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

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

public class LabeledExtract
extends BioMaterial
implements java.io.Serializable, org.biomage.Interface.HasLabels

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasLabels
org.biomage.Interface.HasLabels.Labels_list
 
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.HasLabels.Labels_list labels
          Compound used to label the extract.
 
Fields inherited from class org.biomage.BioMaterial.BioMaterial
 
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
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
 org.biomage.Interface.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(org.biomage.Interface.HasLabels.Labels_list labels)
          Set method for labels
 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.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

private org.biomage.Interface.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

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

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

setLabels

public void setLabels(org.biomage.Interface.HasLabels.Labels_list labels)
Set method for labels

Specified by:
setLabels in interface org.biomage.Interface.HasLabels

getLabels

public org.biomage.Interface.HasLabels.Labels_list getLabels()
Get method for labels

Specified by:
getLabels in interface org.biomage.Interface.HasLabels

addToLabels

public void addToLabels(Compound compound)
Method to add Compound to Labels_list

Specified by:
addToLabels in interface org.biomage.Interface.HasLabels

addToLabels

public void addToLabels(int position,
                        Compound compound)
Method to add Compound at position to Labels_list

Specified by:
addToLabels in interface org.biomage.Interface.HasLabels

getFromLabels

public Compound getFromLabels(int position)
Method to get Compound from Labels_list

Specified by:
getFromLabels in interface org.biomage.Interface.HasLabels

removeElementAtFromLabels

public void removeElementAtFromLabels(int position)
Method to remove by position from Labels_list

Specified by:
removeElementAtFromLabels in interface org.biomage.Interface.HasLabels

removeFromLabels

public void removeFromLabels(Compound compound)
Method to remove first Compound from Labels_list

Specified by:
removeFromLabels in interface org.biomage.Interface.HasLabels