org.biomage.DesignElement
Class FeatureInformation

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.DesignElement.FeatureInformation

All Implemented Interfaces:

HasFeature, HasMismatchInformation, HasPropertySets, java.io.Serializable

public class FeatureInformation

extends Extendable

implements java.io.Serializable, HasFeature, HasMismatchInformation

As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter. Useful for control purposes such as in Affymetrix probe pairs.

See Also:

Serialized Form

Nested Class Summary

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

HasMismatchInformation.MismatchInformation_list

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

HasPropertySets.PropertySets_list

Field Summary

protected Feature	feature The feature the FeatureInformation is supplying information for.
protected HasMismatchInformation.MismatchInformation_list	mismatchInformation Differences in how the feature matches the reporter's sequence, typical examples is the Affymetrix probe pair where one of the features is printed with a mismatch to the other feature's perfect match.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

FeatureInformation()
Default constructor.

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

Method Summary

void	addToMismatchInformation(int position, MismatchInformation mismatchInformation) Method to add MismatchInformation at position to MismatchInformation_list
void	addToMismatchInformation(MismatchInformation mismatchInformation) Method to add MismatchInformation to MismatchInformation_list
Feature	getFeature() Get method for feature
MismatchInformation	getFromMismatchInformation(int position) Method to get MismatchInformation from MismatchInformation_list
HasMismatchInformation.MismatchInformation_list	getMismatchInformation() Get method for mismatchInformation
void	removeElementAtFromMismatchInformation(int position) Method to remove by position from MismatchInformation_list
void	removeFromMismatchInformation(MismatchInformation mismatchInformation) Method to remove first MismatchInformation from MismatchInformation_list
void	setFeature(Feature feature) Set method for feature
void	setMismatchInformation(HasMismatchInformation.MismatchInformation_list mismatchInformation) Set method for mismatchInformation
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.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

feature

protected Feature feature

The feature the FeatureInformation is supplying information for.

mismatchInformation

protected HasMismatchInformation.MismatchInformation_list mismatchInformation

Differences in how the feature matches the reporter's sequence, typical examples is the Affymetrix probe pair where one of the features is printed with a mismatch to the other feature's perfect match.

Constructor Detail

FeatureInformation

public FeatureInformation()

Default constructor.

FeatureInformation

public FeatureInformation(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 Extendable

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 Extendable

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 Extendable

java.io.IOException

setFeature

public void setFeature(Feature feature)

Set method for feature

Specified by:

setFeature in interface HasFeature

getFeature

public Feature getFeature()

Get method for feature

Specified by:

getFeature in interface HasFeature

Returns:

value of the attribute

setMismatchInformation

public void setMismatchInformation(HasMismatchInformation.MismatchInformation_list mismatchInformation)

Set method for mismatchInformation

Specified by:

setMismatchInformation in interface HasMismatchInformation

getMismatchInformation

public HasMismatchInformation.MismatchInformation_list getMismatchInformation()

Get method for mismatchInformation

Specified by:

getMismatchInformation in interface HasMismatchInformation

Returns:

value of the attribute

addToMismatchInformation

public void addToMismatchInformation(MismatchInformation mismatchInformation)

Method to add MismatchInformation to MismatchInformation_list

Specified by:

addToMismatchInformation in interface HasMismatchInformation

addToMismatchInformation

public void addToMismatchInformation(int position,
                                     MismatchInformation mismatchInformation)

Method to add MismatchInformation at position to MismatchInformation_list

Specified by:

addToMismatchInformation in interface HasMismatchInformation

getFromMismatchInformation

public MismatchInformation getFromMismatchInformation(int position)

Method to get MismatchInformation from MismatchInformation_list

Specified by:

getFromMismatchInformation in interface HasMismatchInformation

removeElementAtFromMismatchInformation

public void removeElementAtFromMismatchInformation(int position)

Method to remove by position from MismatchInformation_list

Specified by:

removeElementAtFromMismatchInformation in interface HasMismatchInformation

removeFromMismatchInformation

public void removeFromMismatchInformation(MismatchInformation mismatchInformation)

Method to remove first MismatchInformation from MismatchInformation_list

Specified by:

removeFromMismatchInformation in interface HasMismatchInformation