org.biomage.BioMaterial
Class BioMaterial

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioMaterial.BioMaterial

All Implemented Interfaces:

HasAuditTrail, HasCharacteristics, HasDescriptions, HasMaterialType, HasPropertySets, HasQualityControlStatistics, HasSecurity, HasTreatments, java.io.Serializable

Direct Known Subclasses:

BioSample, BioSource, LabeledExtract

public abstract class BioMaterial

extends Identifiable

implements java.io.Serializable, HasTreatments, HasMaterialType, HasCharacteristics, 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)).

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasTreatments

HasTreatments.Treatments_list

Nested classes inherited from class org.biomage.Interface.HasCharacteristics

HasCharacteristics.Characteristics_list

Nested classes inherited from class org.biomage.Interface.HasQualityControlStatistics

HasQualityControlStatistics.QualityControlStatistics_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasCharacteristics.Characteristics_list	characteristics Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.
protected OntologyEntry	materialType The type of material used, i.e.
protected HasQualityControlStatistics.QualityControlStatistics_list	qualityControlStatistics Measures of the quality of the BioMaterial.
protected HasTreatments.Treatments_list	treatments This association is one way from BioMaterial to Treatment.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioMaterial()
Default constructor.

BioMaterial(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToCharacteristics(int position, OntologyEntry ontologyEntry) Method to add OntologyEntry at position to Characteristics_list
void	addToCharacteristics(OntologyEntry ontologyEntry) Method to add OntologyEntry to Characteristics_list
void	addToQualityControlStatistics(int position, NameValueType nameValueType) Method to add NameValueType at position to QualityControlStatistics_list
void	addToQualityControlStatistics(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
HasCharacteristics.Characteristics_list	getCharacteristics() Get method for characteristics
OntologyEntry	getFromCharacteristics(int position) Method to get OntologyEntry from Characteristics_list
NameValueType	getFromQualityControlStatistics(int position) Method to get NameValueType from QualityControlStatistics_list
Treatment	getFromTreatments(int position) Method to get Treatment from Treatments_list
OntologyEntry	getMaterialType() Get method for materialType
HasQualityControlStatistics.QualityControlStatistics_list	getQualityControlStatistics() Get method for qualityControlStatistics
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(OntologyEntry ontologyEntry) Method to remove first OntologyEntry from Characteristics_list
void	removeFromQualityControlStatistics(NameValueType nameValueType) Method to remove first NameValueType from QualityControlStatistics_list
void	removeFromTreatments(Treatment treatment) Method to remove first Treatment from Treatments_list
void	setCharacteristics(HasCharacteristics.Characteristics_list characteristics) Set method for characteristics
void	setMaterialType(OntologyEntry materialType) Set method for materialType
void	setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics) Set method for qualityControlStatistics
void	setTreatments(HasTreatments.Treatments_list treatments) Set method for treatments
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 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

qualityControlStatistics

protected HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics

Measures of the quality of the BioMaterial.

characteristics

protected HasCharacteristics.Characteristics_list characteristics

Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.

materialType

protected OntologyEntry materialType

The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.

treatments

protected 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.

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.

Overrides:

writeMAGEML in class Identifiable

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.

Overrides:

writeAttributes in class Identifiable

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.

Overrides:

writeAssociations in class Identifiable

java.io.IOException

setQualityControlStatistics

public void setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)

Set method for qualityControlStatistics

Specified by:

setQualityControlStatistics in interface HasQualityControlStatistics

getQualityControlStatistics

public HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()

Get method for qualityControlStatistics

Specified by:

getQualityControlStatistics in interface HasQualityControlStatistics

Returns:

value of the attribute

addToQualityControlStatistics

public void addToQualityControlStatistics(NameValueType nameValueType)

Method to add NameValueType to QualityControlStatistics_list

Specified by:

addToQualityControlStatistics in interface HasQualityControlStatistics

addToQualityControlStatistics

public void addToQualityControlStatistics(int position,
                                          NameValueType nameValueType)

Method to add NameValueType at position to QualityControlStatistics_list

Specified by:

addToQualityControlStatistics in interface HasQualityControlStatistics

getFromQualityControlStatistics

public NameValueType getFromQualityControlStatistics(int position)

Method to get NameValueType from QualityControlStatistics_list

Specified by:

getFromQualityControlStatistics in interface HasQualityControlStatistics

removeElementAtFromQualityControlStatistics

public void removeElementAtFromQualityControlStatistics(int position)

Method to remove by position from QualityControlStatistics_list

Specified by:

removeElementAtFromQualityControlStatistics in interface HasQualityControlStatistics

removeFromQualityControlStatistics

public void removeFromQualityControlStatistics(NameValueType nameValueType)

Method to remove first NameValueType from QualityControlStatistics_list

Specified by:

removeFromQualityControlStatistics in interface HasQualityControlStatistics

setCharacteristics

public void setCharacteristics(HasCharacteristics.Characteristics_list characteristics)

Set method for characteristics

Specified by:

setCharacteristics in interface HasCharacteristics

getCharacteristics

public HasCharacteristics.Characteristics_list getCharacteristics()

Get method for characteristics

Specified by:

getCharacteristics in interface HasCharacteristics

Returns:

value of the attribute

addToCharacteristics

public void addToCharacteristics(OntologyEntry ontologyEntry)

Method to add OntologyEntry to Characteristics_list

Specified by:

addToCharacteristics in interface HasCharacteristics

addToCharacteristics

public void addToCharacteristics(int position,
                                 OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to Characteristics_list

Specified by:

addToCharacteristics in interface HasCharacteristics

getFromCharacteristics

public OntologyEntry getFromCharacteristics(int position)

Method to get OntologyEntry from Characteristics_list

Specified by:

getFromCharacteristics in interface HasCharacteristics

removeElementAtFromCharacteristics

public void removeElementAtFromCharacteristics(int position)

Method to remove by position from Characteristics_list

Specified by:

removeElementAtFromCharacteristics in interface HasCharacteristics

removeFromCharacteristics

public void removeFromCharacteristics(OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from Characteristics_list

Specified by:

removeFromCharacteristics in interface HasCharacteristics

setMaterialType

public void setMaterialType(OntologyEntry materialType)

Set method for materialType

Specified by:

setMaterialType in interface HasMaterialType

getMaterialType

public OntologyEntry getMaterialType()

Get method for materialType

Specified by:

getMaterialType in interface HasMaterialType

Returns:

value of the attribute

setTreatments

public void setTreatments(HasTreatments.Treatments_list treatments)

Set method for treatments

Specified by:

setTreatments in interface HasTreatments

getTreatments

public HasTreatments.Treatments_list getTreatments()

Get method for treatments

Specified by:

getTreatments in interface HasTreatments

Returns:

value of the attribute

addToTreatments

public void addToTreatments(Treatment treatment)

Method to add Treatment to Treatments_list

Specified by:

addToTreatments in interface HasTreatments

addToTreatments

public void addToTreatments(int position,
                            Treatment treatment)

Method to add Treatment at position to Treatments_list

Specified by:

addToTreatments in interface HasTreatments

getFromTreatments

public Treatment getFromTreatments(int position)

Method to get Treatment from Treatments_list

Specified by:

getFromTreatments in interface HasTreatments

removeElementAtFromTreatments

public void removeElementAtFromTreatments(int position)

Method to remove by position from Treatments_list

Specified by:

removeElementAtFromTreatments in interface HasTreatments

removeFromTreatments

public void removeFromTreatments(Treatment treatment)

Method to remove first Treatment from Treatments_list

Specified by:

removeFromTreatments in interface HasTreatments