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

Description

FeatureDbReferenceInfo(String database, String id)
Method Summary

Modifier and Type

Method

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)

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 Details
- FeatureDbReferenceInfo
  
  public FeatureDbReferenceInfo(String database, String id)
Method Details
- 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 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>

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Constructor Details

FeatureDbReferenceInfo

Method Details

getShortDescription

setShortDescription

getDescription

setDescription

getLocations

setLocation

getType

setType

getSource

setSource

setParentFeature

getParentFeature

getChildrenFeatures

setChildrenFeatures

getUserObject

setUserObject

getQualifiers

setQualifiers

addQualifier