org.biomage.BioAssay
Class Channel

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioAssay.Channel
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasLabels, HasPropertySets, HasSecurity

public class Channel
extends Identifiable
implements java.io.Serializable, HasLabels

A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasLabels
HasLabels.Labels_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List labels
          The compound used to label the extract.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Channel()
          Default constructor.
Channel(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
 boolean emptyMAGEobject()
           
 Compound getFromLabels(int position)
          Method to get Compound from Labels_list
 HasLabels.Labels_list getLabels()
          Get method for labels
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

labels

protected java.util.List labels
The compound used to label the extract.

Constructor Detail

Channel

public Channel()
Default constructor.


Channel

public Channel(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setLabels

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

Specified by:
setLabels in interface HasLabels
Parameters:
value - to set

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