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The NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of scientific data formats.
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/*
 * Copyright 1998-2014 University Corporation for Atmospheric Research/Unidata
 *
 *   Portions of this software were developed by the Unidata Program at the
 *   University Corporation for Atmospheric Research.
 *
 *   Access and use of this software shall impose the following obligations
 *   and understandings on the user. The user is granted the right, without
 *   any fee or cost, to use, copy, modify, alter, enhance and distribute
 *   this software, and any derivative works thereof, and its supporting
 *   documentation for any purpose whatsoever, provided that this entire
 *   notice appears in all copies of the software, derivative works and
 *   supporting documentation.  Further, UCAR requests that the user credit
 *   UCAR/Unidata in any publications that result from the use of this
 *   software or in any product that includes this software. The names UCAR
 *   and/or Unidata, however, may not be used in any advertising or publicity
 *   to endorse or promote any products or commercial entity unless specific
 *   written permission is obtained from UCAR/Unidata. The user also
 *   understands that UCAR/Unidata is not obligated to provide the user with
 *   any support, consulting, training or assistance of any kind with regard
 *   to the use, operation and performance of this software nor to provide
 *   the user with any updates, revisions, new versions or "bug fixes."
 *
 *   THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
 *   IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 *   WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 *   DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
 *   INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
 *   FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 *   NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 *   WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
 */

package ucar.ma2;

/**
 * Abstraction for vector operations.
 * A vector is a rank-1 Array.
 * All operations done in double precision
 *
 * @author @caron
 */

public class MAVector {
  private Array a;
  private int nelems;
  private Index ima;

  /**
   * Create an MAVector out of a double array
   */
  public MAVector( double[] values) {
    this( Array.factory( values));
  }

  /**
   * Create an MAVector of the given length.
   */
  public MAVector( int nelems) {
    this.a = new ArrayDouble.D1(nelems);
    this.nelems = nelems;
    ima = a.getIndex();
  }

  /**
   * Create an MAVector using the given rank-1 array.
   * @param a rank-1 array
   * @exception IllegalArgumentException is a is not rank 1
   */
  public MAVector( Array a) {
    this.a = a;
    if (a.getRank() != 1)
      throw new IllegalArgumentException("rank != 1, instead = "+ a.getRank());
    nelems = a.getShape()[0];
    ima = a.getIndex();
  }

  public int getNelems() { return nelems; }
  public double getDouble(int i) { return a.getDouble(ima.set(i)); }
  public void setDouble(int i, double val) { a.setDouble(ima.set(i), val); }

  /**
   * Create a new MAVector that is the same as this one, with a copy of the backing store.
   */
  public MAVector copy() {
    return new MAVector( a.copy());
  }

  /**
   * Cos between two vectors = dot(v) / norm() * norm(v)
   * @param v cosine with this vector
   * @return double result: cos between this and v
   * @exception IllegalArgumentException if nelems != v.getNelems().
   */
  public double cos(MAVector v) {

    if (nelems != v.getNelems())
      throw new IllegalArgumentException("MAVector.cos "+nelems+" != "+ v.getNelems());

    double norm = norm();
    double normV = v.norm();
    if ((norm == 0.0) || (normV == 0.0))
      return 0.0;
    else
      return dot(v)/(norm*normV);
  }

  /**
   * Dot product of 2 vectors
   * @param v dot product with this vector
   * @return double result: dot product
   * @exception IllegalArgumentException if nelems != v.getNelems().
   */
  public double dot(MAVector v) {

    if (nelems != v.getNelems())
      throw new IllegalArgumentException("MAVector.dot "+nelems+" != "+ v.getNelems());

    double sum = 0.0;
    for (int k=0; k