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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:

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

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public class FeatureGroup

extends DesignElementGroup

implements java.io.Serializable, org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasFeatures, org.biomage.Interface.HasTechnologyType, org.biomage.Interface.HasFeatureShape

A collection of like features.

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Nested Class Summary

 

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

org.biomage.Interface.HasFeatures.Features_list

 

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

org.biomage.Interface.HasTypes.Types_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.Measurement.DistanceUnit	distanceUnit           The unit for the feature measures.
(package private)  float	featureHeight           The height of the feature.
(package private)  float	featureLength           The length of the feature.
private  org.biomage.Interface.HasFeatures.Features_list	features           The features that belong to this group.
private  org.biomage.Description.OntologyEntry	featureShape           The expected shape of the feature on the array: circular, oval, square, etc.
(package private)  float	featureWidth           The width of the feature.
private  org.biomage.Description.OntologyEntry	technologyType           The technology type of this design.

 

Fields inherited from class org.biomage.ArrayDesign.DesignElementGroup

 

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

FeatureGroup()           Default constructor.

FeatureGroup(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
void	addToFeatures(org.biomage.DesignElement.Feature feature)           Method to add Feature to Features_list
void	addToFeatures(int position, org.biomage.DesignElement.Feature feature)           Method to add Feature at position to Features_list
org.biomage.Measurement.DistanceUnit	getDistanceUnit()           Get method for distanceUnit
float	getFeatureHeight()           Get method for featureHeight
float	getFeatureLength()           Get method for featureLength
org.biomage.Interface.HasFeatures.Features_list	getFeatures()           Get method for features
org.biomage.Description.OntologyEntry	getFeatureShape()           Get method for featureShape
float	getFeatureWidth()           Get method for featureWidth
org.biomage.DesignElement.Feature	getFromFeatures(int position)           Method to get Feature from Features_list
org.biomage.Description.OntologyEntry	getTechnologyType()           Get method for technologyType
void	removeElementAtFromFeatures(int position)           Method to remove by position from Features_list
void	removeFromFeatures(org.biomage.DesignElement.Feature feature)           Method to remove first Feature from Features_list
void	setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)           Set method for distanceUnit
void	setFeatureHeight(float featureHeight)           Set method for featureHeight
void	setFeatureLength(float featureLength)           Set method for featureLength
void	setFeatures(org.biomage.Interface.HasFeatures.Features_list features)           Set method for features
void	setFeatureShape(org.biomage.Description.OntologyEntry featureShape)           Set method for featureShape
void	setFeatureWidth(float featureWidth)           Set method for featureWidth
void	setTechnologyType(org.biomage.Description.OntologyEntry technologyType)           Set method for technologyType
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.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

featureWidth

float featureWidth

The width of the feature.

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featureLength

float featureLength

The length of the feature.

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featureHeight

float featureHeight

The height of the feature.

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distanceUnit

private org.biomage.Measurement.DistanceUnit distanceUnit

The unit for the feature measures.

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features

private org.biomage.Interface.HasFeatures.Features_list features

The features that belong to this group.

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technologyType

private org.biomage.Description.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.

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featureShape

private org.biomage.Description.OntologyEntry featureShape

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

Constructor Detail

FeatureGroup

public FeatureGroup()

Default constructor.

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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

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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.

Overrides:

writeAttributes in class DesignElementGroup

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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.

Overrides:

writeAssociations in class DesignElementGroup

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setFeatureWidth

public void setFeatureWidth(float featureWidth)

Set method for featureWidth

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getFeatureWidth

public float getFeatureWidth()

Get method for featureWidth

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setFeatureLength

public void setFeatureLength(float featureLength)

Set method for featureLength

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getFeatureLength

public float getFeatureLength()

Get method for featureLength

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setFeatureHeight

public void setFeatureHeight(float featureHeight)

Set method for featureHeight

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getFeatureHeight

public float getFeatureHeight()

Get method for featureHeight

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setDistanceUnit

public void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)

Set method for distanceUnit

Specified by:

setDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

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getDistanceUnit

public org.biomage.Measurement.DistanceUnit getDistanceUnit()

Get method for distanceUnit

Specified by:

getDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

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setFeatures

public void setFeatures(org.biomage.Interface.HasFeatures.Features_list features)

Set method for features

Specified by:

setFeatures in interface org.biomage.Interface.HasFeatures

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getFeatures

public org.biomage.Interface.HasFeatures.Features_list getFeatures()

Get method for features

Specified by:

getFeatures in interface org.biomage.Interface.HasFeatures

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addToFeatures

public void addToFeatures(org.biomage.DesignElement.Feature feature)

Method to add Feature to Features_list

Specified by:

addToFeatures in interface org.biomage.Interface.HasFeatures

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addToFeatures

public void addToFeatures(int position,
                          org.biomage.DesignElement.Feature feature)

Method to add Feature at position to Features_list

Specified by:

addToFeatures in interface org.biomage.Interface.HasFeatures

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getFromFeatures

public org.biomage.DesignElement.Feature getFromFeatures(int position)

Method to get Feature from Features_list

Specified by:

getFromFeatures in interface org.biomage.Interface.HasFeatures

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removeElementAtFromFeatures

public void removeElementAtFromFeatures(int position)

Method to remove by position from Features_list

Specified by:

removeElementAtFromFeatures in interface org.biomage.Interface.HasFeatures

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removeFromFeatures

public void removeFromFeatures(org.biomage.DesignElement.Feature feature)

Method to remove first Feature from Features_list

Specified by:

removeFromFeatures in interface org.biomage.Interface.HasFeatures

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setTechnologyType

public void setTechnologyType(org.biomage.Description.OntologyEntry technologyType)

Set method for technologyType

Specified by:

setTechnologyType in interface org.biomage.Interface.HasTechnologyType

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getTechnologyType

public org.biomage.Description.OntologyEntry getTechnologyType()

Get method for technologyType

Specified by:

getTechnologyType in interface org.biomage.Interface.HasTechnologyType

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setFeatureShape

public void setFeatureShape(org.biomage.Description.OntologyEntry featureShape)

Set method for featureShape

Specified by:

setFeatureShape in interface org.biomage.Interface.HasFeatureShape

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getFeatureShape

public org.biomage.Description.OntologyEntry getFeatureShape()

Get method for featureShape

Specified by:

getFeatureShape in interface org.biomage.Interface.HasFeatureShape

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

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