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 Details

    • 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.

    • getAttributes

      HashMap<String,String> getAttributes()