Package org.snpeff.binseq

Class GenomicSequences

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable<MarkerSeq>
    public class GenomicSequences
extends java.lang.Object
implements java.lang.Iterable<MarkerSeq>, java.io.Serializable
    This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval
    Author:
    pcingola
    See Also:
    Serialized Form

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addChromosomeSequence​(java.lang.String chr, java.lang.String chrSeq)
      Create a sequence for the whole chromsome (mostly used in test cases)
      int addGeneSequences​(java.lang.String chr, java.lang.String chrSeq)
      Add sequences for each gene in the genome
      void build()
      Build interval forest
      void clear()  
      boolean hasChromosome​(java.lang.String chr)
      Do we have sequence information for this chromosome?
      boolean isEmpty()  
      java.util.Iterator<MarkerSeq> iterator()  
      boolean load()
      Load sequences for all 'small chromosomes" (from "sequence.bin" file)
      boolean load​(java.lang.String chr)
      Load sequences for a single chromosome (from "sequence.chr.bin" file)
      boolean loadOrCreateFromGenome​(java.lang.String chr)
      Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.
      MarkerSeq queryMarkerSequence​(Marker marker)
      Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database
      java.lang.String querySequence​(Marker marker)
      Get sequence for a marker
      void reset()  
      void save​(Config config)
      Save genomic sequence into separate files (per chromosome)
      void setDisableLoad​(boolean disableLoad)  
      void setVerbose​(boolean verbose)  
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Constructor Detail

      • GenomicSequences

        public GenomicSequences​(Genome genome)

    • Method Detail

      • addChromosomeSequence

        public void addChromosomeSequence​(java.lang.String chr,
                                  java.lang.String chrSeq)
        Create a sequence for the whole chromsome (mostly used in test cases)

      • addGeneSequences

        public int addGeneSequences​(java.lang.String chr,
                            java.lang.String chrSeq)
        Add sequences for each gene in the genome

      • build

        public void build()
        Build interval forest

      • clear

        public void clear()

      • hasChromosome

        public boolean hasChromosome​(java.lang.String chr)
        Do we have sequence information for this chromosome?

      • isEmpty

        public boolean isEmpty()

      • iterator

        public java.util.Iterator<MarkerSeq> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<MarkerSeq>

      • load

        public boolean load()
        Load sequences for all 'small chromosomes" (from "sequence.bin" file)

      • load

        public boolean load​(java.lang.String chr)
        Load sequences for a single chromosome (from "sequence.chr.bin" file)

      • loadOrCreateFromGenome

        public boolean loadOrCreateFromGenome​(java.lang.String chr)
        Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.

      • queryMarkerSequence

        public MarkerSeq queryMarkerSequence​(Marker marker)
        Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database
        Returns:
        A markerSeq containing 'marker' or null if nothing is found

      • querySequence

        public java.lang.String querySequence​(Marker marker)
        Get sequence for a marker

      • reset

        public void reset()

      • save

        public void save​(Config config)
        Save genomic sequence into separate files (per chromosome)

      • setDisableLoad

        public void setDisableLoad​(boolean disableLoad)

      • setVerbose

        public void setVerbose​(boolean verbose)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object