org.biojava.nbio.core.sequence.features

Class AbstractFeature<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.features.AbstractFeature<S,C>

All Implemented Interfaces:

FeatureInterface<S,C>

Direct Known Subclasses:

QualityFeature, QuantityFeature, TextFeature

public abstract class AbstractFeature<S extends AbstractSequence<C>,C extends Compound>
extends Object
implements FeatureInterface<S,C>

A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature

Author:

Scooter Willis

Field Summary

Fields

Modifier and Type	Field and Description
static Comparator<FeatureInterface<?,?>>	LENGTH Sort features by length.
static Comparator<FeatureInterface<?,?>>	LOCATION_LENGTH Sort features by start position and then longest length.
static Comparator<FeatureInterface<?,?>>	TYPE Sort features by type

Constructor Summary

Constructors

Constructor and Description
AbstractFeature(String type, String source) A feature has a type and a source

Method Summary

Modifier and Type	Method and Description
void	addQualifier(String key, Qualifier qualifier) Add a qualifier
List<FeatureInterface<S,C>>	getChildrenFeatures() Get the children features
String	getDescription() Get the description that can be used to describe the feature
AbstractLocation	getLocations() A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
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 feature source
String	getType() The feature type
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) A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
void	setParentFeature(FeatureInterface<S,C> feature) A feature can be the child or contained by a 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) Set the feature source
void	setType(String type) Set the feature type
void	setUserObject(Object userObject) Allow the user to associate an object with the feature.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LOCATION_LENGTH

public static final Comparator<FeatureInterface<?,?>> LOCATION_LENGTH

Sort features by start position and then longest length. When features are added having them sorted by start position and then longest length helps on the layout of overlapping features so they are delivered in a proper order.

LENGTH

public static final Comparator<FeatureInterface<?,?>> LENGTH

Sort features by length. //TODO need to handle cases where features have multiple locations, strand etc

TYPE

public static final Comparator<FeatureInterface<?,?>> TYPE

Sort features by type

Constructor Detail

AbstractFeature

public AbstractFeature(String type,
                       String source)

A feature has a type and a source

Parameters:

type -

source -

Method Detail

getLocations

public AbstractLocation getLocations()

A feature could be a single sequence position like a mutation or a post translational modification of an amino acid. It could also be the docking interface of N number of amino acids on the surface. The location wold then be a collection of sequence positions instead of a single sequence position or the begin and end of a sequence segment.

Specified by:

getLocations in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

setLocation

public void setLocation(AbstractLocation loc)

A feature could be a single sequence position like a mutation or a post translational modification of an amino acid. It could also be the docking interface of N number of amino acids on the surface. The location wold then be a collection of sequence positions instead of a single sequence position or the begin and end of a sequence segment.

Specified by:

setLocation in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

loc -

getType

public String getType()

The feature type

Specified by:

getType in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

setType

public void setType(String type)

Set the feature type

Specified by:

setType in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

type -

getSource

public String getSource()

The feature source

Specified by:

getSource in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

setSource

public void setSource(String source)

Set the feature source

Specified by:

setSource in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

source -

setParentFeature

public void setParentFeature(FeatureInterface<S,C> feature)

A feature can be the child or contained by a parent feature. An example is a Helix feature could contain children features. A PFAM domain could contain secondary structures.

Specified by:

setParentFeature in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

feature -

getParentFeature

public FeatureInterface<S,C> getParentFeature()

Get the parent Feature

Specified by:

getParentFeature in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

getChildrenFeatures

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

Get the children features

Specified by:

getChildrenFeatures in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

setChildrenFeatures

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

Set the children features

Specified by:

setChildrenFeatures in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

features -

getDescription

public String getDescription()

Description copied from interface: FeatureInterface

Get the description that can be used to describe the feature

Specified by:

getDescription in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

the description

setDescription

public void setDescription(String description)

Description copied from interface: FeatureInterface

Set the description that can be used to describe the feature

Specified by:

setDescription in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

description - the description to set

getShortDescription

public String getShortDescription()

Description copied from interface: FeatureInterface

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

Specified by:

getShortDescription in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

the shortDescription

setShortDescription

public void setShortDescription(String shortDescription)

Description copied from interface: FeatureInterface

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

Specified by:

setShortDescription in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

shortDescription - the shortDescription to set

getUserObject

public Object getUserObject()

Specified by:

getUserObject in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

the userObject

setUserObject

public void setUserObject(Object userObject)

Allow the user to associate an object with the feature. This way if a feature which is displayed in a GUI is clicked on the application can then get a user defined object associated with the feature.

Specified by:

setUserObject in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Parameters:

userObject - the userObject to set

getQualifiers

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

Description copied from interface: FeatureInterface

Get the qualifiers for this feature

Specified by:

getQualifiers in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

Returns:

setQualifiers

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

Description copied from interface: FeatureInterface

Set the qualifiers

Specified by:

setQualifiers in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>

addQualifier

public void addQualifier(String key,
                         Qualifier qualifier)

Description copied from interface: FeatureInterface

Add a qualifier

Specified by:

addQualifier in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>