org.biomage.ArrayDesign
Class FeatureGroup

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.ArrayDesign.DesignElementGroup
                  extended by org.biomage.ArrayDesign.FeatureGroup
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasDistanceUnit, HasFeatures, HasFeatureShape, HasPropertySets, HasSecurity, HasSpecies, HasTechnologyType, HasTypes

public class FeatureGroup
extends DesignElementGroup
implements java.io.Serializable, HasDistanceUnit, HasFeatures, HasTechnologyType, HasFeatureShape

A collection of like features.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatures
HasFeatures.Features_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTypes
HasTypes.Types_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  DistanceUnit distanceUnit
          The unit for the feature measures.
protected  java.util.List features
          The features that belong to this group.
protected  OntologyEntry featureShape
          The expected shape of the feature on the array: circular, oval, square, etc.
protected  OntologyEntry technologyType
          The technology type of this design.
 
Fields inherited from class org.biomage.ArrayDesign.DesignElementGroup
ojbConcreteClass, species, types
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
FeatureGroup()
          Default constructor.
FeatureGroup(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToFeatures(Feature feature)
          Method to add Feature to Features_list
 void addToFeatures(int position, Feature feature)
          Method to add Feature at position to Features_list
 boolean emptyMAGEobject()
           
 DistanceUnit getDistanceUnit()
          Get method for distanceUnit
 java.lang.Float getFeatureHeight()
          Get method for featureHeight
 java.lang.Float getFeatureLength()
          Get method for featureLength
 HasFeatures.Features_list getFeatures()
          Get method for features
 OntologyEntry getFeatureShape()
          Get method for featureShape
 java.lang.Float getFeatureWidth()
          Get method for featureWidth
 Feature getFromFeatures(int position)
          Method to get Feature from Features_list
 java.lang.String getModelClassName()
           
 OntologyEntry getTechnologyType()
          Get method for technologyType
 void removeElementAtFromFeatures(int position)
          Method to remove by position from Features_list
 void removeFromFeatures(Feature feature)
          Method to remove first Feature from Features_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setDistanceUnit(DistanceUnit distanceUnit)
          Set method for distanceUnit
 void setFeatureHeight(java.lang.Float featureHeight)
          Set method for featureHeight
 void setFeatureLength(java.lang.Float featureLength)
          Set method for featureLength
 void setFeatures(HasFeatures.Features_list features)
          Set method for features
 void setFeatureShape(OntologyEntry featureShape)
          Set method for featureShape
 void setFeatureWidth(java.lang.Float featureWidth)
          Set method for featureWidth
 void setTechnologyType(OntologyEntry technologyType)
          Set method for technologyType
 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.ArrayDesign.DesignElementGroup
addToTypes, addToTypes, getFromTypes, getSpecies, getTypes, removeElementAtFromTypes, removeFromTypes, setSpecies, setTypes
 
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

technologyType

protected OntologyEntry technologyType
The technology type of this design. By specifying a technology type, higher level analysis can use appropriate algorithms to compare the results from multiple arrays. The technology type may be spotted cDNA or in situ photolithography.


featureShape

protected OntologyEntry featureShape
The expected shape of the feature on the array: circular, oval, square, etc.


distanceUnit

protected DistanceUnit distanceUnit
The unit for the feature measures.


features

protected java.util.List features
The features that belong to this group.

Constructor Detail

FeatureGroup

public FeatureGroup()
Default constructor.


FeatureGroup

public FeatureGroup(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 DesignElementGroup

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 DesignElementGroup
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 DesignElementGroup
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 DesignElementGroup
Throws:
java.io.IOException

setFeatureWidth

public void setFeatureWidth(java.lang.Float featureWidth)
Set method for featureWidth

Parameters:
value - to set

getFeatureWidth

public java.lang.Float getFeatureWidth()
Get method for featureWidth

Returns:
value of the attribute

setFeatureLength

public void setFeatureLength(java.lang.Float featureLength)
Set method for featureLength

Parameters:
value - to set

getFeatureLength

public java.lang.Float getFeatureLength()
Get method for featureLength

Returns:
value of the attribute

setFeatureHeight

public void setFeatureHeight(java.lang.Float featureHeight)
Set method for featureHeight

Parameters:
value - to set

getFeatureHeight

public java.lang.Float getFeatureHeight()
Get method for featureHeight

Returns:
value of the attribute

getModelClassName

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

setTechnologyType

public void setTechnologyType(OntologyEntry technologyType)
Set method for technologyType

Specified by:
setTechnologyType in interface HasTechnologyType
Parameters:
value - to set

getTechnologyType

public OntologyEntry getTechnologyType()
Get method for technologyType

Specified by:
getTechnologyType in interface HasTechnologyType
Returns:
value of the attribute

setFeatureShape

public void setFeatureShape(OntologyEntry featureShape)
Set method for featureShape

Specified by:
setFeatureShape in interface HasFeatureShape
Parameters:
value - to set

getFeatureShape

public OntologyEntry getFeatureShape()
Get method for featureShape

Specified by:
getFeatureShape in interface HasFeatureShape
Returns:
value of the attribute

setDistanceUnit

public void setDistanceUnit(DistanceUnit distanceUnit)
Set method for distanceUnit

Specified by:
setDistanceUnit in interface HasDistanceUnit
Parameters:
value - to set

getDistanceUnit

public DistanceUnit getDistanceUnit()
Get method for distanceUnit

Specified by:
getDistanceUnit in interface HasDistanceUnit
Returns:
value of the attribute

setFeatures

public void setFeatures(HasFeatures.Features_list features)
Set method for features

Specified by:
setFeatures in interface HasFeatures
Parameters:
value - to set

getFeatures

public HasFeatures.Features_list getFeatures()
Get method for features

Specified by:
getFeatures in interface HasFeatures
Returns:
value of the attribute

addToFeatures

public void addToFeatures(Feature feature)
Method to add Feature to Features_list

Specified by:
addToFeatures in interface HasFeatures

addToFeatures

public void addToFeatures(int position,
                          Feature feature)
Method to add Feature at position to Features_list

Specified by:
addToFeatures in interface HasFeatures

getFromFeatures

public Feature getFromFeatures(int position)
Method to get Feature from Features_list

Specified by:
getFromFeatures in interface HasFeatures

removeElementAtFromFeatures

public void removeElementAtFromFeatures(int position)
Method to remove by position from Features_list

Specified by:
removeElementAtFromFeatures in interface HasFeatures

removeFromFeatures

public void removeFromFeatures(Feature feature)
Method to remove first Feature from Features_list

Specified by:
removeFromFeatures in interface HasFeatures