Package org.biojava.nbio.genome.parsers.gff

Interface FeatureI

  • All Known Implementing Classes:
    Feature
    public interface FeatureI
    A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
    Author:
    Hanno Hinsch

    • Method Detail

      • location

        Location location()
        Get the location of the feature.
        Returns:
        The location.

      • group

        String group()
        Get the group id of the feature. The group id is defined in the GFF1 format; features that share a common group id are presumed to be part of some logical group. For example, a gene might be represented by several exon features that all share the same group id.

        The exact meaning of a feature's group id, or even its existence, is not guaranteed by this interface. An understanding of a particular file's data format is necessary to properly interpret the group id.
        Returns:
        The group id. This may be an empty string.

      • type

        String type()
        Get the feature type, for example, "exon", "CDS", etc.
        Returns:
        The type.

      • seqname

        String seqname()
        Get the sequence name.
        Returns:
        Sequence name.

      • getAttribute

        String getAttribute​(String key)
        Get the attribute value for this key.
        Parameters:
        key - The key.
        Returns:
        The corresponding value. Null if the key has no value defined .

      • hasAttribute

        boolean hasAttribute​(String key)
        Check if the feature has a value defined for the specified key.
        Parameters:
        key - The key.
        Returns:
        True if a value is defined for this key.

      • hasAttribute

        boolean hasAttribute​(String key,
                     String value)
        Check if the feature attributes include the specified key/value pair.
        Parameters:
        key - The key.
        value - The value.
        Returns:
        True if the feature's value for this key matches the specified value.

      • toString

        String toString()
        A string representation of the feature.
        Overrides:
        toString in class Object
        Returns:
        The string.

      • userData

        HashMap<String,​String> userData()
        Get HashMap of user data.
        Returns:
        The user HashMap.