org.biomage.BioAssay
Class Image

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioAssay.Image
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasChannels, HasDescriptions, HasFormat, HasPropertySets, HasSecurity

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/interfaces inherited from interface org.biomage.Interface.HasChannels
HasChannels.Channels_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.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
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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 getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

channels

protected java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

setURI

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

Parameters:
value - to set

getURI

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

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setChannels

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

Specified by:
setChannels in interface HasChannels
Parameters:
value - to set

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
Parameters:
value - to set

getFormat

public OntologyEntry getFormat()
Get method for format

Specified by:
getFormat in interface HasFormat
Returns:
value of the attribute