org.biomage.QuantitationType
Class QuantitationType_package

java.lang.Object
  extended by org.biomage.QuantitationType.QuantitationType_package
All Implemented Interfaces:
java.io.Serializable

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

This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue. The subclasses of StandardQuantitationType will be the best fit from FeatureExtraction or Transformation Protocol for the values obtained. Other values can be specified using SpecializedQuantitationType.

See Also:
Serialized Form

Nested Class Summary
 class QuantitationType_package.QuantitationType_list
          Inner list class for holding multiple entries for attribute quantitationType.
 
Field Summary
 QuantitationType_package.QuantitationType_list quantitationType_list
          A method for calculating a single datum of the matrix (e.g.
 
Constructor Summary
QuantitationType_package()
          Default constructor.
QuantitationType_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToQuantitationType_list(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to QuantitationType_list
 void addToQuantitationType_list(QuantitationType quantitationType)
          Method to add QuantitationType to QuantitationType_list
 boolean emptyMAGEobject()
           
 QuantitationType getFromQuantitationType_list(int position)
          Method to get QuantitationType from QuantitationType_list
 java.lang.String getModelClassName()
           
 QuantitationType_package.QuantitationType_list getQuantitationType_list()
          Get method for quantitationType_list
 void removeElementAtFromQuantitationType_list(int position)
          Method to remove by position from QuantitationType_list
 void removeFromQuantitationType_list(QuantitationType quantitationType)
          Method to remove first QuantitationType from QuantitationType_list
 void setQuantitationType_list(QuantitationType_package.QuantitationType_list quantitationType_list)
          Set method for quantitationType_list
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

quantitationType_list

public QuantitationType_package.QuantitationType_list quantitationType_list
A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).

Constructor Detail

QuantitationType_package

public QuantitationType_package()
Default constructor.


QuantitationType_package

public QuantitationType_package(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

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.

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.

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.

Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()

setQuantitationType_list

public void setQuantitationType_list(QuantitationType_package.QuantitationType_list quantitationType_list)
Set method for quantitationType_list

Parameters:
value - to set

getQuantitationType_list

public QuantitationType_package.QuantitationType_list getQuantitationType_list()
Get method for quantitationType_list

Returns:
value of the attribute

addToQuantitationType_list

public void addToQuantitationType_list(QuantitationType quantitationType)
Method to add QuantitationType to QuantitationType_list


addToQuantitationType_list

public void addToQuantitationType_list(int position,
                                       QuantitationType quantitationType)
Method to add QuantitationType at position to QuantitationType_list


getFromQuantitationType_list

public QuantitationType getFromQuantitationType_list(int position)
Method to get QuantitationType from QuantitationType_list


removeElementAtFromQuantitationType_list

public void removeElementAtFromQuantitationType_list(int position)
Method to remove by position from QuantitationType_list


removeFromQuantitationType_list

public void removeFromQuantitationType_list(QuantitationType quantitationType)
Method to remove first QuantitationType from QuantitationType_list