Package org.snpeff.interval

Class GffMarker

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Custom
org.snpeff.interval.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:

  • Field Details

  • 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()

    • getProteinId

      public String getProteinId()

    • getTranscriptBiotype

      public BioType getTranscriptBiotype()

    • getTags

      public String getTags()

    • getTranscriptTsl

      public String getTranscriptTsl()

    • 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)

    • isMultipleValues

      public boolean isMultipleValues(String key)
      Does the key have mutiple values

    • 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