Package org.snpeff.serializer

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