Package org.snpeff.interval

Class Interval

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

Note: Intervals are assumed to be zero-based and "closed" i.e. an interval includes the first and the last base. e.g.: an interval including the first base, up to base (and including) X would be [0,X]

Author:
pcingola
See Also:

  • Field Details

    • start

      protected int start

    • end

      protected int end

    • strandMinus

      protected boolean strandMinus

    • id

      protected String id

    • chromosomeNameOri

      protected String chromosomeNameOri

    • parent

      protected Interval parent

  • Constructor Details

    • Interval

      protected Interval()

    • Interval

      public Interval(Interval parent, int start, int end, boolean strandMinus, String id)

  • Method Details

    • clone

      public Interval clone()
      Overrides:
      clone in class Object

    • compareTo

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

    • equals

      public boolean equals(Interval interval)

    • findParent

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

    • getChromosome

      public Chromosome getChromosome()

    • getChromosomeName

      public String getChromosomeName()
      Find chromosome name

    • getChromosomeNameOri

      public String getChromosomeNameOri()

    • setChromosomeNameOri

      public void setChromosomeNameOri(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 String getGenomeName()
      Find genome name

    • getId

      public String getId()

    • setId

      public void setId(String id)

    • getParent

      public Interval getParent()

    • setParent

      public void setParent(Interval parent)

    • getStart

      public int getStart()

    • setStart

      public void setStart(int start)

    • getStrand

      public String getStrand()

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class 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 String toStr()
      To string as a simple "chr:start-end" format

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toStringAsciiArt

      public String toStringAsciiArt(int maxLen)
      Show it as an ASCII art

    • toStrPos

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