org.biomage.BioAssay
Class ImageAcquisition

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioEvent.BioEvent
                          |
                          +--org.biomage.BioAssay.BioAssayTreatment
                                |
                                +--org.biomage.BioAssay.ImageAcquisition

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasImages, HasPhysicalBioAssay, HasPropertySets, HasProtocolApplications, HasSecurity, HasTarget, java.io.Serializable

public class ImageAcquisition

extends BioAssayTreatment

implements java.io.Serializable, HasImages

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

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasImages

HasImages.Images_list

Nested classes inherited from class org.biomage.Interface.HasProtocolApplications

HasProtocolApplications.ProtocolApplications_list

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 HasImages.Images_list

images The images produced by the ImageAcquisition event.

Fields inherited from class org.biomage.BioAssay.BioAssayTreatment

physicalBioAssay, target

Fields inherited from class org.biomage.BioEvent.BioEvent

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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(HasImages.Images_list images) Set method for images
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.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

protected 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

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 BioAssayTreatment

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 BioAssayTreatment

java.io.IOException

setImages

public void setImages(HasImages.Images_list images)

Set method for images

Specified by:

setImages in interface HasImages

getImages

public HasImages.Images_list getImages()

Get method for images

Specified by:

getImages in interface HasImages

Returns:

value of the attribute

addToImages

public void addToImages(Image image)

Method to add Image to Images_list

Specified by:

addToImages in interface HasImages

addToImages

public void addToImages(int position,
                        Image image)

Method to add Image at position to Images_list

Specified by:

addToImages in interface HasImages

getFromImages

public Image getFromImages(int position)

Method to get Image from Images_list

Specified by:

getFromImages in interface HasImages

removeElementAtFromImages

public void removeElementAtFromImages(int position)

Method to remove by position from Images_list

Specified by:

removeElementAtFromImages in interface HasImages

removeFromImages

public void removeFromImages(Image image)

Method to remove first Image from Images_list

Specified by:

removeFromImages in interface HasImages