AbstractFeature

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 java.lang.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 java.util.Comparator<FeatureInterface<?,?>>`	`LENGTH` Sort features by length.
`static java.util.Comparator<FeatureInterface<?,?>>`	`LOCATION_LENGTH` Sort features by start position and then longest length.
`static java.util.Comparator<FeatureInterface<?,?>>`	`TYPE` Sort features by type

Constructor Summary

Constructors
Constructor and Description

AbstractFeature(java.lang.String type, java.lang.String source)
A feature has a type and a source

Constructors
Constructor and Description
`AbstractFeature(java.lang.String type, java.lang.String source)` A feature has a type and a source

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addQualifier(java.lang.String key, Qualifier qualifier)` Add a qualifier
`java.util.List<FeatureInterface<S,C>>`	`getChildrenFeatures()` Get the children features
`java.lang.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
`java.util.Map<java.lang.String,java.util.List<Qualifier>>`	`getQualifiers()` Get the qualifiers for this feature
`java.lang.String`	`getShortDescription()` Get the short description that can be used to describe the feature
`java.lang.String`	`getSource()` The feature source
`java.lang.String`	`getType()` The feature type
`java.lang.Object`	`getUserObject()`
`void`	`setChildrenFeatures(java.util.List<FeatureInterface<S,C>> features)` Set the children features
`void`	`setDescription(java.lang.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(java.util.Map<java.lang.String,java.util.List<Qualifier>> qualifiers)` Set the qualifiers
`void`	`setShortDescription(java.lang.String shortDescription)` Set the short description that can be used to describe the feature
`void`	`setSource(java.lang.String source)` Set the feature source
`void`	`setType(java.lang.String type)` Set the feature type
`void`	`setUserObject(java.lang.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 java.util.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 java.util.Comparator<FeatureInterface<?,?>> LENGTH
```
    Sort features by length. //TODO need to handle cases where features have multiple locations, strand etc
  - TYPE
```
public static final java.util.Comparator<FeatureInterface<?,?>> TYPE
```
    Sort features by type
- Constructor Detail
  - AbstractFeature
```
public AbstractFeature(java.lang.String type,
                       java.lang.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 java.lang.String getType()
```
    The feature type
    
    Specified by:
    
    getType in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
    
    Returns:
  - setType
```
public void setType(java.lang.String type)
```
    Set the feature type
    
    Specified by:
    
    setType in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
    
    Parameters:
    
    type -
  - getSource
```
public java.lang.String getSource()
```
    The feature source
    
    Specified by:
    
    getSource in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
    
    Returns:
  - setSource
```
public void setSource(java.lang.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 java.util.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(java.util.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 java.lang.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(java.lang.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 java.lang.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(java.lang.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 java.lang.Object getUserObject()
```
    Specified by:
    
    getUserObject in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
    
    Returns:
    
    the userObject
  - setUserObject
```
public void setUserObject(java.lang.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 java.util.Map<java.lang.String,java.util.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(java.util.Map<java.lang.String,java.util.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(java.lang.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 Detail

LOCATION_LENGTH

LENGTH

TYPE

Constructor Detail

AbstractFeature

Method Detail

getLocations

setLocation

getType

setType

getSource

setSource

setParentFeature

getParentFeature

getChildrenFeatures

setChildrenFeatures

getDescription

setDescription

getShortDescription

setShortDescription

getUserObject

setUserObject

getQualifiers

setQualifiers

addQualifier