Class GffMarker

All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, Iterable<KeyValue<String,String>>, TxtSerializable
Direct Known Subclasses:
Gtf2Marker

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

    • GffMarker

      public GffMarker()
    • GffMarker

      public GffMarker(Genome genome, String line)
    • GffMarker

      public GffMarker(Marker parent, int start, int end, boolean strandMinus, String id)
  • Method Details

    • canParseLine

      public static boolean canParseLine(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(String key, String value)
      Add key value pair
    • getAttr

      public String getAttr(String key)
    • getBiotype

      public BioType getBiotype()
    • getBioType

      protected String getBioType()
    • getBiotypeGeneric

      protected BioType getBiotypeGeneric()
    • getFrame

      public int getFrame()
    • getGeneBiotype

      public BioType getGeneBiotype()
    • getGeneId

      public String getGeneId()
    • getGeneName

      public String getGeneName()
    • getGffParentId

      public String getGffParentId(boolean doNotRecurse)
    • getGffParentIds

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

      public GffType getGffType()
    • getTranscriptBiotype

      public BioType getTranscriptBiotype()
    • getTranscriptId

      public String getTranscriptId()
    • getTranscriptVersion

      public 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(String key)
    • isProteingCoding

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

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

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

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

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

      public String toString()
      Overrides:
      toString in class Custom