Package org.biojava.bio.program.gff

Interface GFFRecord

All Known Implementing Classes:
SimpleGFFRecord
public interface GFFRecord
A single GFF record.

This object has fields for each GFF field. It also defines a couple of useful constants.

GFF is described at http://www.sanger.ac.uk/Software/formats/GFF/

Author:
Matthew Pocock, Keith James (docs)

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final Comparator
    NATURAL_ORDER
    Comparator which defines a useful sort order for GFF records.
    static final int
    NO_FRAME
    Deprecated.
    Use GFFTools.NO_FRAME instead
    static final double
    NO_SCORE
    Deprecated.
    Use GFFTools.NO_SCORE instead

  • Method Summary

    Modifier and Type
    Method
    Description
    String
    getComment()
    The feature comment.
    int
    getEnd()
    The end of this feature within the source sequence.
    String
    getFeature()
    The feature type filed.
    int
    getFrame()
    The frame of the feature.
    Map
    getGroupAttributes()
    A Map containing the group / attribute information.
    double
    getScore()
    The score of the feature.
    String
    getSeqName()
    The sequence name field.
    String
    getSource()
    The source, or creator of this feature.
    int
    getStart()
    The start of this feature within the source sequence.
    StrandedFeature.Strand
    getStrand()
    The strand of the feature.

  • Field Details

    • NO_SCORE

      static final double NO_SCORE
      Deprecated.
      Use GFFTools.NO_SCORE instead
      Flag to indicate that there is no score info.

    • NO_FRAME

      static final int NO_FRAME
      Deprecated.
      Use GFFTools.NO_FRAME instead
      Flag to indicate that there is no frame info.

    • NATURAL_ORDER

      static final Comparator NATURAL_ORDER
      Comparator which defines a useful sort order for GFF records. GFFRecord properties are considered in the following order
      1. Sequence name
      2. Feature start
      3. Feature end
      4. Feature type
      5. Feature source
      6. The complete GFF line corresponding to this record

      Two records are equal iff their GFF lines are character-for-character identical.

      Since:
      1.4

  • Method Details

    • getSeqName

      String getSeqName()
      The sequence name field.

      This should be the name of the sequence that this GFF record is within.

      Returns:
      the name of the sequence

    • getSource

      String getSource()
      The source, or creator of this feature.

      This is usualy a program name.

      Returns:
      the feature source

    • getFeature

      String getFeature()
      The feature type filed.

      This is something like "exon" - usualy corresponds to an EMBL term.

      Returns:
      the feature type

    • getStart

      int getStart()
      The start of this feature within the source sequence.
      Returns:
      the start index

    • getEnd

      int getEnd()
      The end of this feature within the source sequence.
      Returns:
      the end index

    • getScore

      double getScore()
      The score of the feature.

      For sequences that have no score, this will be set to GFFRecord.NO_SCORE.

      Returns:
      the score, or NO_SCORE

    • getStrand

      StrandedFeature.Strand getStrand()
      The strand of the feature.

      This will be one of GFFRecord.POSITIVE_STRAND, GFFRecord.NEGATIVE_STRAND, or GFFRecord.NO_STRAND.

      Returns:
      the strand field

    • getFrame

      int getFrame()
      The frame of the feature.

      This will be one of {1, 2, 3} or GFFRecord.NO_FRAME.

      Returns:
      the frame field

    • getGroupAttributes

      Map getGroupAttributes()
      A Map containing the group / attribute information.

      This will be a Map of group-names to List objects.

      Returns:
      a Map containing the group and attribute info.

    • getComment

      String getComment()
      The feature comment.
      Returns:
      null or the feature comment