org.biojava.nbio.core.sequence.features

Interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

All Known Implementing Classes:

AbstractFeature, FeatureDbReferenceInfo, QualityFeature, QuantityFeature, TextFeature

public interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Interface class to handle describing arbitrary features. A feature can be found at multiple locations in a sequence such as the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example. The location in its current form knows the start and stop position in a sequence and thus should contain knowledge about the actual sequence. A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain and other requirements for grouping.

Author:

Scooter Willis , Paolo Pavan

Method Summary

Modifier and Type	Method and Description
void	addQualifier(String key, Qualifier qualifier) Add a qualifier
List<FeatureInterface<S,C>>	getChildrenFeatures() Get the features contained by this feature
String	getDescription() Get the description that can be used to describe the feature
AbstractLocation	getLocations() The location(s) of this feature where the location should contain a reference to parent and sequence etc.
FeatureInterface<S,C>	getParentFeature() Get the parent feature
Map<String,List<Qualifier>>	getQualifiers() Get the qualifiers for this feature
String	getShortDescription() Get the short description that can be used to describe the feature
String	getSource() The source of the feature.
String	getType() The type of the feature.
Object	getUserObject()
void	setChildrenFeatures(List<FeatureInterface<S,C>> features) Set the children features
void	setDescription(String description) Set the description that can be used to describe the feature
void	setLocation(AbstractLocation loc) The new location for this feature.
void	setParentFeature(FeatureInterface<S,C> feature) Set the parent feature
void	setQualifiers(Map<String,List<Qualifier>> qualifiers) Set the qualifiers
void	setShortDescription(String shortDescription) Set the short description that can be used to describe the feature
void	setSource(String source) Change the source of the FeatureInterface.
void	setType(String type) Change the type of this feature.
void	setUserObject(Object userObject)

Method Detail

getShortDescription

String getShortDescription()

Get the short description that can be used to describe the feature

Returns:

setShortDescription

void setShortDescription(String shortDescription)

Set the short description that can be used to describe the feature

Parameters:

shortDescription -

getDescription

String getDescription()

Get the description that can be used to describe the feature

Returns:

setDescription

void setDescription(String description)

Set the description that can be used to describe the feature

getLocations

AbstractLocation getLocations()

The location(s) of this feature where the location should contain a reference to parent and sequence etc.

The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.

Returns:

a Location anchoring this feature

setLocation

void setLocation(AbstractLocation loc)

The new location for this feature.

The location may be complicated or simply a range. The annotation is assumed to apply to the entire region contained within the location. Any values returned from methods that rely on the old location must not be affected.

Parameters:

loc - the new Location for this feature

getType

String getType()

The type of the feature.

Returns:

the type of this sequence

setType

void setType(String type)

Change the type of this feature.

Parameters:

type - new type String

getSource

String getSource()

The source of the feature. This may be a program or process.

Returns:

the source, or generator

setSource

void setSource(String source)

Change the source of the FeatureInterface.

Parameters:

source - the new source String

setParentFeature

void setParentFeature(FeatureInterface<S,C> feature)

Set the parent feature

Parameters:

feature -

getParentFeature

FeatureInterface<S,C> getParentFeature()

Get the parent feature

Returns:

getChildrenFeatures

List<FeatureInterface<S,C>> getChildrenFeatures()

Get the features contained by this feature

Returns:

setChildrenFeatures

void setChildrenFeatures(List<FeatureInterface<S,C>> features)

Set the children features

Parameters:

features -

getUserObject

Object getUserObject()

Returns:

the userObject

setUserObject

void setUserObject(Object userObject)

Parameters:

userObject - the userObject to set

getQualifiers

Map<String,List<Qualifier>> getQualifiers()

Get the qualifiers for this feature

Returns:

setQualifiers

void setQualifiers(Map<String,List<Qualifier>> qualifiers)

Set the qualifiers

Parameters:

qualifiers -

addQualifier

void addQualifier(String key,
                  Qualifier qualifier)

Add a qualifier

Parameters:

qualifier -