org.biomage.BioMaterial
Class LabeledExtract

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

All Implemented Interfaces:

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

public class LabeledExtract

extends BioMaterial

implements java.io.Serializable, HasLabels

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

See Also:

Serialized Form

Nested Class Summary

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

HasLabels.Labels_list

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 HasLabels.Labels_list

labels Compound used to label the extract.

Fields inherited from class org.biomage.BioMaterial.BioMaterial

characteristics, materialType, qualityControlStatistics, treatments

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

LabeledExtract()
Default constructor.

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

Method Summary

void	addToLabels(Compound compound) Method to add Compound to Labels_list
void	addToLabels(int position, Compound compound) Method to add Compound at position to Labels_list
Compound	getFromLabels(int position) Method to get Compound from Labels_list
HasLabels.Labels_list	getLabels() Get method for labels
void	removeElementAtFromLabels(int position) Method to remove by position from Labels_list
void	removeFromLabels(Compound compound) Method to remove first Compound from Labels_list
void	setLabels(HasLabels.Labels_list labels) Set method for labels
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.BioMaterial.BioMaterial

addToCharacteristics, addToCharacteristics, addToQualityControlStatistics, addToQualityControlStatistics, addToTreatments, addToTreatments, getCharacteristics, getFromCharacteristics, getFromQualityControlStatistics, getFromTreatments, getMaterialType, getQualityControlStatistics, getTreatments, removeElementAtFromCharacteristics, removeElementAtFromQualityControlStatistics, removeElementAtFromTreatments, removeFromCharacteristics, removeFromQualityControlStatistics, removeFromTreatments, setCharacteristics, setMaterialType, setQualityControlStatistics, setTreatments

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

labels

protected HasLabels.Labels_list labels

Compound used to label the extract.

Constructor Detail

LabeledExtract

public LabeledExtract()

Default constructor.

LabeledExtract

public LabeledExtract(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 BioMaterial

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 BioMaterial

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 BioMaterial

java.io.IOException

setLabels

public void setLabels(HasLabels.Labels_list labels)

Set method for labels

Specified by:

setLabels in interface HasLabels

getLabels

public HasLabels.Labels_list getLabels()

Get method for labels

Specified by:

getLabels in interface HasLabels

Returns:

value of the attribute

addToLabels

public void addToLabels(Compound compound)

Method to add Compound to Labels_list

Specified by:

addToLabels in interface HasLabels

addToLabels

public void addToLabels(int position,
                        Compound compound)

Method to add Compound at position to Labels_list

Specified by:

addToLabels in interface HasLabels

getFromLabels

public Compound getFromLabels(int position)

Method to get Compound from Labels_list

Specified by:

getFromLabels in interface HasLabels

removeElementAtFromLabels

public void removeElementAtFromLabels(int position)

Method to remove by position from Labels_list

Specified by:

removeElementAtFromLabels in interface HasLabels

removeFromLabels

public void removeFromLabels(Compound compound)

Method to remove first Compound from Labels_list

Specified by:

removeFromLabels in interface HasLabels