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java.lang.Objectorg.biojava3.core.sequence.features.AbstractFeature<S,C>
public abstract class AbstractFeature<S extends AbstractSequence<C>,C extends Compound>
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
Field Summary | |
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static Comparator<FeatureInterface<?,?>> |
LENGTH
Sort features by length. |
static Comparator<FeatureInterface<?,?>> |
LOCATION_LENGTH
Sort features by start position and then longest length. |
Constructor Summary | |
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AbstractFeature(String type,
String source)
A feature has a type and a source |
Method Summary | |
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List<FeatureInterface<S,C>> |
getChildrenFeatures()
Get the children features |
String |
getDescription()
Get the description that can be used to describe the feature |
SequenceLocation<S,C> |
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 |
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(SequenceLocation<S,C> 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 |
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final Comparator<FeatureInterface<?,?>> LOCATION_LENGTH
public static final Comparator<FeatureInterface<?,?>> LENGTH
Constructor Detail |
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public AbstractFeature(String type, String source)
type
- source
- Method Detail |
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public SequenceLocation<S,C> getLocations()
getLocations
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setLocation(SequenceLocation<S,C> loc)
setLocation
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
loc
- public String getType()
getType
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setType(String type)
setType
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
type
- public String getSource()
getSource
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setSource(String source)
setSource
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
source
- public void setParentFeature(FeatureInterface<S,C> feature)
setParentFeature
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
feature
- public FeatureInterface<S,C> getParentFeature()
getParentFeature
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public List<FeatureInterface<S,C>> getChildrenFeatures()
getChildrenFeatures
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setChildrenFeatures(List<FeatureInterface<S,C>> features)
setChildrenFeatures
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
features
- public String getDescription()
FeatureInterface
getDescription
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setDescription(String description)
FeatureInterface
setDescription
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
description
- the description to setpublic String getShortDescription()
FeatureInterface
getShortDescription
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setShortDescription(String shortDescription)
FeatureInterface
setShortDescription
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
shortDescription
- the shortDescription to setpublic Object getUserObject()
getUserObject
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
public void setUserObject(Object userObject)
setUserObject
in interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
userObject
- the userObject to set
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