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org.biomage.Array
Class ArrayGroup  view ArrayGroup download ArrayGroup.java

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

public class ArrayGroup
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasArrays, org.biomage.Interface.HasFiducials, org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.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.


Nested Class Summary
 class ArrayGroup.OrientationMarkPosition
          Inner class for the enumeration values that the attribute orientationMarkPosition can assume.
 
Nested classes inherited from class org.biomage.Interface.HasArrays
org.biomage.Interface.HasArrays.Arrays_list
 
Nested classes inherited from class org.biomage.Interface.HasFiducials
org.biomage.Interface.HasFiducials.Fiducials_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasArrays.Arrays_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.
(package private)  float 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.
(package private)  float 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.
(package private)  java.lang.String barcode
          Identifier for the ArrayGroup.
private  org.biomage.Measurement.DistanceUnit distanceUnit
          The unit of the measurement attributes.
private  org.biomage.Interface.HasFiducials.Fiducials_list fiducials
          Association to the marks on the Array for alignment for the scanner.
(package private)  float length
          The length of the platform.
(package private)  int numArrays
          This attribute defines the number of arrays on a chip or a slide.
(package private)  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 of the glass, etc.
(package private)  ArrayGroup.OrientationMarkPosition orientationMarkPosition
          One of top, bottom, left or right.
private  org.biomage.Description.OntologyEntry substrateType
          Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.
(package private)  float width
          The width of the platform
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
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
 org.biomage.Interface.HasArrays.Arrays_list getArrays()
          Get method for arrays
 float getArraySpacingX()
          Get method for arraySpacingX
 float getArraySpacingY()
          Get method for arraySpacingY
 java.lang.String getBarcode()
          Get method for barcode
 org.biomage.Measurement.DistanceUnit getDistanceUnit()
          Get method for distanceUnit
 org.biomage.Interface.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
 float getLength()
          Get method for length
 int getNumArrays()
          Get method for numArrays
 java.lang.String getOrientationMark()
          Get method for orientationMark
 ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()
          Get method for orientationMarkPosition
 org.biomage.Description.OntologyEntry getSubstrateType()
          Get method for substrateType
 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(org.biomage.Interface.HasArrays.Arrays_list arrays)
          Set method for arrays
 void setArraySpacingX(float arraySpacingX)
          Set method for arraySpacingX
 void setArraySpacingY(float arraySpacingY)
          Set method for arraySpacingY
 void setBarcode(java.lang.String barcode)
          Set method for barcode
 void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)
          Set method for distanceUnit
 void setFiducials(org.biomage.Interface.HasFiducials.Fiducials_list fiducials)
          Set method for fiducials
 void setLength(float length)
          Set method for length
 void setNumArrays(int 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(org.biomage.Description.OntologyEntry substrateType)
          Set method for substrateType
 void setWidth(float width)
          Set method for width
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

barcode

java.lang.String barcode
Identifier for the ArrayGroup.


arraySpacingX

float 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.


arraySpacingY

float 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.


numArrays

int numArrays
This attribute defines the number of arrays on a chip or a slide.


orientationMark

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 of the glass, etc.


orientationMarkPosition

ArrayGroup.OrientationMarkPosition orientationMarkPosition
One of top, bottom, left or right.


width

float width
The width of the platform


length

float length
The length of the platform.


arrays

private org.biomage.Interface.HasArrays.Arrays_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.


fiducials

private org.biomage.Interface.HasFiducials.Fiducials_list fiducials
Association to the marks on the Array for alignment for the scanner.


distanceUnit

private org.biomage.Measurement.DistanceUnit distanceUnit
The unit of the measurement attributes.


substrateType

private org.biomage.Description.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.

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

Method Detail

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.


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.


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.


setBarcode

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


getBarcode

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


setArraySpacingX

public void setArraySpacingX(float arraySpacingX)
Set method for arraySpacingX


getArraySpacingX

public float getArraySpacingX()
Get method for arraySpacingX


setArraySpacingY

public void setArraySpacingY(float arraySpacingY)
Set method for arraySpacingY


getArraySpacingY

public float getArraySpacingY()
Get method for arraySpacingY


setNumArrays

public void setNumArrays(int numArrays)
Set method for numArrays


getNumArrays

public int getNumArrays()
Get method for numArrays


setOrientationMark

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


getOrientationMark

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


setOrientationMarkPosition

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


getOrientationMarkPosition

public ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()
Get method for orientationMarkPosition


setWidth

public void setWidth(float width)
Set method for width


getWidth

public float getWidth()
Get method for width


setLength

public void setLength(float length)
Set method for length


getLength

public float getLength()
Get method for length


setArrays

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

Specified by:
setArrays in interface org.biomage.Interface.HasArrays

getArrays

public org.biomage.Interface.HasArrays.Arrays_list getArrays()
Get method for arrays

Specified by:
getArrays in interface org.biomage.Interface.HasArrays

addToArrays

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

Specified by:
addToArrays in interface org.biomage.Interface.HasArrays

addToArrays

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

Specified by:
addToArrays in interface org.biomage.Interface.HasArrays

getFromArrays

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

Specified by:
getFromArrays in interface org.biomage.Interface.HasArrays

removeElementAtFromArrays

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

Specified by:
removeElementAtFromArrays in interface org.biomage.Interface.HasArrays

removeFromArrays

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

Specified by:
removeFromArrays in interface org.biomage.Interface.HasArrays

setFiducials

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

Specified by:
setFiducials in interface org.biomage.Interface.HasFiducials

getFiducials

public org.biomage.Interface.HasFiducials.Fiducials_list getFiducials()
Get method for fiducials

Specified by:
getFiducials in interface org.biomage.Interface.HasFiducials

addToFiducials

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

Specified by:
addToFiducials in interface org.biomage.Interface.HasFiducials

addToFiducials

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

Specified by:
addToFiducials in interface org.biomage.Interface.HasFiducials

getFromFiducials

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

Specified by:
getFromFiducials in interface org.biomage.Interface.HasFiducials

removeElementAtFromFiducials

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

Specified by:
removeElementAtFromFiducials in interface org.biomage.Interface.HasFiducials

removeFromFiducials

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

Specified by:
removeFromFiducials in interface org.biomage.Interface.HasFiducials

setDistanceUnit

public void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)
Set method for distanceUnit

Specified by:
setDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

getDistanceUnit

public org.biomage.Measurement.DistanceUnit getDistanceUnit()
Get method for distanceUnit

Specified by:
getDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

setSubstrateType

public void setSubstrateType(org.biomage.Description.OntologyEntry substrateType)
Set method for substrateType

Specified by:
setSubstrateType in interface org.biomage.Interface.HasSubstrateType

getSubstrateType

public org.biomage.Description.OntologyEntry getSubstrateType()
Get method for substrateType

Specified by:
getSubstrateType in interface org.biomage.Interface.HasSubstrateType