org.biomage.BioAssay
Class Image

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioAssay.Image

All Implemented Interfaces:

HasAuditTrail, HasChannels, HasDescriptions, HasFormat, HasPropertySets, HasSecurity, java.io.Serializable

public class Image

extends Identifiable

implements java.io.Serializable, HasChannels, HasFormat

An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).

See Also:

Serialized Form

Nested Class Summary

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

HasChannels.Channels_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 HasChannels.Channels_list	channels The channels captured in this image.
protected OntologyEntry	format The file format of the image typically a TIF or a JPEG.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Image()
Default constructor.

Image(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToChannels(Channel channel) Method to add Channel to Channels_list
void	addToChannels(int position, Channel channel) Method to add Channel at position to Channels_list
HasChannels.Channels_list	getChannels() Get method for channels
OntologyEntry	getFormat() Get method for format
Channel	getFromChannels(int position) Method to get Channel from Channels_list
java.lang.String	getURI() Get method for URI
void	removeElementAtFromChannels(int position) Method to remove by position from Channels_list
void	removeFromChannels(Channel channel) Method to remove first Channel from Channels_list
void	setChannels(HasChannels.Channels_list channels) Set method for channels
void	setFormat(OntologyEntry format) Set method for format
void	setURI(java.lang.String URI) Set method for URI
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

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

channels

protected HasChannels.Channels_list channels

The channels captured in this image.

format

protected OntologyEntry format

The file format of the image typically a TIF or a JPEG.

Constructor Detail

Image

public Image()

Default constructor.

Image

public Image(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 Identifiable

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 Identifiable

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

java.io.IOException

setURI

public void setURI(java.lang.String URI)

Set method for URI

getURI

public java.lang.String getURI()

Get method for URI

Returns:

value of the attribute

setChannels

public void setChannels(HasChannels.Channels_list channels)

Set method for channels

Specified by:

setChannels in interface HasChannels

getChannels

public HasChannels.Channels_list getChannels()

Get method for channels

Specified by:

getChannels in interface HasChannels

Returns:

value of the attribute

addToChannels

public void addToChannels(Channel channel)

Method to add Channel to Channels_list

Specified by:

addToChannels in interface HasChannels

addToChannels

public void addToChannels(int position,
                          Channel channel)

Method to add Channel at position to Channels_list

Specified by:

addToChannels in interface HasChannels

getFromChannels

public Channel getFromChannels(int position)

Method to get Channel from Channels_list

Specified by:

getFromChannels in interface HasChannels

removeElementAtFromChannels

public void removeElementAtFromChannels(int position)

Method to remove by position from Channels_list

Specified by:

removeElementAtFromChannels in interface HasChannels

removeFromChannels

public void removeFromChannels(Channel channel)

Method to remove first Channel from Channels_list

Specified by:

removeFromChannels in interface HasChannels

setFormat

public void setFormat(OntologyEntry format)

Set method for format

Specified by:

setFormat in interface HasFormat

getFormat

public OntologyEntry getFormat()

Get method for format

Specified by:

getFormat in interface HasFormat

Returns:

value of the attribute