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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.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

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).


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.


channels

private org.biomage.Interface.HasChannels.Channels_list channels
The channels captured in this image.


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.


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.


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.


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.


setURI

public void setURI(java.lang.String URI)
Set method for URI


getURI

public java.lang.String getURI()
Get method for URI


setChannels

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

Specified by:
setChannels in interface org.biomage.Interface.HasChannels

getChannels

public org.biomage.Interface.HasChannels.Channels_list getChannels()
Get method for channels

Specified by:
getChannels in interface org.biomage.Interface.HasChannels

addToChannels

public void addToChannels(Channel channel)
Method to add Channel to Channels_list

Specified by:
addToChannels in interface org.biomage.Interface.HasChannels

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

getFromChannels

public Channel getFromChannels(int position)
Method to get Channel from Channels_list

Specified by:
getFromChannels in interface org.biomage.Interface.HasChannels

removeElementAtFromChannels

public void removeElementAtFromChannels(int position)
Method to remove by position from Channels_list

Specified by:
removeElementAtFromChannels in interface org.biomage.Interface.HasChannels

removeFromChannels

public void removeFromChannels(Channel channel)
Method to remove first Channel from Channels_list

Specified by:
removeFromChannels in interface org.biomage.Interface.HasChannels

setFormat

public void setFormat(org.biomage.Description.OntologyEntry format)
Set method for format

Specified by:
setFormat in interface org.biomage.Interface.HasFormat

getFormat

public org.biomage.Description.OntologyEntry getFormat()
Get method for format

Specified by:
getFormat in interface org.biomage.Interface.HasFormat