Package beagleutil

Class Samples

  • public final class Samples
extends java.lang.Object

    Class Samples stores a list of samples.

    Instances of class Samples are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      Samples​(int[] idIndices)
      Constructs a new instance of Samples corresponding to the specified list of sample identifier indices.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean equals​(java.lang.Object obj)
      Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.
      static Samples fromIds​(java.lang.String[] ids)
      Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.
      int hashCode()
      Returns a hash code value for the object.
      java.lang.String id​(int index)
      Returns the identifier for the sample with the specified index in this list of samples.
      int idIndex​(int index)
      Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.
      java.lang.String[] ids()
      Returns this list of samples as an array of sample identifiers.
      int index​(int idIndex)
      Returns the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples.
      int index​(java.lang.String id)
      Returns the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples.
      int nSamples()
      Returns the number of samples in this list.
      java.lang.String toString()
      Returns java.util.Arrays.toString(this.ids()).

      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • Samples

        public Samples​(int[] idIndices)
        Constructs a new instance of Samples corresponding to the specified list of sample identifier indices.
        Parameters:
        idIndices - an array of sample identifier indices
        Throws:
        java.lang.IllegalArgumentException - if the specified array has two or more elements that are equal
        java.lang.IndexOutOfBoundsException - if any element of the specified array is negative or greater than or equal to beagleutil.SampleIds.size()
        java.lang.NullPointerException - if idIndices == null

    • Method Detail

      • fromIds

        public static Samples fromIds​(java.lang.String[] ids)
        Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.
        Parameters:
        ids - an array of sample identifiers.
        Returns:
        a Samples instance corresponding to the specified list of sample identifiers
        Throws:
        java.lang.IllegalArgumentException - if the specified array has two or more elements that are equal as strings
        java.lang.NullPointerException - if ids == null

      • hashCode

        public int hashCode()

        Returns a hash code value for the object.

        The hash code is defined by the following calculation: 

                int hash = 1;
        for (int j, n=this.nSamples(); j<n; ++j) {
            hash = 31 * hash + this.idIndex(j);
        }
        Overrides:
        hashCode in class java.lang.Object
        Returns:
        a hash code value for the object.

      • equals

        public boolean equals​(java.lang.Object obj)
        Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.
        Overrides:
        equals in class java.lang.Object
        Parameters:
        obj - the object to be tested for equality with this
        Returns:
        true if the specified object is a Samples object which represents the same ordered list of samples as this

      • idIndex

        public int idIndex​(int index)
        Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.
        Parameters:
        index - a sample index
        Returns:
        the sample identifier index corresponding to the sample with the specified index in this list of samples
        Throws:
        java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nSamples()

      • index

        public int index​(int idIndex)
        Returns the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples.
        Parameters:
        idIndex - a sample identifier index
        Returns:
        the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples
        Throws:
        java.lang.IndexOutOfBoundsException - if index < 0

      • index

        public int index​(java.lang.String id)
        Returns the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples.
        Parameters:
        id - a sample identifier
        Returns:
        the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples
        Throws:
        java.lang.NullPointerException - if id == null

      • nSamples

        public int nSamples()
        Returns the number of samples in this list.
        Returns:
        the number of samples in this list

      • id

        public java.lang.String id​(int index)
        Returns the identifier for the sample with the specified index in this list of samples.
        Parameters:
        index - a sample index
        Returns:
        the identifier for the sample with the specified index in this list of samples
        Throws:
        java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nSamples()

      • ids

        public java.lang.String[] ids()
        Returns this list of samples as an array of sample identifiers. The returned array has length this.nSamples(), and it satisfies this.ids()[j].equals(this.id(j)) for 0 <= j && j < this.nSamples()
        Returns:
        this list of samples as an array of sample 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