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

java.lang.Object
  extended byorg.biomage.Array.Array_package
All Implemented Interfaces:
java.io.Serializable

public class Array_package
extends java.lang.Object
implements java.io.Serializable

Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters.


Nested Class Summary
 class Array_package.Array_list
          Inner list class for holding multiple entries for attribute array_list.
 class Array_package.ArrayGroup_list
          Inner list class for holding multiple entries for attribute arrayGroup_list.
 class Array_package.ArrayManufacture_list
          Inner list class for holding multiple entries for attribute arrayManufacture_list.
 
Field Summary
 Array_package.Array_list array_list
          The physical substrate along with its features and their annotation
 Array_package.ArrayGroup_list arrayGroup_list
          An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
 Array_package.ArrayManufacture_list arrayManufacture_list
          Describes the process by which arrays are produced.
 
Constructor Summary
Array_package()
          Default constructor.
Array_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArray_list(Array array)
          Method to add Array to Array_list
 void addToArray_list(int position, Array array)
          Method to add Array at position to Array_list
 void addToArrayGroup_list(ArrayGroup arrayGroup)
          Method to add ArrayGroup to ArrayGroup_list
 void addToArrayGroup_list(int position, ArrayGroup arrayGroup)
          Method to add ArrayGroup at position to ArrayGroup_list
 void addToArrayManufacture_list(ArrayManufacture arrayManufacture)
          Method to add ArrayManufacture to ArrayManufacture_list
 void addToArrayManufacture_list(int position, ArrayManufacture arrayManufacture)
          Method to add ArrayManufacture at position to ArrayManufacture_list
 Array_package.Array_list getArray_list()
          Get method for array_list
 Array_package.ArrayGroup_list getArrayGroup_list()
          Get method for arrayGroup_list
 Array_package.ArrayManufacture_list getArrayManufacture_list()
          Get method for arrayManufacture_list
 Array getFromArray_list(int position)
          Method to get Array from Array_list
 ArrayGroup getFromArrayGroup_list(int position)
          Method to get ArrayGroup from ArrayGroup_list
 ArrayManufacture getFromArrayManufacture_list(int position)
          Method to get ArrayManufacture from ArrayManufacture_list
 void removeElementAtFromArray_list(int position)
          Method to remove by position from Array_list
 void removeElementAtFromArrayGroup_list(int position)
          Method to remove by position from ArrayGroup_list
 void removeElementAtFromArrayManufacture_list(int position)
          Method to remove by position from ArrayManufacture_list
 void removeFromArray_list(Array array)
          Method to remove first Array from Array_list
 void removeFromArrayGroup_list(ArrayGroup arrayGroup)
          Method to remove first ArrayGroup from ArrayGroup_list
 void removeFromArrayManufacture_list(ArrayManufacture arrayManufacture)
          Method to remove first ArrayManufacture from ArrayManufacture_list
 void setArray_list(Array_package.Array_list array_list)
          Set method for array_list
 void setArrayGroup_list(Array_package.ArrayGroup_list arrayGroup_list)
          Set method for arrayGroup_list
 void setArrayManufacture_list(Array_package.ArrayManufacture_list arrayManufacture_list)
          Set method for arrayManufacture_list
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

array_list

public Array_package.Array_list array_list
The physical substrate along with its features and their annotation


arrayGroup_list

public Array_package.ArrayGroup_list arrayGroup_list
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.


arrayManufacture_list

public Array_package.ArrayManufacture_list arrayManufacture_list
Describes the process by which arrays are produced.

Constructor Detail

Array_package

public Array_package()
Default constructor.


Array_package

public Array_package(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.


setArray_list

public void setArray_list(Array_package.Array_list array_list)
Set method for array_list


getArray_list

public Array_package.Array_list getArray_list()
Get method for array_list


addToArray_list

public void addToArray_list(Array array)
Method to add Array to Array_list


addToArray_list

public void addToArray_list(int position,
                            Array array)
Method to add Array at position to Array_list


getFromArray_list

public Array getFromArray_list(int position)
Method to get Array from Array_list


removeElementAtFromArray_list

public void removeElementAtFromArray_list(int position)
Method to remove by position from Array_list


removeFromArray_list

public void removeFromArray_list(Array array)
Method to remove first Array from Array_list


setArrayGroup_list

public void setArrayGroup_list(Array_package.ArrayGroup_list arrayGroup_list)
Set method for arrayGroup_list


getArrayGroup_list

public Array_package.ArrayGroup_list getArrayGroup_list()
Get method for arrayGroup_list


addToArrayGroup_list

public void addToArrayGroup_list(ArrayGroup arrayGroup)
Method to add ArrayGroup to ArrayGroup_list


addToArrayGroup_list

public void addToArrayGroup_list(int position,
                                 ArrayGroup arrayGroup)
Method to add ArrayGroup at position to ArrayGroup_list


getFromArrayGroup_list

public ArrayGroup getFromArrayGroup_list(int position)
Method to get ArrayGroup from ArrayGroup_list


removeElementAtFromArrayGroup_list

public void removeElementAtFromArrayGroup_list(int position)
Method to remove by position from ArrayGroup_list


removeFromArrayGroup_list

public void removeFromArrayGroup_list(ArrayGroup arrayGroup)
Method to remove first ArrayGroup from ArrayGroup_list


setArrayManufacture_list

public void setArrayManufacture_list(Array_package.ArrayManufacture_list arrayManufacture_list)
Set method for arrayManufacture_list


getArrayManufacture_list

public Array_package.ArrayManufacture_list getArrayManufacture_list()
Get method for arrayManufacture_list


addToArrayManufacture_list

public void addToArrayManufacture_list(ArrayManufacture arrayManufacture)
Method to add ArrayManufacture to ArrayManufacture_list


addToArrayManufacture_list

public void addToArrayManufacture_list(int position,
                                       ArrayManufacture arrayManufacture)
Method to add ArrayManufacture at position to ArrayManufacture_list


getFromArrayManufacture_list

public ArrayManufacture getFromArrayManufacture_list(int position)
Method to get ArrayManufacture from ArrayManufacture_list


removeElementAtFromArrayManufacture_list

public void removeElementAtFromArrayManufacture_list(int position)
Method to remove by position from ArrayManufacture_list


removeFromArrayManufacture_list

public void removeFromArrayManufacture_list(ArrayManufacture arrayManufacture)
Method to remove first ArrayManufacture from ArrayManufacture_list