Package htsjdk.samtools.util

Class Interval

java.lang.Object
htsjdk.samtools.util.Interval
All Implemented Interfaces:
Locatable, Feature, NamedFeature, Cloneable, Comparable<Interval>
public class Interval extends Object implements Comparable<Interval>, Cloneable, NamedFeature
Represents a simple interval on a sequence. Coordinates are 1-based closed ended.

  • Constructor Details

    • Interval

      public Interval(String sequence, int start, int end)
      Constructs an interval with the supplied sequence and start and end. If the end position is less than the start position an exception is thrown.
      Parameters:
      sequence - the name of the sequence
      start - the start position of the interval on the sequence
      end - the end position of the interval on the sequence

    • Interval

      public Interval(Locatable locatable)
      Constructs an interval with the supplied Locatable.

    • Interval

      public Interval(String sequence, int start, int end, boolean negative, String name)
      Constructs an interval with the supplied sequence and start, end, strand and name. If the end position is less than the start position an exception is thrown.
      Parameters:
      sequence - the name of the sequence
      start - the start position of the interval on the sequence
      end - the end position of the interval on the sequence
      negative - true to indicate negative strand, false otherwise
      name - the name (possibly null) of the interval

  • Method Details

    • getSequence

      @Deprecated public String getSequence()
      Deprecated.
      use getContig() instead
      Gets the name of the sequence on which the interval resides. This is a simple alias of getContig()

    • isNegativeStrand

      public boolean isNegativeStrand()
      Returns true if the interval is on the negative strand, otherwise false.

    • isPositiveStrand

      public boolean isPositiveStrand()
      Returns true if the interval is on the positive strand, otherwise false.

    • getStrand

      public Strand getStrand()
      Return the Strand this interval is on.

    • getName

      public String getName()
      Returns the name of the interval, possibly null.
      Specified by:
      getName in interface NamedFeature

    • intersects

      public boolean intersects(Interval other)
      Returns true if this interval overlaps the other interval, otherwise false.

    • getIntersectionLength

      public int getIntersectionLength(Interval other)

    • intersect

      public Interval intersect(Interval that)
      Returns a new Interval that represents the intersection between the two intervals.

    • abuts

      public boolean abuts(Interval other)
      Returns true if this interval overlaps the other interval, otherwise false.

    • length

      public int length()
      Gets the length of this interval.

    • pad

      public Interval pad(int left, int right)
      Returns a new interval that is padded by the amount of bases specified on either side.

    • countBases

      public static long countBases(Collection<Interval> intervals)
      Counts the total number of bases a collection of intervals.

    • compareTo

      public int compareTo(Interval that)
      Sort based on sequence.compareTo, then start pos, then end pos with null objects coming lexically last
      Specified by:
      compareTo in interface Comparable<Interval>

    • equals

      public boolean equals(Object other)
      Equals method that agrees with compareTo(Interval).
      Overrides:
      equals in class Object

    • equalsWithStrandAndName

      public boolean equalsWithStrandAndName(Object other)
      Equals method that also checks strand and name

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • clone

      public Interval clone()
      Overrides:
      clone in class Object

    • getContig

      public String getContig()
      Description copied from interface: Locatable
      Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.
      Specified by:
      getContig in interface Locatable
      Returns:
      name of the contig this is mapped to, potentially null

    • getStart

      public int getStart()
      Specified by:
      getStart in interface Locatable
      Returns:
      1-based start position, undefined if getContig() == null

    • getEnd

      public int getEnd()
      Specified by:
      getEnd in interface Locatable
      Returns:
      1-based closed-ended position, undefined if getContig() == null