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

Description

static final Comparator<FeatureInterface<?,?>>

LENGTH

Sort features by length.

static final Comparator<FeatureInterface<?,?>>

LOCATION_LENGTH

Sort features by start position and then longest length.

static final Comparator<FeatureInterface<?,?>>

TYPE

Sort features by type
Constructor Summary

Constructors

Constructor

Description

AbstractFeature(String type, String source)

A feature has a type and a source
Method Summary

Modifier and Type

Method

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 Details
- 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 Details
- AbstractFeature
  
  public AbstractFeature(String type, String source)
  
  A feature has a type and a source
  
  Parameters:
  
  type -
  
  source -
Method Details
- 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>

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

LOCATION_LENGTH

LENGTH

TYPE

Constructor Details

AbstractFeature

Method Details

getLocations

setLocation

getType

setType

getSource

setSource

setParentFeature

getParentFeature

getChildrenFeatures

setChildrenFeatures

getDescription

setDescription

getShortDescription

setShortDescription

getUserObject

setUserObject

getQualifiers

setQualifiers

addQualifier