Class Interval

    • Constructor Detail

      • 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 Detail

      • 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.
      • 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>
      • equalsWithStrandAndName

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

        public int hashCode()
        Overrides:
        hashCode 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