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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.
Method Summary | |
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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 |
SequenceLocation<S,C> |
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 |
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(SequenceLocation<S,C> loc)
The new location for this feature. |
void |
setParentFeature(FeatureInterface<S,C> feature)
Set the parent feature |
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)
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Method Detail |
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String getShortDescription()
void setShortDescription(String shortDescription)
shortDescription
- String getDescription()
void setDescription(String description)
SequenceLocation<S,C> getLocations()
The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.
void setLocation(SequenceLocation<S,C> loc)
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.
loc
- the new Location for this featureString getType()
void setType(String type)
type
- new type StringString getSource()
void setSource(String source)
source
- the new source Stringvoid setParentFeature(FeatureInterface<S,C> feature)
feature
- FeatureInterface<S,C> getParentFeature()
List<FeatureInterface<S,C>> getChildrenFeatures()
void setChildrenFeatures(List<FeatureInterface<S,C>> features)
features
- Object getUserObject()
void setUserObject(Object userObject)
userObject
- the userObject to set
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