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org.biomage.BioMaterial
Class BioMaterial_package  

java.lang.Object
  org.biomage.BioMaterial.BioMaterial_package

All Implemented Interfaces:

java.io.Serializable

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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.

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Nested Class Summary
class	BioMaterial_package.BioMaterial_list           Inner list class for holding multiple entries for attribute bioMaterial_list.
class	BioMaterial_package.BioSample_list           Inner list class for holding multiple entries for attribute bioSample_list.
class	BioMaterial_package.BioSource_list           Inner list class for holding multiple entries for attribute bioSource_list.
class	BioMaterial_package.Compound_list           Inner list class for holding multiple entries for attribute compound_list.
class	BioMaterial_package.LabeledExtract_list           Inner list class for holding multiple entries for attribute labeledExtract_list.

 

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.BioSample_list	bioSample_list           BioSamples are products of treatments that are of interest.
BioMaterial_package.BioSource_list	bioSource_list           The BioSource is the original source material before any treatment events.
BioMaterial_package.Compound_list	compound_list           A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
BioMaterial_package.LabeledExtract_list	labeledExtract_list           LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).

 

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	addToBioSample_list(BioSample bioSample)           Method to add BioSample to BioSample_list
void	addToBioSample_list(int position, BioSample bioSample)           Method to add BioSample at position to BioSample_list
void	addToBioSource_list(BioSource bioSource)           Method to add BioSource to BioSource_list
void	addToBioSource_list(int position, BioSource bioSource)           Method to add BioSource at position to BioSource_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
void	addToLabeledExtract_list(int position, LabeledExtract labeledExtract)           Method to add LabeledExtract at position to LabeledExtract_list
void	addToLabeledExtract_list(LabeledExtract labeledExtract)           Method to add LabeledExtract to LabeledExtract_list
BioMaterial_package.BioMaterial_list	getBioMaterial_list()           Get method for bioMaterial_list
BioMaterial_package.BioSample_list	getBioSample_list()           Get method for bioSample_list
BioMaterial_package.BioSource_list	getBioSource_list()           Get method for bioSource_list
BioMaterial_package.Compound_list	getCompound_list()           Get method for compound_list
BioMaterial	getFromBioMaterial_list(int position)           Method to get BioMaterial from BioMaterial_list
BioSample	getFromBioSample_list(int position)           Method to get BioSample from BioSample_list
BioSource	getFromBioSource_list(int position)           Method to get BioSource from BioSource_list
Compound	getFromCompound_list(int position)           Method to get Compound from Compound_list
LabeledExtract	getFromLabeledExtract_list(int position)           Method to get LabeledExtract from LabeledExtract_list
BioMaterial_package.LabeledExtract_list	getLabeledExtract_list()           Get method for labeledExtract_list
void	removeElementAtFromBioMaterial_list(int position)           Method to remove by position from BioMaterial_list
void	removeElementAtFromBioSample_list(int position)           Method to remove by position from BioSample_list
void	removeElementAtFromBioSource_list(int position)           Method to remove by position from BioSource_list
void	removeElementAtFromCompound_list(int position)           Method to remove by position from Compound_list
void	removeElementAtFromLabeledExtract_list(int position)           Method to remove by position from LabeledExtract_list
void	removeFromBioMaterial_list(BioMaterial bioMaterial)           Method to remove first BioMaterial from BioMaterial_list
void	removeFromBioSample_list(BioSample bioSample)           Method to remove first BioSample from BioSample_list
void	removeFromBioSource_list(BioSource bioSource)           Method to remove first BioSource from BioSource_list
void	removeFromCompound_list(Compound compound)           Method to remove first Compound from Compound_list
void	removeFromLabeledExtract_list(LabeledExtract labeledExtract)           Method to remove first LabeledExtract from LabeledExtract_list
void	setBioMaterial_list(BioMaterial_package.BioMaterial_list bioMaterial_list)           Set method for bioMaterial_list
void	setBioSample_list(BioMaterial_package.BioSample_list bioSample_list)           Set method for bioSample_list
void	setBioSource_list(BioMaterial_package.BioSource_list bioSource_list)           Set method for bioSource_list
void	setCompound_list(BioMaterial_package.Compound_list compound_list)           Set method for compound_list
void	setLabeledExtract_list(BioMaterial_package.LabeledExtract_list labeledExtract_list)           Set method for labeledExtract_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

bioSource_list

public BioMaterial_package.BioSource_list bioSource_list

The BioSource is the original source material before any treatment events. It is also a top node of the directed acyclic graph generated by treatments. The association to OntologyEntry allows enumeration of a BioSource's inherent properties.

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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)).

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labeledExtract_list

public BioMaterial_package.LabeledExtract_list labeledExtract_list

LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).

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bioSample_list

public BioMaterial_package.BioSample_list bioSample_list

BioSamples are products of treatments that are of interest. BioSamples are often used as the sources for other biosamples. The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.

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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.

Constructor Detail

BioMaterial_package

public BioMaterial_package()

Default constructor.

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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.

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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.

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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.

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setBioSource_list

public void setBioSource_list(BioMaterial_package.BioSource_list bioSource_list)

Set method for bioSource_list

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getBioSource_list

public BioMaterial_package.BioSource_list getBioSource_list()

Get method for bioSource_list

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addToBioSource_list

public void addToBioSource_list(BioSource bioSource)

Method to add BioSource to BioSource_list

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addToBioSource_list

public void addToBioSource_list(int position,
                                BioSource bioSource)

Method to add BioSource at position to BioSource_list

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getFromBioSource_list

public BioSource getFromBioSource_list(int position)

Method to get BioSource from BioSource_list

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removeElementAtFromBioSource_list

public void removeElementAtFromBioSource_list(int position)

Method to remove by position from BioSource_list

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removeFromBioSource_list

public void removeFromBioSource_list(BioSource bioSource)

Method to remove first BioSource from BioSource_list

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setBioMaterial_list

public void setBioMaterial_list(BioMaterial_package.BioMaterial_list bioMaterial_list)

Set method for bioMaterial_list

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getBioMaterial_list

public BioMaterial_package.BioMaterial_list getBioMaterial_list()

Get method for bioMaterial_list

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addToBioMaterial_list

public void addToBioMaterial_list(BioMaterial bioMaterial)

Method to add BioMaterial to BioMaterial_list

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addToBioMaterial_list

public void addToBioMaterial_list(int position,
                                  BioMaterial bioMaterial)

Method to add BioMaterial at position to BioMaterial_list

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getFromBioMaterial_list

public BioMaterial getFromBioMaterial_list(int position)

Method to get BioMaterial from BioMaterial_list

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removeElementAtFromBioMaterial_list

public void removeElementAtFromBioMaterial_list(int position)

Method to remove by position from BioMaterial_list

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removeFromBioMaterial_list

public void removeFromBioMaterial_list(BioMaterial bioMaterial)

Method to remove first BioMaterial from BioMaterial_list

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setLabeledExtract_list

public void setLabeledExtract_list(BioMaterial_package.LabeledExtract_list labeledExtract_list)

Set method for labeledExtract_list

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getLabeledExtract_list

public BioMaterial_package.LabeledExtract_list getLabeledExtract_list()

Get method for labeledExtract_list

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addToLabeledExtract_list

public void addToLabeledExtract_list(LabeledExtract labeledExtract)

Method to add LabeledExtract to LabeledExtract_list

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addToLabeledExtract_list

public void addToLabeledExtract_list(int position,
                                     LabeledExtract labeledExtract)

Method to add LabeledExtract at position to LabeledExtract_list

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getFromLabeledExtract_list

public LabeledExtract getFromLabeledExtract_list(int position)

Method to get LabeledExtract from LabeledExtract_list

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removeElementAtFromLabeledExtract_list

public void removeElementAtFromLabeledExtract_list(int position)

Method to remove by position from LabeledExtract_list

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removeFromLabeledExtract_list

public void removeFromLabeledExtract_list(LabeledExtract labeledExtract)

Method to remove first LabeledExtract from LabeledExtract_list

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setBioSample_list

public void setBioSample_list(BioMaterial_package.BioSample_list bioSample_list)

Set method for bioSample_list

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getBioSample_list

public BioMaterial_package.BioSample_list getBioSample_list()

Get method for bioSample_list

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addToBioSample_list

public void addToBioSample_list(BioSample bioSample)

Method to add BioSample to BioSample_list

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addToBioSample_list

public void addToBioSample_list(int position,
                                BioSample bioSample)

Method to add BioSample at position to BioSample_list

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getFromBioSample_list

public BioSample getFromBioSample_list(int position)

Method to get BioSample from BioSample_list

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removeElementAtFromBioSample_list

public void removeElementAtFromBioSample_list(int position)

Method to remove by position from BioSample_list

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removeFromBioSample_list

public void removeFromBioSample_list(BioSample bioSample)

Method to remove first BioSample from BioSample_list

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setCompound_list

public void setCompound_list(BioMaterial_package.Compound_list compound_list)

Set method for compound_list

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getCompound_list

public BioMaterial_package.Compound_list getCompound_list()

Get method for compound_list

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addToCompound_list

public void addToCompound_list(Compound compound)

Method to add Compound to Compound_list

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addToCompound_list

public void addToCompound_list(int position,
                               Compound compound)

Method to add Compound at position to Compound_list

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getFromCompound_list

public Compound getFromCompound_list(int position)

Method to get Compound from Compound_list

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removeElementAtFromCompound_list

public void removeElementAtFromCompound_list(int position)

Method to remove by position from Compound_list

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removeFromCompound_list

public void removeFromCompound_list(Compound compound)

Method to remove first Compound from Compound_list

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioMaterial overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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