org.biomage.Array
Class ArrayGroup

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.Array.ArrayGroup
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasArrays, HasAuditTrail, HasDescriptions, HasDistanceUnit, HasFiducials, HasPropertySets, HasSecurity, HasSubstrateType

public class ArrayGroup
extends Identifiable
implements java.io.Serializable, HasArrays, HasFiducials, HasDistanceUnit, HasSubstrateType

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.

See Also:
Serialized Form

Nested Class Summary
 class ArrayGroup.OrientationMarkPosition
          Inner class for the enumeration values that the attribute orientationMarkPosition can assume.
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasArrays
HasArrays.Arrays_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFiducials
HasFiducials.Fiducials_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List arrays
          Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.
protected  DistanceUnit distanceUnit
          The unit of the measurement attributes.
protected  java.util.List fiducials
          Association to the marks on the Array for alignment for the scanner.
protected  OntologyEntry substrateType
          Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ArrayGroup()
          Default constructor.
ArrayGroup(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArrays(Array array)
          Method to add Array to Arrays_list
 void addToArrays(int position, Array array)
          Method to add Array at position to Arrays_list
 void addToFiducials(Fiducial fiducial)
          Method to add Fiducial to Fiducials_list
 void addToFiducials(int position, Fiducial fiducial)
          Method to add Fiducial at position to Fiducials_list
 boolean emptyMAGEobject()
           
 HasArrays.Arrays_list getArrays()
          Get method for arrays
 java.lang.Float getArraySpacingX()
          Get method for arraySpacingX
 java.lang.Float getArraySpacingY()
          Get method for arraySpacingY
 java.lang.String getBarcode()
          Get method for barcode
 DistanceUnit getDistanceUnit()
          Get method for distanceUnit
 HasFiducials.Fiducials_list getFiducials()
          Get method for fiducials
 Array getFromArrays(int position)
          Method to get Array from Arrays_list
 Fiducial getFromFiducials(int position)
          Method to get Fiducial from Fiducials_list
 java.lang.Float getLength()
          Get method for length
 java.lang.String getModelClassName()
           
 java.lang.String getNameByValueOrientationMarkPosition(int val)
          For OrientationMarkPosition get the Name of the Enumeration type by passing a Value to it.
 java.lang.String getNameOrientationMarkPosition()
          Return the current name of the Enumeration type of OrientationMarkPosition.
 java.lang.Integer getNumArrays()
          Get method for numArrays
 java.lang.String getOrientationMark()
          Get method for orientationMark
 ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()
          Get method for orientationMarkPosition
 OntologyEntry getSubstrateType()
          Get method for substrateType
 int getValueByNameOrientationMarkPosition(java.lang.String name)
          For OrientationMarkPosition get the Value of the Enumeration type by passing a Name to it.
 int getValueOrientationMarkPosition()
          Return the currrent value of the Enumeration type of OrientationMarkPosition.
 java.lang.Float getWidth()
          Get method for width
 void removeElementAtFromArrays(int position)
          Method to remove by position from Arrays_list
 void removeElementAtFromFiducials(int position)
          Method to remove by position from Fiducials_list
 void removeFromArrays(Array array)
          Method to remove first Array from Arrays_list
 void removeFromFiducials(Fiducial fiducial)
          Method to remove first Fiducial from Fiducials_list
 void setArrays(HasArrays.Arrays_list arrays)
          Set method for arrays
 void setArraySpacingX(java.lang.Float arraySpacingX)
          Set method for arraySpacingX
 void setArraySpacingY(java.lang.Float arraySpacingY)
          Set method for arraySpacingY
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBarcode(java.lang.String barcode)
          Set method for barcode
 void setDistanceUnit(DistanceUnit distanceUnit)
          Set method for distanceUnit
 void setFiducials(HasFiducials.Fiducials_list fiducials)
          Set method for fiducials
 void setLength(java.lang.Float length)
          Set method for length
 java.lang.String setNameByValueOrientationMarkPosition(int val)
          For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int)
 void setNameOrientationMarkPosition(java.lang.String name)
          Return the current name of the Enumeration type of OrientationMarkPosition.
 void setNumArrays(java.lang.Integer numArrays)
          Set method for numArrays
 void setOrientationMark(java.lang.String orientationMark)
          Set method for orientationMark
 void setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition)
          Set method for orientationMarkPosition
 void setSubstrateType(OntologyEntry substrateType)
          Set method for substrateType
 int setValueByNameOrientationMarkPosition(java.lang.String name)
          For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it.
 void setWidth(java.lang.Float width)
          Set method for width
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

fiducials

protected java.util.List fiducials
Association to the marks on the Array for alignment for the scanner.


arrays

protected java.util.List arrays
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.


substrateType

protected OntologyEntry substrateType
Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.


distanceUnit

protected DistanceUnit distanceUnit
The unit of the measurement attributes.

Constructor Detail

ArrayGroup

public ArrayGroup()
Default constructor.


ArrayGroup

public ArrayGroup(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:
writeMAGEML in class Identifiable
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:
writeAttributes in class Identifiable
Throws:
java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:
writeAssociations in class Identifiable
Throws:
java.io.IOException

setBarcode

public void setBarcode(java.lang.String barcode)
Set method for barcode

Parameters:
value - to set

getBarcode

public java.lang.String getBarcode()
Get method for barcode

Returns:
value of the attribute

setArraySpacingX

public void setArraySpacingX(java.lang.Float arraySpacingX)
Set method for arraySpacingX

Parameters:
value - to set

getArraySpacingX

public java.lang.Float getArraySpacingX()
Get method for arraySpacingX

Returns:
value of the attribute

setArraySpacingY

public void setArraySpacingY(java.lang.Float arraySpacingY)
Set method for arraySpacingY

Parameters:
value - to set

getArraySpacingY

public java.lang.Float getArraySpacingY()
Get method for arraySpacingY

Returns:
value of the attribute

setNumArrays

public void setNumArrays(java.lang.Integer numArrays)
Set method for numArrays

Parameters:
value - to set

getNumArrays

public java.lang.Integer getNumArrays()
Get method for numArrays

Returns:
value of the attribute

setOrientationMark

public void setOrientationMark(java.lang.String orientationMark)
Set method for orientationMark

Parameters:
value - to set

getOrientationMark

public java.lang.String getOrientationMark()
Get method for orientationMark

Returns:
value of the attribute

setOrientationMarkPosition

public void setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition)
Set method for orientationMarkPosition

Parameters:
value - to set

getOrientationMarkPosition

public ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()
Get method for orientationMarkPosition

Returns:
value of the attribute

setNameByValueOrientationMarkPosition

public java.lang.String setNameByValueOrientationMarkPosition(int val)
For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int)

Parameters:
int - value The value to be mapped to the name

setValueByNameOrientationMarkPosition

public int setValueByNameOrientationMarkPosition(java.lang.String name)
For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it.

Parameters:
String - name The name to be mapped to a value

getNameByValueOrientationMarkPosition

public java.lang.String getNameByValueOrientationMarkPosition(int val)
For OrientationMarkPosition get the Name of the Enumeration type by passing a Value to it.

Parameters:
int - val The value for which the Mapped String will be returned.

getValueByNameOrientationMarkPosition

public int getValueByNameOrientationMarkPosition(java.lang.String name)
For OrientationMarkPosition get the Value of the Enumeration type by passing a Name to it.

Parameters:
String - name The name to be mapped to a value.

getNameOrientationMarkPosition

public java.lang.String getNameOrientationMarkPosition()
Return the current name of the Enumeration type of OrientationMarkPosition.


setNameOrientationMarkPosition

public void setNameOrientationMarkPosition(java.lang.String name)
Return the current name of the Enumeration type of OrientationMarkPosition.


getValueOrientationMarkPosition

public int getValueOrientationMarkPosition()
Return the currrent value of the Enumeration type of OrientationMarkPosition.


setWidth

public void setWidth(java.lang.Float width)
Set method for width

Parameters:
value - to set

getWidth

public java.lang.Float getWidth()
Get method for width

Returns:
value of the attribute

setLength

public void setLength(java.lang.Float length)
Set method for length

Parameters:
value - to set

getLength

public java.lang.Float getLength()
Get method for length

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setFiducials

public void setFiducials(HasFiducials.Fiducials_list fiducials)
Set method for fiducials

Specified by:
setFiducials in interface HasFiducials
Parameters:
value - to set

getFiducials

public HasFiducials.Fiducials_list getFiducials()
Get method for fiducials

Specified by:
getFiducials in interface HasFiducials
Returns:
value of the attribute

addToFiducials

public void addToFiducials(Fiducial fiducial)
Method to add Fiducial to Fiducials_list

Specified by:
addToFiducials in interface HasFiducials

addToFiducials

public void addToFiducials(int position,
                           Fiducial fiducial)
Method to add Fiducial at position to Fiducials_list

Specified by:
addToFiducials in interface HasFiducials

getFromFiducials

public Fiducial getFromFiducials(int position)
Method to get Fiducial from Fiducials_list

Specified by:
getFromFiducials in interface HasFiducials

removeElementAtFromFiducials

public void removeElementAtFromFiducials(int position)
Method to remove by position from Fiducials_list

Specified by:
removeElementAtFromFiducials in interface HasFiducials

removeFromFiducials

public void removeFromFiducials(Fiducial fiducial)
Method to remove first Fiducial from Fiducials_list

Specified by:
removeFromFiducials in interface HasFiducials

setArrays

public void setArrays(HasArrays.Arrays_list arrays)
Set method for arrays

Specified by:
setArrays in interface HasArrays
Parameters:
value - to set

getArrays

public HasArrays.Arrays_list getArrays()
Get method for arrays

Specified by:
getArrays in interface HasArrays
Returns:
value of the attribute

addToArrays

public void addToArrays(Array array)
Method to add Array to Arrays_list

Specified by:
addToArrays in interface HasArrays

addToArrays

public void addToArrays(int position,
                        Array array)
Method to add Array at position to Arrays_list

Specified by:
addToArrays in interface HasArrays

getFromArrays

public Array getFromArrays(int position)
Method to get Array from Arrays_list

Specified by:
getFromArrays in interface HasArrays

removeElementAtFromArrays

public void removeElementAtFromArrays(int position)
Method to remove by position from Arrays_list

Specified by:
removeElementAtFromArrays in interface HasArrays

removeFromArrays

public void removeFromArrays(Array array)
Method to remove first Array from Arrays_list

Specified by:
removeFromArrays in interface HasArrays

setSubstrateType

public void setSubstrateType(OntologyEntry substrateType)
Set method for substrateType

Specified by:
setSubstrateType in interface HasSubstrateType
Parameters:
value - to set

getSubstrateType

public OntologyEntry getSubstrateType()
Get method for substrateType

Specified by:
getSubstrateType in interface HasSubstrateType
Returns:
value of the attribute

setDistanceUnit

public void setDistanceUnit(DistanceUnit distanceUnit)
Set method for distanceUnit

Specified by:
setDistanceUnit in interface HasDistanceUnit
Parameters:
value - to set

getDistanceUnit

public DistanceUnit getDistanceUnit()
Get method for distanceUnit

Specified by:
getDistanceUnit in interface HasDistanceUnit
Returns:
value of the attribute