrayGroup.getWidth()public void setLength(java.lang.Float p_length)
ArrayGroup object.
setLength in interface ArrayGroupp_length - The new value for length.ArrayGroup.getLength()public java.lang.Float getLength()
ArrayGroupArrayGroup object's length attribute.
Description of length:
The length of the platform.
getLength in interface ArrayGroupfloat The value of length.ArrayGroup.getLength()public void setArrays(Array[] p_arrays)
ArrayGroup object.
setArrays in interface ArrayGroupp_arrays - The new value for arrays.ArrayGroup.getArrays()public Array[] getArrays()
ArrayGroupArrayGroup object's arrays attribute.
getArrays in interface ArrayGroupgov.nih.nci.mageom.bean.Array.Array[] The value of arrays.ArrayGroup.getArrays()public void setFiducials(Fiducial[] p_fiducials)
ArrayGroup object.
setFiducials in interface ArrayGroupp_fiducials - The new value for fiducials.ArrayGroup.getFiducials()public Fiducial[] getFiducials()
ArrayGroupArrayGroup object's fiducials attribute.
getFiducials in interface ArrayGroupgov.nih.nci.mageom.bean.Array.Fiducial[] The value of fiducials.ArrayGroup.getFiducials()public void setDistanceUnit(DistanceUnit p_distanceUnit)
ArrayGroup object.
setDistanceUnit in interface ArrayGroupp_distanceUnit - The new value for distanceUnit.ArrayGroup.getDistanceUnit()public DistanceUnit getDistanceUnit()
ArrayGroupArrayGroup object's distanceUnit attribute.
getDistanceUnit in interface ArrayGroupgov.nih.nci.mageom.bean.Measurement.DistanceUnit The value of distanceUnit.ArrayGroup.getDistanceUnit()public void setSubstrateType(OntologyEntry p_substrateType)
ArrayGroup object.
setSubstrateType in interface ArrayGroupp_substrateType - The new value for substrateType.ArrayGroup.getSubstrateType()public OntologyEntry getSubstrateType()
ArrayGroupArrayGroup object's substrateType attribute.
getSubstrateType in interface ArrayGroupgov.nih.nci.mageom.bean.Description.OntologyEntry The value of substrateType.ArrayGroup.getSubstrateType()public int getArraysCount()
Array
associated with this ArrayGroup object.
ArrayGroup.getArrays()public int getFiducialsCount()
Fiducial
associated with this ArrayGroup object.
ArrayGroup.getFiducials()public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
toXML in class IdentifiableImplpublic org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
toXMLDoc in class IdentifiableImpl
public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
java.util.ArrayList fillOutValues)
toXMLProcessor in class IdentifiableImpldoc - the working documentfillOutValues - a list of attribute names that should have
full XML for their values.
public java.util.Hashtable getXMLMethodDescriptors()
XMLMethodDescriptors descriptors of
the association methods of this object.
getXMLMethodDescriptors in class IdentifiableImplpublic java.lang.String toString()
toString in class IdentifiableImpl
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| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | |||||||||