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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:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasChannels, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasFormat, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class Image

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasChannels, org.biomage.Interface.HasFormat

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

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Nested Class Summary

 

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

org.biomage.Interface.HasChannels.Channels_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.HasChannels.Channels_list	channels           The channels captured in this image.
private  org.biomage.Description.OntologyEntry	format           The file format of the image typically a TIF or a JPEG.
(package private)  java.lang.String	URI           The file location in which an image may be found.

 

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

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
org.biomage.Interface.HasChannels.Channels_list	getChannels()           Get method for channels
org.biomage.Description.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(org.biomage.Interface.HasChannels.Channels_list channels)           Set method for channels
void	setFormat(org.biomage.Description.OntologyEntry format)           Set method for format
void	setURI(java.lang.String URI)           Set method for URI
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.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

URI

java.lang.String URI

The file location in which an image may be found.

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channels

private org.biomage.Interface.HasChannels.Channels_list channels

The channels captured in this image.

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format

private org.biomage.Description.OntologyEntry format

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

Constructor Detail

Image

public Image()

Default constructor.

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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.

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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.

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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.

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setURI

public void setURI(java.lang.String URI)

Set method for URI

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getURI

public java.lang.String getURI()

Get method for URI

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setChannels

public void setChannels(org.biomage.Interface.HasChannels.Channels_list channels)

Set method for channels

Specified by:

setChannels in interface org.biomage.Interface.HasChannels

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getChannels

public org.biomage.Interface.HasChannels.Channels_list getChannels()

Get method for channels

Specified by:

getChannels in interface org.biomage.Interface.HasChannels

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addToChannels

public void addToChannels(Channel channel)

Method to add Channel to Channels_list

Specified by:

addToChannels in interface org.biomage.Interface.HasChannels

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addToChannels

public void addToChannels(int position,
                          Channel channel)

Method to add Channel at position to Channels_list

Specified by:

addToChannels in interface org.biomage.Interface.HasChannels

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getFromChannels

public Channel getFromChannels(int position)

Method to get Channel from Channels_list

Specified by:

getFromChannels in interface org.biomage.Interface.HasChannels

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removeElementAtFromChannels

public void removeElementAtFromChannels(int position)

Method to remove by position from Channels_list

Specified by:

removeElementAtFromChannels in interface org.biomage.Interface.HasChannels

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removeFromChannels

public void removeFromChannels(Channel channel)

Method to remove first Channel from Channels_list

Specified by:

removeFromChannels in interface org.biomage.Interface.HasChannels

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setFormat

public void setFormat(org.biomage.Description.OntologyEntry format)

Set method for format

Specified by:

setFormat in interface org.biomage.Interface.HasFormat

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getFormat

public org.biomage.Description.OntologyEntry getFormat()

Get method for format

Specified by:

getFormat in interface org.biomage.Interface.HasFormat

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssay overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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