Package beagleutil

Class SampleIds

java.lang.Object
beagleutil.SampleIds
public final class SampleIds extends Object

Class SampleIds is a singleton class that represents a list of sample identifiers.

The singleton instance of SampleIds is thread-safe.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    getIndex(String id)
    Returns the index of the specified sample identifier.
    int
    getIndexIfIndexed(String id)
    Returns the index of the specified sampled identifier, or returns -1 if the specified sample identifier is not indexed.
    int[]
    getIndices(String[] ids)
    Returns an array of sample identifier indices corresponding to the specified array of sample identifiers.
    String
    id(int index)
    Returns the sample identifier with the specified index.
    int[]
    idIndexToIndex(Samples samples)
    Returns an array mapping sample identifier indices to sample indices.
    String[]
    ids()
    Returns the list of indexed sample identifiers as an array.
    String[]
    ids(int[] indices)
    Returns a list of sample identifiers with the specified indices.
    static SampleIds
    instance()
    Returns the singleton SampleIds instance.
    int
    size()
    Returns the number of indexed sample identifiers.
    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 Details

    • instance

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

    • getIndex

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

    • getIndices

      public int[] getIndices(String[] ids)
      Returns an array of sample identifier indices corresponding to the specified array of sample 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:
      IllegalArgumentException - if there is a j satisfying (0 <= j && j < ids.length) && ids[j].isEmpty()
      NullPointerException - if ids == null
      NullPointerException - if there is a j satisfying (0 <= j && j < ids.length) && (ids[j] == null)

    • idIndexToIndex

      public int[] idIndexToIndex(Samples samples)
      Returns an array mapping sample identifier indices to sample indices. Indices for sample identifiers not present in this list of samples are mapped to -1.
      Parameters:
      samples - a list of sample identifiers
      Returns:
      an array mapping sample identifier indices to sample indices
      Throws:
      IllegalArgumentException - if two sample identifiers are the same string
      NullPointerException - if samples == null

    • getIndexIfIndexed

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

    • size

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

    • id

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

    • ids

      public String[] ids(int[] indices)
      Returns a list of sample identifiers with the specified indices.
      Parameters:
      indices - an array of sample identifiers indices
      Returns:
      a list of sample identifiers with the specified indices
      Throws:
      IndexOutOfBoundsException - if there exists a j satisfying (0 <= j && j < indices.length) && (indices[j] < 0 || indices[j] >= this.size())

    • ids

      public String[] ids()
      Returns the list of indexed sample 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 && k < this.size().
      Returns:
      an array of sample identifiers

    • toString

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