org.biomage.BioMaterial
Class BioMaterial_package

java.lang.Object
  extended by org.biomage.BioMaterial.BioMaterial_package
All Implemented Interfaces:
java.io.Serializable

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

The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay. A set of treatments are typically linear in time but can form a Directed Acyclic Graph.

See Also:
Serialized Form

Nested Class Summary
 class BioMaterial_package.BioMaterial_list
          Inner list class for holding multiple entries for attribute bioMaterial.
 class BioMaterial_package.Compound_list
          Inner list class for holding multiple entries for attribute compound.
 
Field Summary
 BioMaterial_package.BioMaterial_list bioMaterial_list
          BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
 BioMaterial_package.Compound_list compound_list
          A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
 
Constructor Summary
BioMaterial_package()
          Default constructor.
BioMaterial_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioMaterial_list(BioMaterial bioMaterial)
          Method to add BioMaterial to BioMaterial_list
 void addToBioMaterial_list(int position, BioMaterial bioMaterial)
          Method to add BioMaterial at position to BioMaterial_list
 void addToCompound_list(Compound compound)
          Method to add Compound to Compound_list
 void addToCompound_list(int position, Compound compound)
          Method to add Compound at position to Compound_list
 boolean emptyMAGEobject()
           
 BioMaterial_package.BioMaterial_list getBioMaterial_list()
          Get method for bioMaterial_list
 BioMaterial_package.Compound_list getCompound_list()
          Get method for compound_list
 BioMaterial getFromBioMaterial_list(int position)
          Method to get BioMaterial from BioMaterial_list
 Compound getFromCompound_list(int position)
          Method to get Compound from Compound_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromBioMaterial_list(int position)
          Method to remove by position from BioMaterial_list
 void removeElementAtFromCompound_list(int position)
          Method to remove by position from Compound_list
 void removeFromBioMaterial_list(BioMaterial bioMaterial)
          Method to remove first BioMaterial from BioMaterial_list
 void removeFromCompound_list(Compound compound)
          Method to remove first Compound from Compound_list
 void setBioMaterial_list(BioMaterial_package.BioMaterial_list bioMaterial_list)
          Set method for bioMaterial_list
 void setCompound_list(BioMaterial_package.Compound_list compound_list)
          Set method for compound_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

compound_list

public BioMaterial_package.Compound_list compound_list
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). It may also be made of other Compounds in proportions using CompoundMeasurements to enumerate the Compounds and their amounts such as LB (Luria Broth) Media.


bioMaterial_list

public BioMaterial_package.BioMaterial_list bioMaterial_list
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... Biomaterials can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)).

Constructor Detail

BioMaterial_package

public BioMaterial_package()
Default constructor.


BioMaterial_package

public BioMaterial_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()

setCompound_list

public void setCompound_list(BioMaterial_package.Compound_list compound_list)
Set method for compound_list

Parameters:
value - to set

getCompound_list

public BioMaterial_package.Compound_list getCompound_list()
Get method for compound_list

Returns:
value of the attribute

addToCompound_list

public void addToCompound_list(Compound compound)
Method to add Compound to Compound_list


addToCompound_list

public void addToCompound_list(int position,
                               Compound compound)
Method to add Compound at position to Compound_list


getFromCompound_list

public Compound getFromCompound_list(int position)
Method to get Compound from Compound_list


removeElementAtFromCompound_list

public void removeElementAtFromCompound_list(int position)
Method to remove by position from Compound_list


removeFromCompound_list

public void removeFromCompound_list(Compound compound)
Method to remove first Compound from Compound_list


setBioMaterial_list

public void setBioMaterial_list(BioMaterial_package.BioMaterial_list bioMaterial_list)
Set method for bioMaterial_list

Parameters:
value - to set

getBioMaterial_list

public BioMaterial_package.BioMaterial_list getBioMaterial_list()
Get method for bioMaterial_list

Returns:
value of the attribute

addToBioMaterial_list

public void addToBioMaterial_list(BioMaterial bioMaterial)
Method to add BioMaterial to BioMaterial_list


addToBioMaterial_list

public void addToBioMaterial_list(int position,
                                  BioMaterial bioMaterial)
Method to add BioMaterial at position to BioMaterial_list


getFromBioMaterial_list

public BioMaterial getFromBioMaterial_list(int position)
Method to get BioMaterial from BioMaterial_list


removeElementAtFromBioMaterial_list

public void removeElementAtFromBioMaterial_list(int position)
Method to remove by position from BioMaterial_list


removeFromBioMaterial_list

public void removeFromBioMaterial_list(BioMaterial bioMaterial)
Method to remove first BioMaterial from BioMaterial_list