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org.biomage.BioAssay
Class ImageAcquisition  view ImageAcquisition download ImageAcquisition.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioAssay.BioAssayTreatment
                      extended byorg.biomage.BioAssay.ImageAcquisition
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasImages, org.biomage.Interface.HasPhysicalBioAssay, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasTarget, java.io.Serializable

public class ImageAcquisition
extends BioAssayTreatment
implements java.io.Serializable, org.biomage.Interface.HasImages

The process by which an image is generated (typically scanning).


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasImages
org.biomage.Interface.HasImages.Images_list
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_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.HasImages.Images_list images
          The images produced by the ImageAcquisition event.
 
Fields inherited from class org.biomage.BioAssay.BioAssayTreatment
 
Fields inherited from class org.biomage.BioEvent.BioEvent
 
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
ImageAcquisition()
          Default constructor.
ImageAcquisition(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToImages(Image image)
          Method to add Image to Images_list
 void addToImages(int position, Image image)
          Method to add Image at position to Images_list
 Image getFromImages(int position)
          Method to get Image from Images_list
 org.biomage.Interface.HasImages.Images_list getImages()
          Get method for images
 void removeElementAtFromImages(int position)
          Method to remove by position from Images_list
 void removeFromImages(Image image)
          Method to remove first Image from Images_list
 void setImages(org.biomage.Interface.HasImages.Images_list images)
          Set method for images
 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.BioAssay.BioAssayTreatment
getPhysicalBioAssay, getTarget, setPhysicalBioAssay, setTarget
 
Methods inherited from class org.biomage.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
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

images

private org.biomage.Interface.HasImages.Images_list images
The images produced by the ImageAcquisition event.

Constructor Detail

ImageAcquisition

public ImageAcquisition()
Default constructor.


ImageAcquisition

public ImageAcquisition(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 BioAssayTreatment

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 BioAssayTreatment

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 BioAssayTreatment

setImages

public void setImages(org.biomage.Interface.HasImages.Images_list images)
Set method for images

Specified by:
setImages in interface org.biomage.Interface.HasImages

getImages

public org.biomage.Interface.HasImages.Images_list getImages()
Get method for images

Specified by:
getImages in interface org.biomage.Interface.HasImages

addToImages

public void addToImages(Image image)
Method to add Image to Images_list

Specified by:
addToImages in interface org.biomage.Interface.HasImages

addToImages

public void addToImages(int position,
                        Image image)
Method to add Image at position to Images_list

Specified by:
addToImages in interface org.biomage.Interface.HasImages

getFromImages

public Image getFromImages(int position)
Method to get Image from Images_list

Specified by:
getFromImages in interface org.biomage.Interface.HasImages

removeElementAtFromImages

public void removeElementAtFromImages(int position)
Method to remove by position from Images_list

Specified by:
removeElementAtFromImages in interface org.biomage.Interface.HasImages

removeFromImages

public void removeFromImages(Image image)
Method to remove first Image from Images_list

Specified by:
removeFromImages in interface org.biomage.Interface.HasImages