Package org.biojava.nbio.core.sequence.features

Interface FeatureInterface<S extends AbstractSequence<C>,​C extends Compound>

  • 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

    • Method Detail

      • getShortDescription

        java.lang.String getShortDescription()
        Get the short description that can be used to describe the feature
        Returns:

      • setShortDescription

        void setShortDescription​(java.lang.String shortDescription)
        Set the short description that can be used to describe the feature
        Parameters:
        shortDescription -

      • getDescription

        java.lang.String getDescription()
        Get the description that can be used to describe the feature
        Returns:

      • setDescription

        void setDescription​(java.lang.String description)
        Set the description that can be used to describe the feature

      • 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

      • 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

      • getType

        java.lang.String getType()
        The type of the feature.
        Returns:
        the type of this sequence

      • setType

        void setType​(java.lang.String type)
        Change the type of this feature.
        Parameters:
        type - new type String

      • getSource

        java.lang.String getSource()
        The source of the feature. This may be a program or process.
        Returns:
        the source, or generator

      • setSource

        void setSource​(java.lang.String source)
        Change the source of the FeatureInterface.
        Parameters:
        source - the new source String

      • setParentFeature

        void setParentFeature​(FeatureInterface<S,​C> feature)
        Set the parent feature
        Parameters:
        feature -

      • getParentFeature

        FeatureInterface<S,​C> getParentFeature()
        Get the parent feature
        Returns:

      • getChildrenFeatures

        java.util.List<FeatureInterface<S,​C>> getChildrenFeatures()
        Get the features contained by this feature
        Returns:

      • setChildrenFeatures

        void setChildrenFeatures​(java.util.List<FeatureInterface<S,​C>> features)
        Set the children features
        Parameters:
        features -

      • getUserObject

        java.lang.Object getUserObject()
        Returns:
        the userObject

      • setUserObject

        void setUserObject​(java.lang.Object userObject)
        Parameters:
        userObject - the userObject to set

      • getQualifiers

        java.util.Map<java.lang.String,​java.util.List<Qualifier>> getQualifiers()
        Get the qualifiers for this feature
        Returns:

      • setQualifiers

        void setQualifiers​(java.util.Map<java.lang.String,​java.util.List<Qualifier>> qualifiers)
        Set the qualifiers
        Parameters:
        qualifiers -

      • addQualifier

        void addQualifier​(java.lang.String key,
                  Qualifier qualifier)
        Add a qualifier
        Parameters:
        qualifier -