org.biomage.BioMaterial
Class BioMaterial_package

java.lang.Object
  |
  +--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
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
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

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.

java.io.IOException

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.

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.

java.io.IOException

setCompound_list

public void setCompound_list(BioMaterial_package.Compound_list compound_list)

Set method for compound_list

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

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