Interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
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- All Known Implementing Classes:
AbstractFeature
,FeatureDbReferenceInfo
,QualityFeature
,QuantityFeature
,TextFeature
public interface FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
Interface class to handle describing arbitrary features. A feature can be found at multiple locations in a sequence such as the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example. The location in its current form knows the start and stop position in a sequence and thus should contain knowledge about the actual sequence. A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain and other requirements for grouping.- Author:
- Scooter Willis
, Paolo Pavan
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addQualifier(String key, Qualifier qualifier)
Add a qualifierList<FeatureInterface<S,C>>
getChildrenFeatures()
Get the features contained by this featureString
getDescription()
Get the description that can be used to describe the featureAbstractLocation
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 featureMap<String,List<Qualifier>>
getQualifiers()
Get the qualifiers for this featureString
getShortDescription()
Get the short description that can be used to describe the featureString
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 featuresvoid
setDescription(String description)
Set the description that can be used to describe the featurevoid
setLocation(AbstractLocation loc)
The new location for this feature.void
setParentFeature(FeatureInterface<S,C> feature)
Set the parent featurevoid
setQualifiers(Map<String,List<Qualifier>> qualifiers)
Set the qualifiersvoid
setShortDescription(String shortDescription)
Set the short description that can be used to describe the featurevoid
setSource(String source)
Change the source of the FeatureInterface.void
setType(String type)
Change the type of this feature.void
setUserObject(Object userObject)
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Method Detail
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getShortDescription
String getShortDescription()
Get the short description that can be used to describe the feature- Returns:
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setShortDescription
void setShortDescription(String shortDescription)
Set the short description that can be used to describe the feature- Parameters:
shortDescription
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getDescription
String getDescription()
Get the description that can be used to describe the feature- Returns:
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setDescription
void setDescription(String description)
Set the description that can be used to describe the feature
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getLocations
AbstractLocation getLocations()
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.
- Returns:
- a Location anchoring this feature
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setLocation
void setLocation(AbstractLocation loc)
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.
- Parameters:
loc
- the new Location for this feature
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setType
void setType(String type)
Change the type of this feature.- Parameters:
type
- new type String
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getSource
String getSource()
The source of the feature. This may be a program or process.- Returns:
- the source, or generator
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setSource
void setSource(String source)
Change the source of the FeatureInterface.- Parameters:
source
- the new source String
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setParentFeature
void setParentFeature(FeatureInterface<S,C> feature)
Set the parent feature- Parameters:
feature
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getParentFeature
FeatureInterface<S,C> getParentFeature()
Get the parent feature- Returns:
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getChildrenFeatures
List<FeatureInterface<S,C>> getChildrenFeatures()
Get the features contained by this feature- Returns:
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setChildrenFeatures
void setChildrenFeatures(List<FeatureInterface<S,C>> features)
Set the children features- Parameters:
features
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getUserObject
Object getUserObject()
- Returns:
- the userObject
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setUserObject
void setUserObject(Object userObject)
- Parameters:
userObject
- the userObject to set
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getQualifiers
Map<String,List<Qualifier>> getQualifiers()
Get the qualifiers for this feature- Returns:
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setQualifiers
void setQualifiers(Map<String,List<Qualifier>> qualifiers)
Set the qualifiers- Parameters:
qualifiers
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addQualifier
void addQualifier(String key, Qualifier qualifier)
Add a qualifier- Parameters:
qualifier
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