Package beagleutil

Class ChromIds

  • public final class ChromIds
extends java.lang.Object

    Class ChromIds is a singleton class that represents a list of chromosome identifiers.

    The singleton instance of ChromIds is thread-safe.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getIndex​(java.lang.String id)
      Returns the index of the specified chromosome identifier.
      int getIndexIfIndexed​(java.lang.String id)
      Returns the index of the specified chromosome identifier, or returns -1 if the specified chromosome identifier is not indexed.
      int[] getIndices​(java.lang.String[] ids)
      Returns an array of chromosome identifier indices corresponding to the specified array of chromosome identifiers.
      java.lang.String id​(int index)
      Returns the chromosome identifier with the specified index.
      java.lang.String[] ids()
      Returns the list of chromosome identifiers as an array.
      static ChromIds instance()
      Returns the singleton ChromIds instance.
      int size()
      Returns the number of indexed chromosomes identifiers.
      java.lang.String toString()
      Returns java.util.Arrays.toString(this.ids()).

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Method Detail

      • instance

        public static ChromIds instance()
        Returns the singleton ChromIds instance.
        Returns:
        the singleton ChromIds instance

      • getIndex

        public int getIndex​(java.lang.String id)
        Returns the index of the specified chromosome identifier. If the chromosome identifiers is not yet indexed, the chromosome identifier will be indexed. Chromosome identifier indices are assigned in consecutive order beginning with 0.
        Parameters:
        id - a chromosome identifier
        Returns:
        the index of the specified chromosome identifier
        Throws:
        java.lang.IllegalArgumentException - if id.isEmpty()
        java.lang.NullPointerException - if id == null

      • getIndices

        public int[] getIndices​(java.lang.String[] ids)
        Returns an array of chromosome identifier indices corresponding to the specified array of chromosome identifiers. If a sample identifier is not yet indexed, the sample identifier will be indexed. Sample identifier indices are assigned in increasing order starting with 0.
        Parameters:
        ids - an array of sample identifiers
        Returns:
        an array of sample identifier indices
        Throws:
        java.lang.IllegalArgumentException - if there is a j satisfying (0 <= j && j < ids.length) && ids[j].isEmpty()
        java.lang.NullPointerException - if ids == null
        java.lang.NullPointerException - if there is a j satisfying (0 <= j && j < ids.length) && (ids[j] == null)

      • getIndexIfIndexed

        public int getIndexIfIndexed​(java.lang.String id)
        Returns the index of the specified chromosome identifier, or returns -1 if the specified chromosome identifier is not indexed.
        Parameters:
        id - a chromosome identifier.
        Returns:
        the index of the specified chromosome identifier, or -1 if the specified chromosome identifier is not indexed.
        Throws:
        java.lang.IllegalArgumentException - if id.isEmpty()
        java.lang.NullPointerException - if id == null

      • size

        public int size()
        Returns the number of indexed chromosomes identifiers.
        Returns:
        the number of indexed chromosomes identifiers

      • id

        public java.lang.String id​(int index)
        Returns the chromosome identifier with the specified index.
        Parameters:
        index - a chromosome identifier index.
        Returns:
        the specified chromosome identifier.
        Throws:
        java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.size()

      • ids

        public java.lang.String[] ids()
        Returns the list of chromosome identifiers as an array. The returned array will have length this.size(), and it will satisfy this.ids()[k].equals(this.id(k)) == true for 0 <= k < this.size().
        Returns:
        an array of chromosome identifiers

      • toString

        public java.lang.String toString()
        Returns java.util.Arrays.toString(this.ids()).
        Overrides:
        toString in class java.lang.Object
        Returns:
        a string representation of this