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org.biomage.Array
Class ManufactureLIMS  view ManufactureLIMS download ManufactureLIMS.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Array.ManufactureLIMS
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioMaterial, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasFeature, org.biomage.Interface.HasIdentifierLIMS, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable
Direct Known Subclasses:
ManufactureLIMSBiomaterial

public class ManufactureLIMS
extends org.biomage.Common.Describable
implements java.io.Serializable, org.biomage.Interface.HasFeature, org.biomage.Interface.HasIdentifierLIMS, org.biomage.Interface.HasBioMaterial

Information on the physical production of arrays within the laboratory.


Nested Class Summary
 
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.BioMaterial.BioMaterial bioMaterial
          The BioMaterial used for the feature.
private  org.biomage.DesignElement.Feature feature
          The feature whose LIMS information is being described.
private  org.biomage.Description.DatabaseEntry identifierLIMS
          Association to a LIMS data source for further information on the manufacturing process.
(package private)  java.lang.String quality
          A brief description of the quality of the array manufacture process.
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
ManufactureLIMS()
          Default constructor.
ManufactureLIMS(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 org.biomage.BioMaterial.BioMaterial getBioMaterial()
          Get method for bioMaterial
 org.biomage.DesignElement.Feature getFeature()
          Get method for feature
 org.biomage.Description.DatabaseEntry getIdentifierLIMS()
          Get method for identifierLIMS
 java.lang.String getQuality()
          Get method for quality
 void setBioMaterial(org.biomage.BioMaterial.BioMaterial bioMaterial)
          Set method for bioMaterial
 void setFeature(org.biomage.DesignElement.Feature feature)
          Set method for feature
 void setIdentifierLIMS(org.biomage.Description.DatabaseEntry identifierLIMS)
          Set method for identifierLIMS
 void setQuality(java.lang.String quality)
          Set method for quality
 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.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

quality

java.lang.String quality
A brief description of the quality of the array manufacture process.


feature

private org.biomage.DesignElement.Feature feature
The feature whose LIMS information is being described.


identifierLIMS

private org.biomage.Description.DatabaseEntry identifierLIMS
Association to a LIMS data source for further information on the manufacturing process.


bioMaterial

private org.biomage.BioMaterial.BioMaterial bioMaterial
The BioMaterial used for the feature.

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.


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.


setQuality

public void setQuality(java.lang.String quality)
Set method for quality


getQuality

public java.lang.String getQuality()
Get method for quality


setFeature

public void setFeature(org.biomage.DesignElement.Feature feature)
Set method for feature

Specified by:
setFeature in interface org.biomage.Interface.HasFeature

getFeature

public org.biomage.DesignElement.Feature getFeature()
Get method for feature

Specified by:
getFeature in interface org.biomage.Interface.HasFeature

setIdentifierLIMS

public void setIdentifierLIMS(org.biomage.Description.DatabaseEntry identifierLIMS)
Set method for identifierLIMS

Specified by:
setIdentifierLIMS in interface org.biomage.Interface.HasIdentifierLIMS

getIdentifierLIMS

public org.biomage.Description.DatabaseEntry getIdentifierLIMS()
Get method for identifierLIMS

Specified by:
getIdentifierLIMS in interface org.biomage.Interface.HasIdentifierLIMS

setBioMaterial

public void setBioMaterial(org.biomage.BioMaterial.BioMaterial bioMaterial)
Set method for bioMaterial

Specified by:
setBioMaterial in interface org.biomage.Interface.HasBioMaterial

getBioMaterial

public org.biomage.BioMaterial.BioMaterial getBioMaterial()
Get method for bioMaterial

Specified by:
getBioMaterial in interface org.biomage.Interface.HasBioMaterial