Class MarkerSerializer

java.lang.Object
org.snpeff.serializer.MarkerSerializer

public class MarkerSerializer extends Object
Serialize markers to (and from) file

Note: Marker's children are serialized first (e.g. a transcript get all exons serialized first).

Note: Since Marker is a tree-like structure, we first load all the markers and then assign parents. Markers are assigned a fake parent object (MarkerParentId) which is later replaced by the 'real' parent.

Note: All 'IDs' used have not meaning outside this serialization process.

Author:
pcingola
  • Constructor Details

    • MarkerSerializer

      public MarkerSerializer(Genome genome)
  • Method Details

    • doNotSave

      public void doNotSave(Marker m)
    • getById

      protected TxtSerializable getById(int id)
    • getIdByMarker

      public int getIdByMarker(Marker m)
    • getMarkerById

      protected Marker getMarkerById(int id)
    • getNextField

      public String getNextField()
    • getNextFieldBoolean

      public boolean getNextFieldBoolean()
    • getNextFieldInt

      public int getNextFieldInt()
    • getNextFieldMarker

      public Marker getNextFieldMarker()
    • getNextFieldMarkers

      public Markers getNextFieldMarkers()
    • getNextId

      protected int getNextId()
    • load

      public Markers load(String fileName)
      Load data from file
    • save

      public String save(Iterable<Marker> markersCollection)
      Save all markers
    • save

      public int save(Marker m)
      Save a marker
    • save

      public void save(String fileName, Markers markers)
      Save data to file