org.biomage.Array
Class ManufactureLIMS

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Array.ManufactureLIMS

All Implemented Interfaces:

HasAuditTrail, HasBioMaterial, HasDescriptions, HasFeature, HasIdentifierLIMS, HasPropertySets, HasSecurity, java.io.Serializable

Direct Known Subclasses:

ManufactureLIMSBiomaterial

public class ManufactureLIMS

extends Describable

implements java.io.Serializable, HasFeature, HasIdentifierLIMS, HasBioMaterial

Information on the physical production of arrays within the laboratory.

See Also:

Serialized Form

Nested Class Summary

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 BioMaterial	bioMaterial The BioMaterial used for the feature.
protected Feature	feature The feature whose LIMS information is being described.
protected DatabaseEntry	identifierLIMS Association to a LIMS data source for further information on the manufacturing process.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ManufactureLIMS()
Default constructor.

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

Method Summary

BioMaterial	getBioMaterial() Get method for bioMaterial
Feature	getFeature() Get method for feature
DatabaseEntry	getIdentifierLIMS() Get method for identifierLIMS
java.lang.String	getQuality() Get method for quality
void	setBioMaterial(BioMaterial bioMaterial) Set method for bioMaterial
void	setFeature(Feature feature) Set method for feature
void	setIdentifierLIMS(DatabaseEntry identifierLIMS) Set method for identifierLIMS
void	setQuality(java.lang.String quality) Set method for quality
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.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

feature

protected Feature feature

The feature whose LIMS information is being described.

bioMaterial

protected BioMaterial bioMaterial

The BioMaterial used for the feature.

identifierLIMS

protected DatabaseEntry identifierLIMS

Association to a LIMS data source for further information on the manufacturing process.

Constructor Detail

ManufactureLIMS

public ManufactureLIMS()

Default constructor.

ManufactureLIMS

public ManufactureLIMS(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 Describable

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 Describable

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 Describable

java.io.IOException

setQuality

public void setQuality(java.lang.String quality)

Set method for quality

getQuality

public java.lang.String getQuality()

Get method for quality

Returns:

value of the attribute

setFeature

public void setFeature(Feature feature)

Set method for feature

Specified by:

setFeature in interface HasFeature

getFeature

public Feature getFeature()

Get method for feature

Specified by:

getFeature in interface HasFeature

Returns:

value of the attribute

setBioMaterial

public void setBioMaterial(BioMaterial bioMaterial)

Set method for bioMaterial

Specified by:

setBioMaterial in interface HasBioMaterial

getBioMaterial

public BioMaterial getBioMaterial()

Get method for bioMaterial

Specified by:

getBioMaterial in interface HasBioMaterial

Returns:

value of the attribute

setIdentifierLIMS

public void setIdentifierLIMS(DatabaseEntry identifierLIMS)

Set method for identifierLIMS

Specified by:

setIdentifierLIMS in interface HasIdentifierLIMS

getIdentifierLIMS

public DatabaseEntry getIdentifierLIMS()

Get method for identifierLIMS

Specified by:

getIdentifierLIMS in interface HasIdentifierLIMS

Returns:

value of the attribute