Class SimpleGFFRecord

  • All Implemented Interfaces:
    GFFRecord

    public class SimpleGFFRecord
    extends Object
    implements GFFRecord
    A no-frills implementation of a GFFRecord.
    Author:
    Matthew Pocock, Greg Cox, Aroul Ramadass, Len Trigg, Richard Holland
    • Method Detail

      • setSeqName

        public void setSeqName​(String seqName)
        Set the sequence name to seqName.
        Parameters:
        seqName - the new name
      • getSeqName

        public String getSeqName()
        Description copied from interface: GFFRecord
        The sequence name field.

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

        Specified by:
        getSeqName in interface GFFRecord
        Returns:
        the name of the sequence
      • setSource

        public void setSource​(String source)
        Set the feature source to source.
        Parameters:
        source - the new source
      • getSource

        public String getSource()
        Description copied from interface: GFFRecord
        The source, or creator of this feature.

        This is usualy a program name.

        Specified by:
        getSource in interface GFFRecord
        Returns:
        the feature source
      • setFeature

        public void setFeature​(String feature)
        Set the feature type to type.
        Parameters:
        feature - the new feature type
      • getFeature

        public String getFeature()
        Description copied from interface: GFFRecord
        The feature type filed.

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

        Specified by:
        getFeature in interface GFFRecord
        Returns:
        the feature type
      • setStart

        public void setStart​(int start)
        Set the start coordinate to start.
        Parameters:
        start - the new start coordinate
      • getStart

        public int getStart()
        Description copied from interface: GFFRecord
        The start of this feature within the source sequence.
        Specified by:
        getStart in interface GFFRecord
        Returns:
        the start index
      • setEnd

        public void setEnd​(int end)
        Set the end coordinate to end.
        Parameters:
        end - the new end coordinate
      • getEnd

        public int getEnd()
        Description copied from interface: GFFRecord
        The end of this feature within the source sequence.
        Specified by:
        getEnd in interface GFFRecord
        Returns:
        the end index
      • setScore

        public void setScore​(double score)
        Set the score to score.

        The score must be a double, inclusive of 0. If you wish to indicate that there is no score, then use GFFRecord.NO_SCORE.

        Parameters:
        score - the new score
      • getScore

        public double getScore()
        Description copied from interface: GFFRecord
        The score of the feature.

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

        Specified by:
        getScore in interface GFFRecord
        Returns:
        the score, or NO_SCORE
      • getStrand

        public StrandedFeature.Strand getStrand()
        Description copied from interface: GFFRecord
        The strand of the feature.

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

        Specified by:
        getStrand in interface GFFRecord
        Returns:
        the strand field
      • setFrame

        public void setFrame​(int frame)
        Set the frame to frame.

        The score must be one of {0, 1, 2} or GFFRecord.NO_FRAME.

        Parameters:
        frame - the frame
        Throws:
        IllegalArgumentException - if score is not valid.
      • getFrame

        public int getFrame()
        Description copied from interface: GFFRecord
        The frame of the feature.

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

        Specified by:
        getFrame in interface GFFRecord
        Returns:
        the frame field
      • setGroupAttributes

        public void setGroupAttributes​(Map ga)
        Replace the group-attribute Map with ga.

        To efficiently add a key, call getGroupAttributes() and modify the Map.

        Parameters:
        ga - the new group-attribute Map
      • getGroupAttributes

        public Map getGroupAttributes()
        Description copied from interface: GFFRecord
        A Map containing the group / attribute information.

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

        Specified by:
        getGroupAttributes in interface GFFRecord
        Returns:
        a Map containing the group and attribute info.
      • setComment

        public void setComment​(String comment)
        Set the comment to comment.

        If you set it to null, then the comment for this line will be ignored.

        Parameters:
        comment - the new comment
      • stringifyAttributes

        public static String stringifyAttributes​(Map attMap)
        Create a String representation of attMap. attMap is assumed to contain String keys and List values.
        Parameters:
        attMap - the Map of attributes and value lists
        Returns:
        a GFF attribute/value String