org.biojava.nbio.core.sequence.features

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

java.lang.Object

org.biojava.nbio.core.sequence.features.Qualifier

org.biojava.nbio.core.sequence.features.DBReferenceInfo

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

Type Parameters:

S -

C -

All Implemented Interfaces:

FeatureInterface<S,C>

public class FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound>
extends DBReferenceInfo
implements FeatureInterface<S,C>

It is DBReferenceInfo which implements FeatureInterface. It allows to keep a dbReferenceInfo as a feature.

Author:

Jacek Grzebyta, Paolo Pavan

Constructor Summary

Constructors

Constructor and Description
FeatureDbReferenceInfo(String database, String id)

Method Summary

Methods

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
HashMap<String,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(HashMap<String,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)

Methods inherited from class org.biojava.nbio.core.sequence.features.DBReferenceInfo

addProperty, getDatabase, getId, getProperties, setDatabase, setId, setProperties, toString

Methods inherited from class org.biojava.nbio.core.sequence.features.Qualifier

getName, getValue, needsQuotes, setName, setNeedsQuotes, setValue

Methods inherited from class java.lang.Object

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

Constructor Detail

FeatureDbReferenceInfo

public FeatureDbReferenceInfo(String database,
                      String id)

Method Detail

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:

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>

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:

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>

getLocations

public AbstractLocation getLocations()

Description copied from interface: FeatureInterface

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.

Specified by:

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

Returns:

a Location anchoring this feature

setLocation

public void setLocation(AbstractLocation loc)

Description copied from interface: FeatureInterface

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.

Specified by:

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

Parameters:

loc - the new Location for this feature

getType

public String getType()

Description copied from interface: FeatureInterface

The type of the feature.

Specified by:

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

Returns:

the type of this sequence

setType

public void setType(String type)

Description copied from interface: FeatureInterface

Change the type of this feature.

Specified by:

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

Parameters:

type - new type String

getSource

public String getSource()

Description copied from interface: FeatureInterface

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

Specified by:

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

Returns:

the source, or generator

setSource

public void setSource(String source)

Description copied from interface: FeatureInterface

Change the source of the FeatureInterface.

Specified by:

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

Parameters:

source - the new source String

setParentFeature

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

Description copied from interface: FeatureInterface

Set the parent feature

Specified by:

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

getParentFeature

public FeatureInterface<S,C> getParentFeature()

Description copied from interface: FeatureInterface

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()

Description copied from interface: FeatureInterface

Get the features contained by this feature

Specified by:

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

Returns:

setChildrenFeatures

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

Description copied from interface: FeatureInterface

Set the children features

Specified by:

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

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)

Specified by:

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

Parameters:

userObject - the userObject to set

getQualifiers

public HashMap<String,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(HashMap<String,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>