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org.biomage.BioMaterial
Class BioMaterial_package  view BioMaterial_package download BioMaterial_package.java

java.lang.Object
  extended byorg.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.


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.


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)).


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).


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.


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.


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.


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.


setBioSource_list

public void setBioSource_list(BioMaterial_package.BioSource_list bioSource_list)
Set method for bioSource_list


getBioSource_list

public BioMaterial_package.BioSource_list getBioSource_list()
Get method for bioSource_list


addToBioSource_list

public void addToBioSource_list(BioSource bioSource)
Method to add BioSource to BioSource_list


addToBioSource_list

public void addToBioSource_list(int position,
                                BioSource bioSource)
Method to add BioSource at position to BioSource_list


getFromBioSource_list

public BioSource getFromBioSource_list(int position)
Method to get BioSource from BioSource_list


removeElementAtFromBioSource_list

public void removeElementAtFromBioSource_list(int position)
Method to remove by position from BioSource_list


removeFromBioSource_list

public void removeFromBioSource_list(BioSource bioSource)
Method to remove first BioSource from BioSource_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


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


setLabeledExtract_list

public void setLabeledExtract_list(BioMaterial_package.LabeledExtract_list labeledExtract_list)
Set method for labeledExtract_list


getLabeledExtract_list

public BioMaterial_package.LabeledExtract_list getLabeledExtract_list()
Get method for labeledExtract_list


addToLabeledExtract_list

public void addToLabeledExtract_list(LabeledExtract labeledExtract)
Method to add LabeledExtract to LabeledExtract_list


addToLabeledExtract_list

public void addToLabeledExtract_list(int position,
                                     LabeledExtract labeledExtract)
Method to add LabeledExtract at position to LabeledExtract_list


getFromLabeledExtract_list

public LabeledExtract getFromLabeledExtract_list(int position)
Method to get LabeledExtract from LabeledExtract_list


removeElementAtFromLabeledExtract_list

public void removeElementAtFromLabeledExtract_list(int position)
Method to remove by position from LabeledExtract_list


removeFromLabeledExtract_list

public void removeFromLabeledExtract_list(LabeledExtract labeledExtract)
Method to remove first LabeledExtract from LabeledExtract_list


setBioSample_list

public void setBioSample_list(BioMaterial_package.BioSample_list bioSample_list)
Set method for bioSample_list


getBioSample_list

public BioMaterial_package.BioSample_list getBioSample_list()
Get method for bioSample_list


addToBioSample_list

public void addToBioSample_list(BioSample bioSample)
Method to add BioSample to BioSample_list


addToBioSample_list

public void addToBioSample_list(int position,
                                BioSample bioSample)
Method to add BioSample at position to BioSample_list


getFromBioSample_list

public BioSample getFromBioSample_list(int position)
Method to get BioSample from BioSample_list


removeElementAtFromBioSample_list

public void removeElementAtFromBioSample_list(int position)
Method to remove by position from BioSample_list


removeFromBioSample_list

public void removeFromBioSample_list(BioSample bioSample)
Method to remove first BioSample from BioSample_list


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


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