Class MarkerSerializer


  • public class MarkerSerializer
    extends java.lang.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 Detail

      • MarkerSerializer

        public MarkerSerializer​(Genome genome)
    • Method Detail

      • doNotSave

        public void doNotSave​(Marker m)
      • getIdByMarker

        public int getIdByMarker​(Marker m)
      • getMarkerById

        protected Marker getMarkerById​(int id)
      • getNextField

        public java.lang.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​(java.lang.String fileName)
        Load data from file
      • save

        public java.lang.String save​(java.lang.Iterable<Marker> markersCollection)
        Save all markers
      • save

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

        public void save​(java.lang.String fileName,
                         Markers markers)
        Save data to file