Package org.snpeff.interval

Class Genes

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable<Gene>
    public class Genes
extends java.lang.Object
implements java.lang.Iterable<Gene>, java.io.Serializable
    A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genome
    Author:
    pcingola
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      boolean debug  

    • Constructor Summary

      Constructors 
      Constructor Description
      Genes​(Genome genome)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(Gene gene)
      Add a gene interval to this collection
      void createCircularGenes()
      In a circular genome, a gene can have negative coordinates or crosses over chromosome end.
      java.util.List<Intergenic> createIntergenic()
      Creates a list of Intergenic regions
      void createSpliceSites​(int spliceSiteSize, int spliceRegionExonSize, int spliceRegionIntronMin, int spliceRegionIntronMax)
      Create splice sites.
      java.util.List<Marker> createUpDownStream​(int upDownLength)
      Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is created
      Transcript findTranscript​(java.lang.String trId)
      Find a transcript by ID
      Gene get​(java.lang.String geneId)
      Obtain a gene interval
      Gene getGeneByName​(java.lang.String geneName)
      Obtain a gene by GeneName WARNING: The first match is returned.
      java.util.Iterator<Gene> iterator()  
      int size()  
      java.util.Collection<Gene> sorted()  
      java.lang.String toString()  
      java.util.Collection<Gene> values()  

      • 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

    • Field Detail

      • debug

        public boolean debug

    • Constructor Detail

      • Genes

        public Genes​(Genome genome)

    • Method Detail

      • add

        public void add​(Gene gene)
        Add a gene interval to this collection

      • createCircularGenes

        public void createCircularGenes()
        In a circular genome, a gene can have negative coordinates or crosses over chromosome end. These genes are mirrored to the opposite end of the chromosome so that they can be referenced by both circular coordinates.

      • createIntergenic

        public java.util.List<Intergenic> createIntergenic()
        Creates a list of Intergenic regions

      • createSpliceSites

        public void createSpliceSites​(int spliceSiteSize,
                              int spliceRegionExonSize,
                              int spliceRegionIntronMin,
                              int spliceRegionIntronMax)
        Create splice sites.
        Parameters:
        createIfMissing - : If true, create canonical splice sites if they are missing. For a definition of splice site, see comments at the beginning of SpliceSite.java

      • createUpDownStream

        public java.util.List<Marker> createUpDownStream​(int upDownLength)
        Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript Note: If upDownLength <=0 no interval is created

      • findTranscript

        public Transcript findTranscript​(java.lang.String trId)
        Find a transcript by ID

      • get

        public Gene get​(java.lang.String geneId)
        Obtain a gene interval

      • getGeneByName

        public Gene getGeneByName​(java.lang.String geneName)
        Obtain a gene by GeneName WARNING: The first match is returned. If multiple genes share the same gene name, no order can be expected for this method.

      • iterator

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

      • size

        public int size()

      • sorted

        public java.util.Collection<Gene> sorted()

      • toString

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

      • values

        public java.util.Collection<Gene> values()