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

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.ArrayImpl
All Implemented Interfaces:
Array, Describable, Extendable, Identifiable, java.io.Serializable

public class ArrayImpl
extends IdentifiableImpl
implements Array

The physical substrate along with its features and their annotation

Version:
%I%, %G%
See Also:
Serialized Form

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected  ArrayDesign arrayDesign
          DOCUMENT ME
protected  java.lang.Long arrayDesignId
          The internal ID of the associated arrayDesign object.
protected  ArrayGroup arrayGroup
          DOCUMENT ME
protected  java.lang.Long arrayGroupId
          The internal ID of the associated arrayGroup object.
protected  java.lang.String arrayIdentifier
          An identifying string, e.g.
protected  ArrayManufactureDeviation[] arrayManufactureDeviations
          DOCUMENT ME
protected  int arrayManufactureDeviationsCount
          The count of ArrayManufactureDeviation objects.
protected  java.lang.Float arrayXOrigin
          This can indicate the x position on a slide, chip, etc.
protected  java.lang.Float arrayYOrigin
          This can indicate the y position on a slide, chip, etc.
protected static java.util.Hashtable associationMethods
           
protected  ArrayManufacture information
          DOCUMENT ME
protected  java.lang.Long informationId
          The internal ID of the associated information object.
protected  java.lang.String originRelativeTo
          What the array origin is relative to, e.g.
 
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
ArrayImpl()
          Default constructor
 
Method Summary
 ArrayDesign getArrayDesign()
          Returns the value of this Array object's arrayDesign attribute.
 ArrayGroup getArrayGroup()
          Returns the value of this Array object's arrayGroup attribute.
 java.lang.String getArrayIdentifier()
          Returns the value of this Array object's arrayIdentifier attribute.
 ArrayManufactureDeviation[] getArrayManufactureDeviations()
          Returns the value of this Array object's arrayManufactureDeviations attribute.
 int getArrayManufactureDeviationsCount()
          Returns the count of all ArrayManufactureDeviation associated with this Array object.
 java.lang.Float getArrayXOrigin()
          Returns the value of this Array object's arrayXOrigin attribute.
 java.lang.Float getArrayYOrigin()
          Returns the value of this Array object's arrayYOrigin attribute.
 ArrayManufacture getInformation()
          Returns the value of this Array object's information attribute.
 java.lang.String getOriginRelativeTo()
          Returns the value of this Array object's originRelativeTo attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 Array[] searchArrays(ArraySearchCriteria criteria)
          Returns an array of Array objects that satisfy the given ArraySearchCriteria.
 void setArrayDesign(ArrayDesign p_arrayDesign)
          Sets the arrayDesign attribute.
 void setArrayGroup(ArrayGroup p_arrayGroup)
          Sets the arrayGroup attribute.
 void setArrayIdentifier(java.lang.String p_arrayIdentifier)
          Sets the arrayIdentifier attribute.
 void setArrayManufactureDeviations(ArrayManufactureDeviation[] p_arrayManufactureDeviations)
          Sets the arrayManufactureDeviations attribute.
 void setArrayXOrigin(java.lang.Float p_arrayXOrigin)
          Sets the arrayXOrigin attribute.
 void setArrayYOrigin(java.lang.Float p_arrayYOrigin)
          Sets the arrayYOrigin attribute.
 void setInformation(ArrayManufacture p_information)
          Sets the information attribute.
 void setOriginRelativeTo(java.lang.String p_originRelativeTo)
          Sets the originRelativeTo 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

arrayIdentifier

protected java.lang.String arrayIdentifier
An identifying string, e.g. a barcode.


arrayXOrigin

protected java.lang.Float arrayXOrigin
This can indicate the x position on a slide, chip, etc. of the first Feature and is usually relative to the fiducial.


arrayYOrigin

protected java.lang.Float arrayYOrigin
This can indicate the y position on a slide, chip, etc. of the first Feature and is usually relative to the fiducial.


originRelativeTo

protected java.lang.String originRelativeTo
What the array origin is relative to, e.g. upper left corner, fiducial, etc.


arrayDesign

protected ArrayDesign arrayDesign
DOCUMENT ME


arrayDesignId

protected java.lang.Long arrayDesignId
The internal ID of the associated arrayDesign object.


arrayGroup

protected ArrayGroup arrayGroup
DOCUMENT ME


arrayGroupId

protected java.lang.Long arrayGroupId
The internal ID of the associated arrayGroup object.


information

protected ArrayManufacture information
DOCUMENT ME


informationId

protected java.lang.Long informationId
The internal ID of the associated information object.


arrayManufactureDeviationsCount

protected int arrayManufactureDeviationsCount
The count of ArrayManufactureDeviation objects.


arrayManufactureDeviations

protected ArrayManufactureDeviation[] arrayManufactureDeviations
DOCUMENT ME

Constructor Detail

ArrayImpl

public ArrayImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchArrays

public Array[] searchArrays(ArraySearchCriteria criteria)
                     throws gov.nih.nci.common.search.SearchException
Returns an array of Array objects that satisfy the given ArraySearchCriteria.

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

setArrayIdentifier

public void setArrayIdentifier(java.lang.String p_arrayIdentifier)
Sets the arrayIdentifier attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setArrayIdentifier in interface Array
Parameters:
p_arrayIdentifier - The new value for arrayIdentifier.
See Also:
Array.getArrayIdentifier()

getArrayIdentifier

public java.lang.String getArrayIdentifier()
Description copied from interface: Array
Returns the value of this Array object's arrayIdentifier attribute. Description of arrayIdentifier: An identifying string, e.g. a barcode.

Specified by:
getArrayIdentifier in interface Array
Returns:
String The value of arrayIdentifier.
See Also:
Array.getArrayIdentifier()

setArrayXOrigin

public void setArrayXOrigin(java.lang.Float p_arrayXOrigin)
Sets the arrayXOrigin attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setArrayXOrigin in interface Array
Parameters:
p_arrayXOrigin - The new value for arrayXOrigin.
See Also:
Array.getArrayXOrigin()

getArrayXOrigin

public java.lang.Float getArrayXOrigin()
Description copied from interface: Array
Returns the value of this Array object's arrayXOrigin attribute. Description of arrayXOrigin: This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

Specified by:
getArrayXOrigin in interface Array
Returns:
float The value of arrayXOrigin.
See Also:
Array.getArrayXOrigin()

setArrayYOrigin

public void setArrayYOrigin(java.lang.Float p_arrayYOrigin)
Sets the arrayYOrigin attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setArrayYOrigin in interface Array
Parameters:
p_arrayYOrigin - The new value for arrayYOrigin.
See Also:
Array.getArrayYOrigin()

getArrayYOrigin

public java.lang.Float getArrayYOrigin()
Description copied from interface: Array
Returns the value of this Array object's arrayYOrigin attribute. Description of arrayYOrigin: This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

Specified by:
getArrayYOrigin in interface Array
Returns:
float The value of arrayYOrigin.
See Also:
Array.getArrayYOrigin()

setOriginRelativeTo

public void setOriginRelativeTo(java.lang.String p_originRelativeTo)
Sets the originRelativeTo attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setOriginRelativeTo in interface Array
Parameters:
p_originRelativeTo - The new value for originRelativeTo.
See Also:
Array.getOriginRelativeTo()

getOriginRelativeTo

public java.lang.String getOriginRelativeTo()
Description copied from interface: Array
Returns the value of this Array object's originRelativeTo attribute. Description of originRelativeTo: What the array origin is relative to, e.g. upper left corner, fiducial, etc.

Specified by:
getOriginRelativeTo in interface Array
Returns:
String The value of originRelativeTo.
See Also:
Array.getOriginRelativeTo()

setArrayDesign

public void setArrayDesign(ArrayDesign p_arrayDesign)
Sets the arrayDesign attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setArrayDesign in interface Array
Parameters:
p_arrayDesign - The new value for arrayDesign.
See Also:
Array.getArrayDesign()

getArrayDesign

public ArrayDesign getArrayDesign()
Description copied from interface: Array
Returns the value of this Array object's arrayDesign attribute.

Specified by:
getArrayDesign in interface Array
Returns:
gov.nih.nci.mageom.bean.ArrayDesign.ArrayDesign The value of arrayDesign.
See Also:
Array.getArrayDesign()

setArrayGroup

public void setArrayGroup(ArrayGroup p_arrayGroup)
Sets the arrayGroup attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setArrayGroup in interface Array
Parameters:
p_arrayGroup - The new value for arrayGroup.
See Also:
Array.getArrayGroup()

getArrayGroup

public ArrayGroup getArrayGroup()
Description copied from interface: Array
Returns the value of this Array object's arrayGroup attribute.

Specified by:
getArrayGroup in interface Array
Returns:
gov.nih.nci.mageom.bean.Array.ArrayGroup The value of arrayGroup.
See Also:
Array.getArrayGroup()

setInformation

public void setInformation(ArrayManufacture p_information)
Sets the information attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setInformation in interface Array
Parameters:
p_information - The new value for information.
See Also:
Array.getInformation()

getInformation

public ArrayManufacture getInformation()
Description copied from interface: Array
Returns the value of this Array object's information attribute.

Specified by:
getInformation in interface Array
Returns:
gov.nih.nci.mageom.bean.Array.ArrayManufacture The value of information.
See Also:
Array.getInformation()

setArrayManufactureDeviations

public void setArrayManufactureDeviations(ArrayManufactureDeviation[] p_arrayManufactureDeviations)
Sets the arrayManufactureDeviations attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Array object.

Specified by:
setArrayManufactureDeviations in interface Array
Parameters:
p_arrayManufactureDeviations - The new value for arrayManufactureDeviations.
See Also:
Array.getArrayManufactureDeviations()

getArrayManufactureDeviations

public ArrayManufactureDeviation[] getArrayManufactureDeviations()
Description copied from interface: Array
Returns the value of this Array object's arrayManufactureDeviations attribute.

Specified by:
getArrayManufactureDeviations in interface Array
Returns:
gov.nih.nci.mageom.bean.Array.ArrayManufactureDeviation[] The value of arrayManufactureDeviations.
See Also:
Array.getArrayManufactureDeviations()

getArrayManufactureDeviationsCount

public int getArrayManufactureDeviationsCount()
Returns the count of all ArrayManufactureDeviation associated with this Array object.

Returns:
the count
See Also:
Array.getArrayManufactureDeviations()

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.