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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.Array.Array
All Implemented Interfaces:
org.biomage.Interface.HasArrayDesign, org.biomage.Interface.HasArrayGroup, org.biomage.Interface.HasArrayManufactureDeviations, org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasInformation, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

public class Array
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasArrayDesign, org.biomage.Interface.HasArrayGroup, org.biomage.Interface.HasInformation, org.biomage.Interface.HasArrayManufactureDeviations

The physical substrate along with its features and their annotation


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasArrayManufactureDeviations
org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_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.ArrayDesign.ArrayDesign arrayDesign
          The association of a physical array with its array design.
private  ArrayGroup arrayGroup
          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)  java.lang.String arrayIdentifier
          An identifying string, e.g.
private  org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations
          Association to classes to describe deviations from the ArrayDesign.
(package private)  float arrayXOrigin
          This can indicate the x position on a slide, chip, etc.
(package private)  float arrayYOrigin
          This can indicate the y position on a slide, chip, etc.
private  ArrayManufacture information
          Association between the manufactured array and the information on that manufacture.
(package private)  java.lang.String originRelativeTo
          What the array origin is relative to, e.g.
 
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
Array()
          Default constructor.
Array(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
          Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list
 void addToArrayManufactureDeviations(int position, ArrayManufactureDeviation arrayManufactureDeviation)
          Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list
 org.biomage.ArrayDesign.ArrayDesign getArrayDesign()
          Get method for arrayDesign
 ArrayGroup getArrayGroup()
          Get method for arrayGroup
 java.lang.String getArrayIdentifier()
          Get method for arrayIdentifier
 org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list getArrayManufactureDeviations()
          Get method for arrayManufactureDeviations
 float getArrayXOrigin()
          Get method for arrayXOrigin
 float getArrayYOrigin()
          Get method for arrayYOrigin
 ArrayManufactureDeviation getFromArrayManufactureDeviations(int position)
          Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list
 ArrayManufacture getInformation()
          Get method for information
 java.lang.String getOriginRelativeTo()
          Get method for originRelativeTo
 void removeElementAtFromArrayManufactureDeviations(int position)
          Method to remove by position from ArrayManufactureDeviations_list
 void removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
          Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list
 void setArrayDesign(org.biomage.ArrayDesign.ArrayDesign arrayDesign)
          Set method for arrayDesign
 void setArrayGroup(ArrayGroup arrayGroup)
          Set method for arrayGroup
 void setArrayIdentifier(java.lang.String arrayIdentifier)
          Set method for arrayIdentifier
 void setArrayManufactureDeviations(org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)
          Set method for arrayManufactureDeviations
 void setArrayXOrigin(float arrayXOrigin)
          Set method for arrayXOrigin
 void setArrayYOrigin(float arrayYOrigin)
          Set method for arrayYOrigin
 void setInformation(ArrayManufacture information)
          Set method for information
 void setOriginRelativeTo(java.lang.String originRelativeTo)
          Set method for originRelativeTo
 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

arrayIdentifier

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


arrayXOrigin

float arrayXOrigin
This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.


arrayYOrigin

float arrayYOrigin
This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.


originRelativeTo

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


arrayDesign

private org.biomage.ArrayDesign.ArrayDesign arrayDesign
The association of a physical array with its array design.


arrayGroup

private ArrayGroup arrayGroup
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.


information

private ArrayManufacture information
Association between the manufactured array and the information on that manufacture.


arrayManufactureDeviations

private org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations
Association to classes to describe deviations from the ArrayDesign.

Constructor Detail

Array

public Array()
Default constructor.


Array

public Array(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.


setArrayIdentifier

public void setArrayIdentifier(java.lang.String arrayIdentifier)
Set method for arrayIdentifier


getArrayIdentifier

public java.lang.String getArrayIdentifier()
Get method for arrayIdentifier


setArrayXOrigin

public void setArrayXOrigin(float arrayXOrigin)
Set method for arrayXOrigin


getArrayXOrigin

public float getArrayXOrigin()
Get method for arrayXOrigin


setArrayYOrigin

public void setArrayYOrigin(float arrayYOrigin)
Set method for arrayYOrigin


getArrayYOrigin

public float getArrayYOrigin()
Get method for arrayYOrigin


setOriginRelativeTo

public void setOriginRelativeTo(java.lang.String originRelativeTo)
Set method for originRelativeTo


getOriginRelativeTo

public java.lang.String getOriginRelativeTo()
Get method for originRelativeTo


setArrayDesign

public void setArrayDesign(org.biomage.ArrayDesign.ArrayDesign arrayDesign)
Set method for arrayDesign

Specified by:
setArrayDesign in interface org.biomage.Interface.HasArrayDesign

getArrayDesign

public org.biomage.ArrayDesign.ArrayDesign getArrayDesign()
Get method for arrayDesign

Specified by:
getArrayDesign in interface org.biomage.Interface.HasArrayDesign

setArrayGroup

public void setArrayGroup(ArrayGroup arrayGroup)
Set method for arrayGroup

Specified by:
setArrayGroup in interface org.biomage.Interface.HasArrayGroup

getArrayGroup

public ArrayGroup getArrayGroup()
Get method for arrayGroup

Specified by:
getArrayGroup in interface org.biomage.Interface.HasArrayGroup

setInformation

public void setInformation(ArrayManufacture information)
Set method for information

Specified by:
setInformation in interface org.biomage.Interface.HasInformation

getInformation

public ArrayManufacture getInformation()
Get method for information

Specified by:
getInformation in interface org.biomage.Interface.HasInformation

setArrayManufactureDeviations

public void setArrayManufactureDeviations(org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)
Set method for arrayManufactureDeviations

Specified by:
setArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

getArrayManufactureDeviations

public org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list getArrayManufactureDeviations()
Get method for arrayManufactureDeviations

Specified by:
getArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

addToArrayManufactureDeviations

public void addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list

Specified by:
addToArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

addToArrayManufactureDeviations

public void addToArrayManufactureDeviations(int position,
                                            ArrayManufactureDeviation arrayManufactureDeviation)
Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list

Specified by:
addToArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

getFromArrayManufactureDeviations

public ArrayManufactureDeviation getFromArrayManufactureDeviations(int position)
Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list

Specified by:
getFromArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

removeElementAtFromArrayManufactureDeviations

public void removeElementAtFromArrayManufactureDeviations(int position)
Method to remove by position from ArrayManufactureDeviations_list

Specified by:
removeElementAtFromArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

removeFromArrayManufactureDeviations

public void removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list

Specified by:
removeFromArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations