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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioMaterial.BioMaterial
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasCharacteristics, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasMaterialType, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasQualityControlStatistics, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasTreatments, java.io.Serializable
Direct Known Subclasses:
BioSample, BioSource, LabeledExtract

public abstract class BioMaterial
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasTreatments, org.biomage.Interface.HasMaterialType, org.biomage.Interface.HasCharacteristics, org.biomage.Interface.HasQualityControlStatistics

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)).


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasTreatments
org.biomage.Interface.HasTreatments.Treatments_list
 
Nested classes inherited from class org.biomage.Interface.HasCharacteristics
org.biomage.Interface.HasCharacteristics.Characteristics_list
 
Nested classes inherited from class org.biomage.Interface.HasQualityControlStatistics
org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasCharacteristics.Characteristics_list characteristics
          Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.
private  org.biomage.Description.OntologyEntry materialType
          The type of material used, i.e.
private  org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics
          Measures of the quality of the BioMaterial.
private  org.biomage.Interface.HasTreatments.Treatments_list treatments
          This association is one way from BioMaterial to Treatment.
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioMaterial()
          Default constructor.
BioMaterial(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToCharacteristics(int position, org.biomage.Description.OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Characteristics_list
 void addToCharacteristics(org.biomage.Description.OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Characteristics_list
 void addToQualityControlStatistics(int position, org.biomage.Common.NameValueType nameValueType)
          Method to add NameValueType at position to QualityControlStatistics_list
 void addToQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
          Method to add NameValueType to QualityControlStatistics_list
 void addToTreatments(int position, Treatment treatment)
          Method to add Treatment at position to Treatments_list
 void addToTreatments(Treatment treatment)
          Method to add Treatment to Treatments_list
 org.biomage.Interface.HasCharacteristics.Characteristics_list getCharacteristics()
          Get method for characteristics
 org.biomage.Description.OntologyEntry getFromCharacteristics(int position)
          Method to get OntologyEntry from Characteristics_list
 org.biomage.Common.NameValueType getFromQualityControlStatistics(int position)
          Method to get NameValueType from QualityControlStatistics_list
 Treatment getFromTreatments(int position)
          Method to get Treatment from Treatments_list
 org.biomage.Description.OntologyEntry getMaterialType()
          Get method for materialType
 org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()
          Get method for qualityControlStatistics
 org.biomage.Interface.HasTreatments.Treatments_list getTreatments()
          Get method for treatments
 void removeElementAtFromCharacteristics(int position)
          Method to remove by position from Characteristics_list
 void removeElementAtFromQualityControlStatistics(int position)
          Method to remove by position from QualityControlStatistics_list
 void removeElementAtFromTreatments(int position)
          Method to remove by position from Treatments_list
 void removeFromCharacteristics(org.biomage.Description.OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Characteristics_list
 void removeFromQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
          Method to remove first NameValueType from QualityControlStatistics_list
 void removeFromTreatments(Treatment treatment)
          Method to remove first Treatment from Treatments_list
 void setCharacteristics(org.biomage.Interface.HasCharacteristics.Characteristics_list characteristics)
          Set method for characteristics
 void setMaterialType(org.biomage.Description.OntologyEntry materialType)
          Set method for materialType
 void setQualityControlStatistics(org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
          Set method for qualityControlStatistics
 void setTreatments(org.biomage.Interface.HasTreatments.Treatments_list treatments)
          Set method for treatments
 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 org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

treatments

private org.biomage.Interface.HasTreatments.Treatments_list treatments
This association is one way from BioMaterial to Treatment. From this a BioMaterial can discover the amount and type of BioMaterial that was part of the treatment that produced it.


materialType

private org.biomage.Description.OntologyEntry materialType
The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.


characteristics

private org.biomage.Interface.HasCharacteristics.Characteristics_list characteristics
Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.


qualityControlStatistics

private org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics
Measures of the quality of the BioMaterial.

Constructor Detail

BioMaterial

public BioMaterial()
Default constructor.


BioMaterial

public BioMaterial(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.


setTreatments

public void setTreatments(org.biomage.Interface.HasTreatments.Treatments_list treatments)
Set method for treatments

Specified by:
setTreatments in interface org.biomage.Interface.HasTreatments

getTreatments

public org.biomage.Interface.HasTreatments.Treatments_list getTreatments()
Get method for treatments

Specified by:
getTreatments in interface org.biomage.Interface.HasTreatments

addToTreatments

public void addToTreatments(Treatment treatment)
Method to add Treatment to Treatments_list

Specified by:
addToTreatments in interface org.biomage.Interface.HasTreatments

addToTreatments

public void addToTreatments(int position,
                            Treatment treatment)
Method to add Treatment at position to Treatments_list

Specified by:
addToTreatments in interface org.biomage.Interface.HasTreatments

getFromTreatments

public Treatment getFromTreatments(int position)
Method to get Treatment from Treatments_list

Specified by:
getFromTreatments in interface org.biomage.Interface.HasTreatments

removeElementAtFromTreatments

public void removeElementAtFromTreatments(int position)
Method to remove by position from Treatments_list

Specified by:
removeElementAtFromTreatments in interface org.biomage.Interface.HasTreatments

removeFromTreatments

public void removeFromTreatments(Treatment treatment)
Method to remove first Treatment from Treatments_list

Specified by:
removeFromTreatments in interface org.biomage.Interface.HasTreatments

setMaterialType

public void setMaterialType(org.biomage.Description.OntologyEntry materialType)
Set method for materialType

Specified by:
setMaterialType in interface org.biomage.Interface.HasMaterialType

getMaterialType

public org.biomage.Description.OntologyEntry getMaterialType()
Get method for materialType

Specified by:
getMaterialType in interface org.biomage.Interface.HasMaterialType

setCharacteristics

public void setCharacteristics(org.biomage.Interface.HasCharacteristics.Characteristics_list characteristics)
Set method for characteristics

Specified by:
setCharacteristics in interface org.biomage.Interface.HasCharacteristics

getCharacteristics

public org.biomage.Interface.HasCharacteristics.Characteristics_list getCharacteristics()
Get method for characteristics

Specified by:
getCharacteristics in interface org.biomage.Interface.HasCharacteristics

addToCharacteristics

public void addToCharacteristics(org.biomage.Description.OntologyEntry ontologyEntry)
Method to add OntologyEntry to Characteristics_list

Specified by:
addToCharacteristics in interface org.biomage.Interface.HasCharacteristics

addToCharacteristics

public void addToCharacteristics(int position,
                                 org.biomage.Description.OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Characteristics_list

Specified by:
addToCharacteristics in interface org.biomage.Interface.HasCharacteristics

getFromCharacteristics

public org.biomage.Description.OntologyEntry getFromCharacteristics(int position)
Method to get OntologyEntry from Characteristics_list

Specified by:
getFromCharacteristics in interface org.biomage.Interface.HasCharacteristics

removeElementAtFromCharacteristics

public void removeElementAtFromCharacteristics(int position)
Method to remove by position from Characteristics_list

Specified by:
removeElementAtFromCharacteristics in interface org.biomage.Interface.HasCharacteristics

removeFromCharacteristics

public void removeFromCharacteristics(org.biomage.Description.OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Characteristics_list

Specified by:
removeFromCharacteristics in interface org.biomage.Interface.HasCharacteristics

setQualityControlStatistics

public void setQualityControlStatistics(org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
Set method for qualityControlStatistics

Specified by:
setQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

getQualityControlStatistics

public org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()
Get method for qualityControlStatistics

Specified by:
getQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

addToQualityControlStatistics

public void addToQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
Method to add NameValueType to QualityControlStatistics_list

Specified by:
addToQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

addToQualityControlStatistics

public void addToQualityControlStatistics(int position,
                                          org.biomage.Common.NameValueType nameValueType)
Method to add NameValueType at position to QualityControlStatistics_list

Specified by:
addToQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

getFromQualityControlStatistics

public org.biomage.Common.NameValueType getFromQualityControlStatistics(int position)
Method to get NameValueType from QualityControlStatistics_list

Specified by:
getFromQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

removeElementAtFromQualityControlStatistics

public void removeElementAtFromQualityControlStatistics(int position)
Method to remove by position from QualityControlStatistics_list

Specified by:
removeElementAtFromQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

removeFromQualityControlStatistics

public void removeFromQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
Method to remove first NameValueType from QualityControlStatistics_list

Specified by:
removeFromQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics