Class GffMarker

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, java.lang.Iterable<KeyValue<java.lang.String,​java.lang.String>>, TxtSerializable
    Direct Known Subclasses:
    Gtf2Marker

    public class GffMarker
    extends Custom
    An interval intended as a mark
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • GffMarker

        public GffMarker()
      • GffMarker

        public GffMarker​(Genome genome,
                         java.lang.String line)
      • GffMarker

        public GffMarker​(Marker parent,
                         int start,
                         int end,
                         boolean strandMinus,
                         java.lang.String id)
    • Method Detail

      • canParseLine

        public static boolean canParseLine​(java.lang.String line)
        Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expected
      • add

        public void add​(java.lang.String key,
                        java.lang.String value)
        Add key value pair
      • getAttr

        public java.lang.String getAttr​(java.lang.String key)
      • getBiotype

        public BioType getBiotype()
      • getBioType

        protected java.lang.String getBioType()
      • getBiotypeGeneric

        protected BioType getBiotypeGeneric()
      • getFrame

        public int getFrame()
      • getGeneBiotype

        public BioType getGeneBiotype()
      • getGeneId

        public java.lang.String getGeneId()
      • getGeneName

        public java.lang.String getGeneName()
      • getGffParentId

        public java.lang.String getGffParentId​(boolean fromGeneId)
      • getGffParentIds

        public java.lang.String[] getGffParentIds()
        Parent can have multiple, comma separated entries
      • getGffType

        public GffType getGffType()
      • getTranscriptBiotype

        public BioType getTranscriptBiotype()
      • getTranscriptId

        public java.lang.String getTranscriptId()
      • getTranscriptVersion

        public java.lang.String getTranscriptVersion()
      • hasAnnotations

        public boolean hasAnnotations()
        When annotating a VCF file, add fields from this GFF
        Overrides:
        hasAnnotations in class Custom
      • hasAttr

        public boolean hasAttr​(java.lang.String key)
      • isProteingCoding

        public boolean isProteingCoding()
        Is biotType considered 'protein coding'?
      • iterator

        public java.util.Iterator<KeyValue<java.lang.String,​java.lang.String>> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<KeyValue<java.lang.String,​java.lang.String>>
        Overrides:
        iterator in class Custom
      • parse

        protected void parse​(Genome genome,
                             java.lang.String line)
        Parse an entry (line) from a GFF file
      • parseAttributes

        protected void parseAttributes​(java.lang.String attrStr)
        Parse attributes (key-value pairs) from a line in a GFF file
      • parseId

        protected java.lang.String parseId()
        Obtain or create an ID
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class Custom