// $Id: vectorx.cpp,v 1.14 2011/04/23 02:02:49 bobgian Exp $

/*
  Copyright 2002  Peter Beerli, Mary Kuhner, Jon Yamato and Joseph Felsenstein

  This software is distributed free of charge for non-commercial use
  and is copyrighted.  Of course, we do not guarantee that the software
  works, and are not responsible for any damage you may cause or have.
*/

#include <cassert>
#include <cmath>

#include "vectorx.h"

#ifdef DMALLOC_FUNC_CHECK
#include "/usr/local/include/dmalloc.h"
#endif

using namespace std;

//------------------------------------------------------------------------------------
// maintenance functions

// forward declarations if helper functions of the maintenace functions
double logsave(const double value);
double log0(const double value);

void LogVec0(const vector<double> &in, vector<double> &out)
{
    assert(in.size() == out.size());
    transform(in.begin(),in.end(),out.begin(),log0);
}

// helper function that keeps the structural zeros intact
// used in LogVec0() in  PostLike::Setup0()
double log0(const double value)
{
    return ((value > 0.0) ? log(value) : 0.0);
}

long LongSquareRootOfLong(long shouldBeASquare)
{
    // this is a funny-looking way to take a square root,
    // necessitated by the fact that the C library only provides
    // floating-point square root, and we don't want to deal with
    // the consequences of rounding error.

    long i;

    for (i = 1; i <= long(shouldBeASquare/2); ++i)
    {
        if (i * i == shouldBeASquare)
        {
            return i;
        }
    }
    throw ("Attempt to take long square root of non-square");
}

//____________________________________________________________________________________