Package org.snpeff.interval

Class Interval

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>
    Direct Known Subclasses:
    Marker
    public class Interval
extends java.lang.Object
implements java.lang.Comparable<Interval>, java.io.Serializable, java.lang.Cloneable
    A genomic interval.

    Note: Intervals are assumed to be zero-based and inclusive i.e. an interval including the first base up to base X would be [0,X] NOT [1,X]

    Author:
    pcingola
    See Also:
    Serialized Form

    • Field Detail

      • start

        protected int start

      • end

        protected int end

      • strandMinus

        protected boolean strandMinus

      • id

        protected java.lang.String id

      • chromosomeNameOri

        protected java.lang.String chromosomeNameOri

    • Constructor Detail

      • Interval

        protected Interval()

      • Interval

        public Interval​(Interval parent,
                int start,
                int end,
                boolean strandMinus,
                java.lang.String id)

    • Method Detail

      • clone

        public Interval clone()
        Overrides:
        clone in class java.lang.Object

      • compareTo

        public int compareTo​(Interval i2)
        Compare by start and end
        Specified by:
        compareTo in interface java.lang.Comparable<Interval>

      • equals

        public boolean equals​(Interval interval)

      • findParent

        public Interval findParent​(java.lang.Class clazz)
        Go up (parent) until we find an instance of 'clazz'

      • getChromosome

        public Chromosome getChromosome()

      • getChromosomeName

        public java.lang.String getChromosomeName()
        Find chromosome name

      • getChromosomeNameOri

        public java.lang.String getChromosomeNameOri()

      • setChromosomeNameOri

        public void setChromosomeNameOri​(java.lang.String chromosomeNameOri)

      • getChromosomeNum

        public double getChromosomeNum()
        Find chromosome and return it's number
        Returns:
        Chromosome number if found, -1 otherwise

      • getEnd

        public int getEnd()

      • setEnd

        public void setEnd​(int end)

      • getGenome

        public Genome getGenome()
        Find genome

      • getGenomeName

        public java.lang.String getGenomeName()
        Find genome name

      • getId

        public java.lang.String getId()

      • setId

        public void setId​(java.lang.String id)

      • getParent

        public Interval getParent()

      • setParent

        public void setParent​(Interval parent)

      • getStart

        public int getStart()

      • setStart

        public void setStart​(int start)

      • getStrand

        public java.lang.String getStrand()

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • intersects

        public boolean intersects​(int iStart,
                          int iEnd)
        Return true if this intersects '[iStart, iEnd]'

      • intersects

        public boolean intersects​(Interval interval)
        Return true if this intersects 'interval'

      • intersects

        public boolean intersects​(long point)
        Returns:
        true if this interval contains point (inclusive)

      • intersects

        public boolean intersects​(Marker interval)
        Do the intervals intersect?
        Returns:
        return true if this intersects 'interval'

      • intersectSize

        public int intersectSize​(Marker interval)
        How much do intervals intersect?
        Returns:
        number of bases these intervals intersect

      • isCircular

        public boolean isCircular()
        Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?

      • isSameChromo

        public boolean isSameChromo​(Marker interval)

      • isStrandMinus

        public boolean isStrandMinus()

      • setStrandMinus

        public void setStrandMinus​(boolean strand)

      • isStrandPlus

        public boolean isStrandPlus()

      • isValid

        public boolean isValid()

      • shiftCoordinates

        public void shiftCoordinates​(int shift)

      • size

        public int size()

      • toStr

        public java.lang.String toStr()
        To string as a simple "chr:start-end" format

      • toString

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

      • toStringAsciiArt

        public java.lang.String toStringAsciiArt​(int maxLen)
        Show it as an ASCII art

      • toStrPos

        public java.lang.String toStrPos()
        To string as a simple "chr:start-end" format