org.biomage.ArrayDesign
Class FeatureGroup

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.ArrayDesign.DesignElementGroup
                          |
                          +--org.biomage.ArrayDesign.FeatureGroup

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasDistanceUnit, HasFeatures, HasFeatureShape, HasPropertySets, HasSecurity, HasSpecies, HasTechnologyType, HasTypes, java.io.Serializable

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 inherited from class org.biomage.Interface.HasFeatures

HasFeatures.Features_list

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

HasTypes.Types_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 DistanceUnit	distanceUnit The unit for the feature measures.
protected HasFeatures.Features_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

species, types

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
DistanceUnit	getDistanceUnit() Get method for distanceUnit
float	getFeatureHeight() Get method for featureHeight
float	getFeatureLength() Get method for featureLength
HasFeatures.Features_list	getFeatures() Get method for features
OntologyEntry	getFeatureShape() Get method for featureShape
float	getFeatureWidth() Get method for featureWidth
Feature	getFromFeatures(int position) Method to get Feature from Features_list
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	setDistanceUnit(DistanceUnit distanceUnit) Set method for distanceUnit
void	setFeatureHeight(float featureHeight) Set method for featureHeight
void	setFeatureLength(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(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

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

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 HasFeatures.Features_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

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 DesignElementGroup

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 DesignElementGroup

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

java.io.IOException

setFeatureWidth

public void setFeatureWidth(float featureWidth)

Set method for featureWidth

getFeatureWidth

public float getFeatureWidth()

Get method for featureWidth

Returns:

value of the attribute

setFeatureLength

public void setFeatureLength(float featureLength)

Set method for featureLength

getFeatureLength

public float getFeatureLength()

Get method for featureLength

Returns:

value of the attribute

setFeatureHeight

public void setFeatureHeight(float featureHeight)

Set method for featureHeight

getFeatureHeight

public float getFeatureHeight()

Get method for featureHeight

Returns:

value of the attribute

setTechnologyType

public void setTechnologyType(OntologyEntry technologyType)

Set method for technologyType

Specified by:

setTechnologyType in interface HasTechnologyType

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

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

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

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