// $Id$
//
//  Copyright (C) 2001-2014 Greg Landrum and Rational Discovery LLC
//
//  @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <cstdlib>
#include <iostream>
#include <sstream>
#include <fstream>
#include <ios>
#include "BitVects.h"
#include "BitOps.h"
#include "BitVectUtils.h"
#include "base64.h"
#include <cmath>
#include "DiscreteValueVect.h"
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Exceptions.h>
#include <DataStructs/SparseIntVect.h>
#include <DataStructs/DatastructsStreamOps.h>
#include <stdlib.h>

using namespace std;
using namespace RDKit;
template <typename T>
inline void TXTMSG(const char *__a__, T __b__) {
  BOOST_LOG(rdInfoLog) << (__a__) << " " << (__b__) << std::endl;
}

bool feq(double v1, double v2, double tol = 1e-4) {
  return fabs(v1 - v2) < tol;
}

template <typename T>
void Test(T arg) {
  (void)arg;
  T t1(20);
  TXTMSG("Set 10:", t1.setBit(10));
  TXTMSG("Set 11:", t1.setBit(11));
  TXTMSG("Set 14:", t1.setBit(14));
  TXTMSG("Set 10:", t1.setBit(10));
  TXTMSG("Get 14:", t1.getBit(14));
  TXTMSG("Num:", t1.getNumBits());
  TXTMSG("NumOn:", t1.getNumOnBits());
  TXTMSG("NumOff:", t1.getNumOffBits());
  TEST_ASSERT(t1 == t1);

  IntVect onBits;
  t1.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  T t2(t1);
  // onBits = t2.getOnBits();
  TXTMSG("t2[19]:", t2[19]);
  TXTMSG("t2[14]:", t2[14]);

  TEST_ASSERT(t2 == t1);

  t2 = t1;
  // onBits = t2.getOnBits();
  TXTMSG("t2[19]:", t2[19]);
  t2.unsetBit(14);
  TXTMSG("t2[14]:", t2[14]);
  t2.setBit(15);
  t2.setBit(17);
  TEST_ASSERT(t2 != t1);

  std::cout << "t1: ";
  t1.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  std::cout << "t2: ";
  t2.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  std::cout << "t1|t2: ";
  T t3 = t1 | t2;
  t3.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  std::cout << "t1&t2: ";
  t3 = t1 & t2;
  t3.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  std::cout << "t1^t2: ";
  t3 = t1 ^ t2;
  t3.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  std::cout << "~t1: ";
  t3 = ~t1;
  t3.getOnBits(onBits);
  std::copy(onBits.begin(), onBits.end(),
            std::ostream_iterator<int>(std::cout, ", "));
  std::cout << std::endl;

  try {
    t3.getBit(4000);
  } catch (IndexErrorException &) {
    std::cout << " except " << endl;
  } catch (...) {
    std::cout << " ERROR EXCEPT " << endl;
  }

  T t4(t1.toString());
  TEST_ASSERT(t4 == t1);
  TEST_ASSERT(feq(TanimotoSimilarity(t1, t4), 1.0));

  T *t5 = FoldFingerprint(t1);
  TEST_ASSERT(t5->getNumBits() == t1.getNumBits() / 2);
  TEST_ASSERT(t5->getBit(0));
  TEST_ASSERT(t5->getBit(1));
  TEST_ASSERT(t5->getBit(4));
  TEST_ASSERT(!t5->getBit(2));
  TEST_ASSERT(!t5->getBit(3));
  delete t5;

  std::string pkl = t1.toString();
  const char *pkl64 = Base64Encode(pkl.c_str(), pkl.size());
  T t6(t1.getNumBits());
  t6.initFromText(pkl64, strlen(pkl64), true);
  delete[] pkl64;
  TEST_ASSERT(t6 == t1);
}

template <typename T>
void TaniTest(T &arg) {
  (void)arg;  // unused var;
  std::string fps[4] = {
      ".b+HHa.EgU6+ibEIr89.CpX0g8FZiXH+R0+Ps.mr6tg.2",
      ".b7HEa..ccc+gWEIr89.8lV8gOF3aXFFR.+Ps.mZ6lg.2",
      ".H+nHq2EcY09y5EIr9e.8p50h0NgiWGNx4+Hm+Gbslw.2",
      ".1.HHa..cUI6i5E2rO8.Op10d0NoiWGVx.+Hm.Gb6lo.2",
  };
  double dists[] = {1.0,      0.788991, 0.677165, 0.686957, 1.0,
                    0.578125, 0.591304, 1.0,      0.732759, 1.0};
  int idx = 0;
  for (int i = 0; i < 4; i++) {
    T v1(256);
    FromDaylightString(v1, fps[i]);
    for (int j = i; j < 4; j++) {
      T v2(256);
      FromDaylightString(v2, fps[j]);
      double tani = TanimotoSimilarity(v1, v2);
      TEST_ASSERT(feq(tani, dists[idx]));
      tani = TverskySimilarity(v1, v2, 1., 1.);
      TEST_ASSERT(feq(tani, dists[idx]));
      tani = SimilarityWrapper(v1, v2, TanimotoSimilarity<T, T>);
      TEST_ASSERT(feq(tani, dists[idx]));
      tani = SimilarityWrapper(v1, v2, 1., 1., TverskySimilarity<T, T>);
      TEST_ASSERT(feq(tani, dists[idx]));
      tani = SimilarityWrapper(v1, v2, TanimotoSimilarity<T, T>, true);
      TEST_ASSERT(feq(tani, 1. - dists[idx]));
      tani = SimilarityWrapper(v1, v2, 1., 1., TverskySimilarity<T, T>, true);
      TEST_ASSERT(feq(tani, 1. - dists[idx]));
      idx++;
    }
  }
}

template <typename T>
void ProbeTest(T &arg) {
  (void)arg;  // unused var
  int sz = 1000;
  T t1(sz), t2(sz);
  for (int i = 0; i < sz; i += 2) {
    t1.setBit(i);
    if (i < 3 * sz / 4) t2.setBit(i);
  }
  std::string pkl = t1.toString();
  TEST_ASSERT(AllProbeBitsMatch(t1, pkl));
  TEST_ASSERT(AllProbeBitsMatch(t2, pkl));
  TEST_ASSERT(AllProbeBitsMatch(t1.toString(), pkl));
  TEST_ASSERT(AllProbeBitsMatch(t2.toString(), pkl));
  TEST_ASSERT(AllProbeBitsMatch(t1.toString().c_str(), pkl.c_str()));
  TEST_ASSERT(AllProbeBitsMatch(t2.toString().c_str(), pkl.c_str()));
  pkl = t2.toString();
  TEST_ASSERT(!AllProbeBitsMatch(t1, pkl));
  TEST_ASSERT(AllProbeBitsMatch(t2, pkl));
  TEST_ASSERT(!AllProbeBitsMatch(t1.toString(), pkl));
  TEST_ASSERT(AllProbeBitsMatch(t2.toString(), pkl));
  TEST_ASSERT(!AllProbeBitsMatch(t1.toString().c_str(), pkl.c_str()));
  TEST_ASSERT(AllProbeBitsMatch(t2.toString().c_str(), pkl.c_str()));
}

void test1DiscreteVect() {
  DiscreteValueVect vect1(DiscreteValueVect::ONEBITVALUE, 30);
  unsigned int i;
  for (i = 0; i < 15; ++i) {
    vect1.setVal(2 * i, 1);
  }

  TEST_ASSERT(vect1.getLength() == 30);
  TEST_ASSERT(vect1.getTotalVal() == 15);
  for (i = 0; i < vect1.getLength(); ++i) {
    TEST_ASSERT(vect1.getVal(i) == (i + 1) % 2);
  }
  try {
    vect1.setVal(28, 2);
  } catch (ValueErrorException &dexp) {
    BOOST_LOG(rdInfoLog) << "Expected failure: " << dexp.message() << "\n";
  }

  // all these tests should fail if unsigned int changes from being
  // 32 bits
  DiscreteValueVect vect2(DiscreteValueVect::TWOBITVALUE, 30);
  for (i = 0; i < vect2.getLength(); ++i) {
    vect2.setVal(i, i % 4);
  }

  for (i = 0; i < vect2.getLength(); ++i) {
    TEST_ASSERT(vect2.getVal(i) == i % 4);
  }
  TEST_ASSERT(vect2.getTotalVal() == 43);
  try {
    vect2.setVal(28, 10);
  } catch (ValueErrorException &dexp) {
    BOOST_LOG(rdInfoLog) << "Expected failure: " << dexp.message() << "\n";
  }

  DiscreteValueVect vect4(DiscreteValueVect::FOURBITVALUE, 30);
  for (i = 0; i < vect4.getLength(); ++i) {
    vect4.setVal(i, i % 16);
  }

  for (i = 0; i < vect4.getLength(); ++i) {
    TEST_ASSERT(vect4.getVal(i) == i % 16);
  }
  TEST_ASSERT(vect4.getTotalVal() == 211);
  try {
    vect4.setVal(28, 16);
  } catch (ValueErrorException &dexp) {
    BOOST_LOG(rdInfoLog) << "Expected failure: " << dexp.message() << "\n";
  }

  DiscreteValueVect vect8(DiscreteValueVect::EIGHTBITVALUE, 32);
  for (i = 0; i < vect8.getLength(); ++i) {
    vect8.setVal(i, i % 256);
  }

  for (i = 0; i < vect8.getLength(); ++i) {
    TEST_ASSERT(vect8.getVal(i) == i % 256);
  }
  TEST_ASSERT(vect8.getTotalVal() == 496);
  try {
    vect8.setVal(28, 257);
  } catch (ValueErrorException &dexp) {
    BOOST_LOG(rdInfoLog) << "Expected failure: " << dexp.message() << "\n";
  }

  DiscreteValueVect vect16(DiscreteValueVect::SIXTEENBITVALUE, 300);
  for (i = 0; i < vect16.getLength(); ++i) {
    vect16.setVal(i, i % 300);
  }

  for (i = 0; i < vect16.getLength(); ++i) {
    TEST_ASSERT(vect16.getVal(i) == i % 300);
  }

  TEST_ASSERT(vect16.getTotalVal() == 44850);
  vect16.setVal(28, 65535);
  try {
    vect16.setVal(28, 65536);
  } catch (ValueErrorException &dexp) {
    BOOST_LOG(rdInfoLog) << "Expected failure: " << dexp.message() << "\n";
  }
}

void test2DiscreteVectDists() {
  DiscreteValueVect v1(DiscreteValueVect::ONEBITVALUE, 30);
  DiscreteValueVect v2(DiscreteValueVect::ONEBITVALUE, 30);
  unsigned int i;
  for (i = 0; i < 15; ++i) {
    v1.setVal(2 * i, 1);
    v2.setVal(2 * i, 1);
  }
  TEST_ASSERT(computeL1Norm(v1, v2) == 0);
  for (i = 0; i < 30; ++i) {
    v2.setVal(i, i % 2);
  }

  TEST_ASSERT(computeL1Norm(v1, v2) == 30);

  for (i = 0; i < 30; ++i) {
    if (i % 3 == 0) {
      v2.setVal(i, 1);
    } else {
      v2.setVal(i, 0);
    }
  }

  TEST_ASSERT(computeL1Norm(v1, v2) == 15);

  DiscreteValueVect v21(DiscreteValueVect::TWOBITVALUE, 30);
  DiscreteValueVect v22(DiscreteValueVect::TWOBITVALUE, 30);
  for (i = 0; i < 30; ++i) {
    v21.setVal(i, i % 4);
    v22.setVal(i, i % 4);
  }
  TEST_ASSERT(computeL1Norm(v21, v22) == 0);
  for (i = 0; i < 30; ++i) {
    v22.setVal(i, (i + 1) % 4);
  }
  TEST_ASSERT(computeL1Norm(v21, v22) == 44);

  DiscreteValueVect v41(DiscreteValueVect::FOURBITVALUE, 16);
  DiscreteValueVect v42(DiscreteValueVect::FOURBITVALUE, 16);
  for (i = 0; i < 16; ++i) {
    v41.setVal(i, i % 16);
    v42.setVal(i, i % 16);
  }
  TEST_ASSERT(computeL1Norm(v41, v42) == 0);

  for (i = 0; i < 16; ++i) {
    v42.setVal(i, i % 5);
  }
  TEST_ASSERT(computeL1Norm(v41, v42) == 90);

  DiscreteValueVect v43(v42);
  TEST_ASSERT(computeL1Norm(v42, v43) == 0);

  DiscreteValueVect v81(DiscreteValueVect::EIGHTBITVALUE, 5);
  DiscreteValueVect v82(DiscreteValueVect::EIGHTBITVALUE, 5);
  v81.setVal(0, 34);
  v82.setVal(0, 34);
  v81.setVal(1, 167);
  v82.setVal(1, 167);
  v81.setVal(2, 3);
  v82.setVal(2, 3);
  v81.setVal(3, 56);
  v82.setVal(3, 56);
  v81.setVal(4, 128);
  v82.setVal(4, 128);
  TEST_ASSERT(computeL1Norm(v81, v82) == 0);

  v82.setVal(0, 14);
  v82.setVal(1, 67);
  v82.setVal(2, 103);
  v82.setVal(3, 6);
  v82.setVal(4, 228);
  TEST_ASSERT(computeL1Norm(v81, v82) == 370);

  DiscreteValueVect v161(DiscreteValueVect::SIXTEENBITVALUE, 3);
  DiscreteValueVect v162(DiscreteValueVect::SIXTEENBITVALUE, 3);
  v161.setVal(0, 2345);
  v162.setVal(0, 2345);
  v161.setVal(1, 64578);
  v162.setVal(1, 64578);
  v161.setVal(2, 34);
  v162.setVal(2, 34);
  TEST_ASSERT(computeL1Norm(v161, v162) == 0);

  v162.setVal(0, 1345);
  v162.setVal(1, 54578);
  v162.setVal(2, 10034);
  TEST_ASSERT(computeL1Norm(v161, v162) == 21000);
}

void test3DiscreteVectPickles() {
  DiscreteValueVect v1(DiscreteValueVect::ONEBITVALUE, 30);
  unsigned int i;
  for (i = 0; i < 15; ++i) {
    v1.setVal(2 * i, 1);
  }
  DiscreteValueVect v2(v1.toString());
  TEST_ASSERT(computeL1Norm(v1, v2) == 0);

  DiscreteValueVect v21(DiscreteValueVect::TWOBITVALUE, 30);
  for (i = 0; i < 30; ++i) {
    v21.setVal(i, i % 4);
  }
  DiscreteValueVect v22(v21.toString());
  TEST_ASSERT(computeL1Norm(v21, v22) == 0);

  DiscreteValueVect v41(DiscreteValueVect::FOURBITVALUE, 16);
  for (i = 0; i < 16; ++i) {
    v41.setVal(i, i % 16);
  }
  DiscreteValueVect v42(v41.toString());
  TEST_ASSERT(computeL1Norm(v41, v42) == 0);

  DiscreteValueVect v81(DiscreteValueVect::EIGHTBITVALUE, 5);
  v81.setVal(0, 34);
  v81.setVal(1, 167);
  v81.setVal(2, 3);
  v81.setVal(3, 56);
  v81.setVal(4, 128);
  DiscreteValueVect v82(v81.toString());
  TEST_ASSERT(computeL1Norm(v81, v82) == 0);

  DiscreteValueVect v161(DiscreteValueVect::SIXTEENBITVALUE, 3);
  v161.setVal(0, 2345);
  v161.setVal(1, 64578);
  v161.setVal(2, 34);
  DiscreteValueVect v162(v161.toString());
  TEST_ASSERT(computeL1Norm(v161, v162) == 0);
}

void test4DiscreteVectOps1() {
  DiscreteValueVect vect1(DiscreteValueVect::ONEBITVALUE, 8);
  for (unsigned int i = 0; i < 4; ++i) {
    vect1.setVal(2 * i, 1);
  }
  TEST_ASSERT(vect1.getLength() == 8);
  TEST_ASSERT(vect1.getTotalVal() == 4);

  DiscreteValueVect vect2(DiscreteValueVect::ONEBITVALUE, 8);
  for (unsigned int i = 0; i < 4; ++i) {
    vect2.setVal(2 * i + 1, 1);
  }
  TEST_ASSERT(vect2.getTotalVal() == 4);

  DiscreteValueVect vect3 = vect1 & vect2;
  TEST_ASSERT(vect3.getLength() == 8);
  TEST_ASSERT(vect3.getTotalVal() == 0);

  DiscreteValueVect vect4 = vect1 | vect2;
  TEST_ASSERT(vect4.getLength() == 8);
  TEST_ASSERT(vect4.getTotalVal() == 8);
#if 0
  DiscreteValueVect vect5=~vect1;
  TEST_ASSERT(vect5.getLength() == 8);
  TEST_ASSERT(vect5.getTotalVal() == 4);

  TEST_ASSERT((vect5&vect1).getTotalVal()==0);
  TEST_ASSERT((vect5&vect2).getTotalVal()==4);
#endif
}

void test5DiscreteVectOps2() {
  DiscreteValueVect vect1(DiscreteValueVect::TWOBITVALUE, 8);
  for (unsigned int i = 0; i < 4; ++i) {
    vect1.setVal(2 * i, 2);
  }
  TEST_ASSERT(vect1.getLength() == 8);
  TEST_ASSERT(vect1.getTotalVal() == 8);

  DiscreteValueVect vect2(DiscreteValueVect::TWOBITVALUE, 8);
  for (unsigned int i = 0; i < 4; ++i) {
    vect2.setVal(2 * i + 1, 2);
    vect2.setVal(2 * i, 1);
  }
  TEST_ASSERT(vect2.getTotalVal() == 12);

  DiscreteValueVect vect3 = vect1 & vect2;
  TEST_ASSERT(vect3.getLength() == 8);
  TEST_ASSERT(vect3.getTotalVal() == 4);

  DiscreteValueVect vect4 = vect1 | vect2;
  TEST_ASSERT(vect4.getLength() == 8);
  TEST_ASSERT(vect4.getTotalVal() == 16);

  DiscreteValueVect vect5 = vect1 + vect2;
  TEST_ASSERT(vect5.getLength() == 8);
  TEST_ASSERT(vect5.getTotalVal() == 20);

  vect5 = vect1 - vect2;
  TEST_ASSERT(vect5.getTotalVal() == 4);
  vect5 = vect2 - vect1;
  TEST_ASSERT(vect5.getTotalVal() == 8);

#if 0
  DiscreteValueVect vect5=~vect1;
  TEST_ASSERT(vect5.getLength() == 8);
  TEST_ASSERT(vect5.getTotalVal() == 16);

  TEST_ASSERT((vect5&vect1).getTotalVal()==4);
  TEST_ASSERT((vect5&vect2).getTotalVal()==12);
#endif
}

void test6SparseIntVect() {
  SparseIntVect<int> iVect(255);

  TEST_ASSERT(iVect.getLength() == 255);
  TEST_ASSERT(iVect.getVal(23) == 0);
  iVect.setVal(23, 14);
  TEST_ASSERT(iVect.getVal(23) == 14);

  SparseIntVect<int> oVect(iVect);
  TEST_ASSERT(oVect.getLength() == 255);
  TEST_ASSERT(oVect.getVal(23) == 14);

  std::vector<int> tmpV(3);
  tmpV[0] = 1;
  tmpV[1] = 5;
  tmpV[2] = 1;
  TEST_ASSERT(iVect.getVal(1) == 0);
  TEST_ASSERT(iVect[1] == 0);
  TEST_ASSERT(iVect.getVal(5) == 0);
  TEST_ASSERT(iVect[5] == 0);
  updateFromSequence(iVect, tmpV);
  TEST_ASSERT(iVect.getVal(1) == 2);
  TEST_ASSERT(iVect[1] == 2);
  TEST_ASSERT(iVect.getVal(5) == 1);
  TEST_ASSERT(iVect[5] == 1);

  iVect.setVal(3, -4);
  TEST_ASSERT(iVect.getTotalVal() == 13);

  try {
    iVect.setVal(-1, 13);
    TEST_ASSERT(0);
  } catch (IndexErrorException &) {
    ;
  }
  try {
    iVect.setVal(255, 42);
    TEST_ASSERT(0);
  } catch (IndexErrorException &) {
    ;
  }
  try {
    iVect.getVal(-1);
    TEST_ASSERT(0);
  } catch (IndexErrorException &) {
    ;
  }
  try {
    iVect.getVal(255);
    TEST_ASSERT(0);
  } catch (IndexErrorException &) {
    ;
  }
  try {
    iVect[-1];
    TEST_ASSERT(0);
  } catch (IndexErrorException &) {
    ;
  }

  {
    SparseIntVect<int> iV1(5);
    iV1.setVal(4, 4);
    iV1.setVal(0, 2);
    iV1.setVal(3, 1);
    auto iter = iV1.getNonzeroElements().begin();
    TEST_ASSERT(iter->first == 0);
    TEST_ASSERT(iter->second == 2);
    ++iter;
    TEST_ASSERT(iter->first == 3);
    TEST_ASSERT(iter->second == 1);
    ++iter;
    TEST_ASSERT(iter->first == 4);
    TEST_ASSERT(iter->second == 4);
    ++iter;
    TEST_ASSERT(iter == iV1.getNonzeroElements().end());
    TEST_ASSERT(feq(DiceSimilarity(iV1, iV1), 1.));
  }

  {  // iV1 &= iV2
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    TEST_ASSERT(feq(DiceSimilarity(iV1, iV2), 18. / 26.));

    iV1 &= iV2;
    TEST_ASSERT(iV1[0] == 0);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);

    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 6);

    TEST_ASSERT(feq(DiceSimilarity(iV1, iV2), 18. / 24.));
    TEST_ASSERT(feq(TverskySimilarity(iV1, iV2, 0.5, 0.5, false), 9. / 12.));
    TEST_ASSERT(feq(TverskySimilarity(iV1, iV2, 1.0, 1.0, false), 9. / 15.));
    TEST_ASSERT(feq(TanimotoSimilarity(iV1, iV2), 9. / 15.));
    TEST_ASSERT(
        feq(TverskySimilarity(iV1, iV2, 0.333333333, 0.66666666667, false),
            9. / 13.));
    TEST_ASSERT(feq(TverskySimilarity(iV1, iV2, 1.0, 0.0, false), 9. / 9.));

    try {
      iV1 &= iVect;
      TEST_ASSERT(0);
    } catch (ValueErrorException &) {
      ;
    }
  }

  {  // iV3 = iv1&iV2
    SparseIntVect<int> iV1(5), iV2(5), iV3(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV3 = iV1 & iV2;
    TEST_ASSERT(iV3[0] == 0);
    TEST_ASSERT(iV3[1] == 0);
    TEST_ASSERT(iV3[2] == 1);
    TEST_ASSERT(iV3[3] == 4);
    TEST_ASSERT(iV3[4] == 4);

    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);

    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 6);
  }

  {  // iV2 &= iV1
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV2 &= iV1;
    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 0);
    TEST_ASSERT(iV2[2] == 1);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 4);

    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);

    try {
      iV2 &= iVect;
      TEST_ASSERT(0);
    } catch (ValueErrorException &) {
      ;
    }
  }

  {  // iV1 |= iV2
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV1 |= iV2;
    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 2);
    TEST_ASSERT(iV1[2] == 3);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 6);

    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 6);

    try {
      iV1 |= iVect;
      TEST_ASSERT(0);
    } catch (ValueErrorException &) {
      ;
    }
  }

  {  // iV3 = iv1 |iV2
    SparseIntVect<int> iV1(5), iV2(5), iV3(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV3 = iV1 | iV2;
    TEST_ASSERT(iV3[0] == 2);
    TEST_ASSERT(iV3[1] == 2);
    TEST_ASSERT(iV3[2] == 3);
    TEST_ASSERT(iV3[3] == 4);
    TEST_ASSERT(iV3[4] == 6);

    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);

    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 6);
  }

  {  // iV2 |= iV1
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV2 |= iV1;
    TEST_ASSERT(iV2[0] == 2);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 6);

    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);
  }

  {  // iV1 += iV2
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, -4);
    iV2.setVal(4, 6);

    iV1 += iV2;
    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 2);
    TEST_ASSERT(iV1[2] == 4);
    TEST_ASSERT(iV1[3] == 0);
    TEST_ASSERT(iV1[4] == 10);

    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == -4);
    TEST_ASSERT(iV2[4] == 6);
  }
  {  // iV3 = IV1 + iV2
    SparseIntVect<int> iV1(5), iV2(5), iV3(5);
    iV1.setVal(2, 1);
    iV1.setVal(0, 2);
    iV1.setVal(4, 4);
    iV1.setVal(3, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, -4);
    iV2.setVal(4, 6);

    iV3 = iV1 + iV2;
    TEST_ASSERT(iV3[0] == 2);
    TEST_ASSERT(iV3[1] == 2);
    TEST_ASSERT(iV3[2] == 4);
    TEST_ASSERT(iV3[3] == 0);
    TEST_ASSERT(iV3[4] == 10);

    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);
    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == -4);
    TEST_ASSERT(iV2[4] == 6);
  }

  {  // iV1 -= iV2
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV1 -= iV2;
    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == -2);
    TEST_ASSERT(iV1[2] == -2);
    TEST_ASSERT(iV1[3] == 0);
    TEST_ASSERT(iV1[4] == -2);

    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[4] == 6);
    TEST_ASSERT(iV2[3] == 4);
  }
  {  // iV3 = IV1 - iV2
    SparseIntVect<int> iV1(5), iV2(5), iV3(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(3, 4);
    iV2.setVal(4, 6);
    iV2.setVal(1, 2);
    iV2.setVal(2, 3);

    iV3 = iV1 - iV2;
    TEST_ASSERT(iV3[0] == 2);
    TEST_ASSERT(iV3[1] == -2);
    TEST_ASSERT(iV3[2] == -2);
    TEST_ASSERT(iV3[3] == 0);
    TEST_ASSERT(iV3[4] == -2);

    TEST_ASSERT(iV1[0] == 2);
    TEST_ASSERT(iV1[1] == 0);
    TEST_ASSERT(iV1[2] == 1);
    TEST_ASSERT(iV1[3] == 4);
    TEST_ASSERT(iV1[4] == 4);
    TEST_ASSERT(iV2[0] == 0);
    TEST_ASSERT(iV2[1] == 2);
    TEST_ASSERT(iV2[2] == 3);
    TEST_ASSERT(iV2[3] == 4);
    TEST_ASSERT(iV2[4] == 6);
  }

  {  // operator== and operator!=
    SparseIntVect<int> iV1(5), iV2(5), iV3(3), iV4(5);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(1, 2);
    iV2.setVal(2, 3);
    iV2.setVal(3, 4);
    iV2.setVal(4, 6);

    iV4.setVal(1, 2);
    iV4.setVal(2, 3);
    iV4.setVal(3, 4);
    iV4.setVal(4, 6);

    TEST_ASSERT(iV1 == iV1);
    TEST_ASSERT(iV2 == iV2);
    TEST_ASSERT(iV3 == iV3);
    TEST_ASSERT(iV1 != iV2);
    TEST_ASSERT(iV1 != iV3);
    TEST_ASSERT(iV2 != iV1);
    TEST_ASSERT(iV3 != iV1);
    TEST_ASSERT(iV1 != iV3);
    TEST_ASSERT(iV1 != iV4);
    TEST_ASSERT(iV2 == iV4);
  }

  {  // test negative values (was sf.net Issue 3295215)
    SparseIntVect<int> iV1(5), iV2(5);
    iV1.setVal(0, -2);
    iV1.setVal(2, 1);
    iV1.setVal(3, -4);
    iV1.setVal(4, 4);

    iV2.setVal(1, -2);
    iV2.setVal(2, 3);
    iV2.setVal(3, -4);
    iV2.setVal(4, 6);

    TEST_ASSERT(feq(DiceSimilarity(iV1, iV2), 18. / 26.));
  }
}

void test7SparseIntVectPickles() {
  {
    SparseIntVect<int> iV1(5), iV2(3);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);
    iV1.setVal(4, 4);

    iV2.setVal(2, 3);
    TEST_ASSERT(iV1 != iV2);
    std::string pkl;
    pkl = iV1.toString();
    iV2.fromString(pkl);
    TEST_ASSERT(iV1 == iV2);
  }

  {
    SparseIntVect<char> iV1(5);
    SparseIntVect<int> iV2(3);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);

    iV2.setVal(1, 1);
    std::string pkl;
    pkl = iV1.toString();
    iV2.fromString(pkl);
    TEST_ASSERT(iV2.getLength() == iV1.getLength());
    TEST_ASSERT(iV2[0] == 2)
    TEST_ASSERT(iV2[1] == 0)
    TEST_ASSERT(iV2[2] == 1)
    TEST_ASSERT(iV2[3] == 4)
  }

  {
    SparseIntVect<int> iV1(5);
    SparseIntVect<char> iV2(3);
    iV1.setVal(0, 2);
    iV1.setVal(2, 1);
    iV1.setVal(3, 4);

    std::string pkl;
    pkl = iV1.toString();
    try {
      iV2.fromString(pkl);
      TEST_ASSERT(0);
    } catch (ValueErrorException &) {
      ;
    }
  }
}

void test8BitVectPickles() {
#if 0
  {
    std::string dirName = getenv("RDBASE");
    dirName+="/Code/DataStructs/testData/";
    std::string pklName = dirName+"test1.bin";
    std::ofstream outS;
    outS.open(pklName.c_str(),std::ios_base::binary);

    ExplicitBitVect bv(32);
    for(int i=0;i<32;i+=2){
      bv.setBit(i);
    }
    std::string pkl=bv.toString();
    unsigned int sz=pkl.size();
    outS<<sz;
    outS<<pkl;
    outS.close();
  }
#endif

  {
    std::string dirName = getenv("RDBASE");
    dirName += "/Code/DataStructs/testData/";
    std::string pklName = dirName + "test1.bin";
    std::ifstream inS;
    inS.open(pklName.c_str(), std::ios_base::binary);
    unsigned int length;
    inS >> length;
    auto *buff = new char[length];
    length = inS.readsome(buff, length);
    inS.close();
    std::string pkl(buff, length);
    delete[] buff;
    ExplicitBitVect bv(pkl);

    TEST_ASSERT(bv.getNumBits() == 32);
    TEST_ASSERT(bv.getNumOnBits() == 16);
    TEST_ASSERT(bv[0]);
    TEST_ASSERT(!bv[1]);
  }
}

void test9BitVectFPS() {
  {
    ExplicitBitVect bv(32);
    std::string fps;

    fps = BitVectToFPSText(bv);
    TEST_ASSERT(fps == "00000000");

    bv.setBit(0);
    bv.setBit(1);
    bv.setBit(17);
    bv.setBit(23);
    bv.setBit(31);

    fps = BitVectToFPSText(bv);
    TEST_ASSERT(fps == "03008280");
  }
  {
    ExplicitBitVect bv(32), bv2(32);
    std::string fps;

    fps = BitVectToFPSText(bv);
    TEST_ASSERT(fps == "00000000");
    UpdateBitVectFromFPSText(bv2, fps);
    TEST_ASSERT(bv == bv2);

    bv.setBit(0);
    bv.setBit(1);
    bv.setBit(4);
    bv.setBit(17);
    bv.setBit(23);
    bv.setBit(31);

    fps = BitVectToFPSText(bv);
    UpdateBitVectFromFPSText(bv2, fps);
    TEST_ASSERT(bv == bv2);
  }
  {
    ExplicitBitVect bv(33);
    std::string fps;

    fps = BitVectToFPSText(bv);
    TEST_ASSERT(fps == "0000000000");

    bv.setBit(0);
    bv.setBit(32);

    fps = BitVectToFPSText(bv);
    TEST_ASSERT(fps == "0100000001");
  }
  {
    ExplicitBitVect bv(33), bv2(33);
    std::string fps;

    fps = BitVectToFPSText(bv);
    TEST_ASSERT(fps == "0000000000");
    UpdateBitVectFromFPSText(bv2, fps);
    TEST_ASSERT(bv == bv2);

    bv.setBit(0);
    bv.setBit(1);
    bv.setBit(4);
    bv.setBit(17);
    bv.setBit(23);
    bv.setBit(32);

    fps = BitVectToFPSText(bv);
    UpdateBitVectFromFPSText(bv2, fps);
    TEST_ASSERT(bv == bv2);
  }
}

void test10BitVectBinaryText() {
  {
    ExplicitBitVect bv(32);
    std::string fps;

    fps = BitVectToBinaryText(bv);
    TEST_ASSERT(fps.size() == 4);
    for (char fp : fps) {
      TEST_ASSERT(fp == 0);
    }

    bv.setBit(0);
    bv.setBit(9);
    bv.setBit(17);
    bv.setBit(26);

    fps = BitVectToBinaryText(bv);
    TEST_ASSERT(fps.size() == 4);
    for (char fp : fps) {
      TEST_ASSERT(fp != 0);
    }
  }
  {
    ExplicitBitVect bv(32), bv2(32);
    std::string fps;

    fps = BitVectToBinaryText(bv);
    TEST_ASSERT(fps.size() == 4);
    for (char fp : fps) {
      TEST_ASSERT(fp == 0);
    }
    UpdateBitVectFromBinaryText(bv2, fps);
    TEST_ASSERT(bv == bv2);

    bv.setBit(0);
    bv.setBit(1);
    bv.setBit(4);
    bv.setBit(17);
    bv.setBit(23);
    bv.setBit(31);

    fps = BitVectToBinaryText(bv);
    UpdateBitVectFromBinaryText(bv2, fps);
    TEST_ASSERT(bv == bv2);
  }
  {
    ExplicitBitVect bv(33);
    std::string fps;

    fps = BitVectToBinaryText(bv);
    TEST_ASSERT(fps.size() == 5);
    for (char fp : fps) {
      TEST_ASSERT(fp == 0);
    }

    bv.setBit(0);
    bv.setBit(32);

    fps = BitVectToBinaryText(bv);
    TEST_ASSERT(fps.size() == 5);
    TEST_ASSERT(fps[0] != 0);
    for (unsigned int i = 1; i < fps.size() - 1; ++i) {
      TEST_ASSERT(fps[i] == 0);
    }
    TEST_ASSERT(fps[fps.size() - 1] != 0);
  }
  {
    ExplicitBitVect bv(33), bv2(33);
    std::string fps;

    fps = BitVectToBinaryText(bv);
    TEST_ASSERT(fps.size() == 5);
    UpdateBitVectFromBinaryText(bv2, fps);
    TEST_ASSERT(bv == bv2);

    bv.setBit(0);
    bv.setBit(1);
    bv.setBit(4);
    bv.setBit(17);
    bv.setBit(23);
    bv.setBit(32);

    fps = BitVectToBinaryText(bv);
    UpdateBitVectFromBinaryText(bv2, fps);
    TEST_ASSERT(bv == bv2);
  }
}

void test11SimilaritiesBV() {
  // similarity = 1.0
  ExplicitBitVect bv(10);
  bv.setBit(0);
  bv.setBit(1);
  bv.setBit(4);
  bv.setBit(6);
  bv.setBit(9);
  ExplicitBitVect bv2 = bv;

  TEST_ASSERT(feq(TanimotoSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(DiceSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(CosineSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(KulczynskiSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(SokalSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(McConnaugheySimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(BraunBlanquetSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(RusselSimilarity(bv, bv2), 0.5));
  TEST_ASSERT(feq(RogotGoldbergSimilarity(bv, bv2), 1.));
  TEST_ASSERT(feq(AllBitSimilarity(bv, bv2), 1.));

  // similarity = 0.0
  bv2 = ExplicitBitVect(10);
  bv2.setBit(2);
  bv2.setBit(3);
  bv2.setBit(5);
  bv2.setBit(7);
  bv2.setBit(8);

  TEST_ASSERT(feq(TanimotoSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(DiceSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(CosineSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(KulczynskiSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(SokalSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(McConnaugheySimilarity(bv, bv2), -1.));
  TEST_ASSERT(feq(BraunBlanquetSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(RusselSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(RogotGoldbergSimilarity(bv, bv2), 0.));
  TEST_ASSERT(feq(AllBitSimilarity(bv, bv2), 0.));

  // similarity ~= 0.5
  bv.setBit(5);
  bv2 = ExplicitBitVect(10);
  bv2.setBit(0);
  bv2.setBit(2);
  bv2.setBit(4);
  bv2.setBit(5);
  bv2.setBit(8);
  bv2.setBit(9);

  TEST_ASSERT(feq(TanimotoSimilarity(bv, bv2), 0.5));
  TEST_ASSERT(feq(DiceSimilarity(bv, bv2), 0.6666));
  TEST_ASSERT(feq(CosineSimilarity(bv, bv2), 0.6666));
  TEST_ASSERT(feq(KulczynskiSimilarity(bv, bv2), 0.6666));
  TEST_ASSERT(feq(SokalSimilarity(bv, bv2), 0.3333));
  TEST_ASSERT(feq(McConnaugheySimilarity(bv, bv2), 0.3333));
  TEST_ASSERT(feq(BraunBlanquetSimilarity(bv, bv2), 0.6666));
  TEST_ASSERT(feq(RusselSimilarity(bv, bv2), 0.4));
  TEST_ASSERT(feq(RogotGoldbergSimilarity(bv, bv2), 0.5833));
  TEST_ASSERT(feq(AllBitSimilarity(bv, bv2), 0.6));
}

void test12SimilaritiesSparseBV() {
  // similarity = 1.0
  SparseBitVect sbv(10);
  sbv.setBit(0);
  sbv.setBit(1);
  sbv.setBit(4);
  sbv.setBit(6);
  sbv.setBit(9);
  SparseBitVect sbv2 = sbv;

  TEST_ASSERT(feq(TanimotoSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(DiceSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(CosineSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(KulczynskiSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(SokalSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(McConnaugheySimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(BraunBlanquetSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(RusselSimilarity(sbv, sbv2), 0.5));
  TEST_ASSERT(feq(RogotGoldbergSimilarity(sbv, sbv2), 1.));
  TEST_ASSERT(feq(AllBitSimilarity(sbv, sbv2), 1.));

  // similarity = 0.0
  sbv2 = SparseBitVect(10);
  sbv2.setBit(2);
  sbv2.setBit(3);
  sbv2.setBit(5);
  sbv2.setBit(7);
  sbv2.setBit(8);

  TEST_ASSERT(feq(TanimotoSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(DiceSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(CosineSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(KulczynskiSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(SokalSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(McConnaugheySimilarity(sbv, sbv2), -1.));
  TEST_ASSERT(feq(BraunBlanquetSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(RusselSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(RogotGoldbergSimilarity(sbv, sbv2), 0.));
  TEST_ASSERT(feq(AllBitSimilarity(sbv, sbv2), 0.));

  // similarity ~= 0.5
  sbv.setBit(5);
  sbv2 = SparseBitVect(10);
  sbv2.setBit(0);
  sbv2.setBit(2);
  sbv2.setBit(4);
  sbv2.setBit(5);
  sbv2.setBit(8);
  sbv2.setBit(9);

  TEST_ASSERT(feq(TanimotoSimilarity(sbv, sbv2), 0.5));
  TEST_ASSERT(feq(DiceSimilarity(sbv, sbv2), 0.6666));
  TEST_ASSERT(feq(CosineSimilarity(sbv, sbv2), 0.6666));
  TEST_ASSERT(feq(KulczynskiSimilarity(sbv, sbv2), 0.6666));
  TEST_ASSERT(feq(SokalSimilarity(sbv, sbv2), 0.3333));
  TEST_ASSERT(feq(McConnaugheySimilarity(sbv, sbv2), 0.3333));
  TEST_ASSERT(feq(BraunBlanquetSimilarity(sbv, sbv2), 0.6666));
  TEST_ASSERT(feq(RusselSimilarity(sbv, sbv2), 0.4));
  TEST_ASSERT(feq(RogotGoldbergSimilarity(sbv, sbv2), 0.5833));
  TEST_ASSERT(feq(AllBitSimilarity(sbv, sbv2), 0.6));
}

void test13BitVectAllOnes() {
  {
    ExplicitBitVect bv(32, false);
    TEST_ASSERT(bv.getNumOnBits() == 0);
    TEST_ASSERT(bv[0] == 0);

    ExplicitBitVect bv2(32, true);
    TEST_ASSERT(bv2.getNumOnBits() == 32);
    TEST_ASSERT(bv2[0] == 1);
  }
}

void test14BitVectConcatenation() {
  {
    ExplicitBitVect bv(32, false);
    ExplicitBitVect bv2(32, true);
    ExplicitBitVect bv3 = bv + bv2;
    TEST_ASSERT(bv3.getNumBits() == 64);
    TEST_ASSERT(bv3.getNumOnBits() == 32);
    TEST_ASSERT(bv3.getNumOffBits() == 32);
  }
}

void test15BitmapOps() {
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    TEST_ASSERT(CalcBitmapPopcount(bv1, 5) == 5);
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x3, 0x1, 0x1};
    TEST_ASSERT(CalcBitmapPopcount(bv1, 5) == 6);
  }
  {
    const unsigned char bv1[5] = {0x0, 0x0, 0x0, 0x0, 0x0};
    TEST_ASSERT(CalcBitmapPopcount(bv1, 5) == 0);
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    TEST_ASSERT(feq(CalcBitmapTanimoto(bv1, bv2, 5), 1.0));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x0, 0x1};
    TEST_ASSERT(feq(CalcBitmapTanimoto(bv1, bv2, 5), 0.8));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    TEST_ASSERT(feq(CalcBitmapTversky(bv1, bv2, 5, 1., 1.), 1.0));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x0, 0x1};
    TEST_ASSERT(feq(CalcBitmapTversky(bv1, bv2, 5, 1., 1.), 0.8));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    TEST_ASSERT(feq(CalcBitmapDice(bv1, bv2, 5), 1.0));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x0, 0x1};
    TEST_ASSERT(feq(CalcBitmapDice(bv1, bv2, 5), 8. / 9));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    TEST_ASSERT(feq(CalcBitmapTversky(bv1, bv2, 5, 0.5, 0.5), 1.0));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x1, 0x1, 0x1, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x1, 0x0, 0x1};
    TEST_ASSERT(feq(CalcBitmapTversky(bv1, bv2, 5, 0.5, 0.5), 8. / 9));
  }

  {
    const unsigned char bv1[5] = {0x1, 0x0, 0x1, 0x0, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x5, 0x1, 0x1};
    TEST_ASSERT(CalcBitmapAllProbeBitsMatch(bv1, bv2, 5));
  }
  {
    const unsigned char bv1[5] = {0x1, 0x0, 0x1, 0x0, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x2, 0x1, 0x1};
    TEST_ASSERT(!CalcBitmapAllProbeBitsMatch(bv1, bv2, 5));
  }

  {
    const unsigned char bv1[5] = {0x1, 0x0, 0x1, 0x0, 0x1};
    const unsigned char bv2[5] = {0x1, 0x1, 0x5, 0x1, 0x1};
    TEST_ASSERT(feq(CalcBitmapTversky(bv1, bv2, 5, 1.0, 0.), 1.0));
  }
}

void test16BitVectProps() {
  ExplicitBitVect bv(32);
  for(int i=0;i<32;i+=2){
    bv.setBit(i);
  }

  ExplicitBitVect bv2(bv.toString());
  TEST_ASSERT(bv == bv2);
  
  Dict d;
  d.setVal<ExplicitBitVect>("exp", bv);
  RDValue &value = d.getData()[0].val;
  
  DataStructsExplicitBitVecPropHandler bv_handler;
  std::vector<CustomPropHandler*> handlers = {&bv_handler,
                                              bv_handler.clone()};
  for(auto handler: handlers)
  {
    TEST_ASSERT(handler->canSerialize(value));
    RDValue bad_value = 1;
    TEST_ASSERT(!handler->canSerialize(bad_value));
    std::stringstream ss;
    TEST_ASSERT(handler->write(ss, value));
    RDValue newValue;
    TEST_ASSERT(handler->read(ss, newValue));
    TEST_ASSERT(from_rdvalue<ExplicitBitVect>(newValue) == bv);
  }
  delete handlers[1];
}


int main() {
  RDLog::InitLogs();
  try {
    throw IndexErrorException(3);
  } catch (IndexErrorException &) {
    BOOST_LOG(rdInfoLog) << "pass" << endl;
  }

  stringstream ss(ios_base::binary | ios_base::out | ios_base::in);
  int v1 = 4, v2 = 5, v3, v4;

  ss.write((const char *)&v1, sizeof(v1));
  ss.write((const char *)&v2, sizeof(v2));
  ss.seekp(0, ios_base::beg);
  RDKit::streamRead(ss, v3);
  RDKit::streamRead(ss, v4);

  TXTMSG("v3", v3);
  TXTMSG("v4", v4);

  BOOST_LOG(rdInfoLog) << " SPARSE -----------------------------------"
                       << std::endl;
  SparseBitVect sparseFoo(10);
  Test(sparseFoo);
  TaniTest(sparseFoo);
  ProbeTest(sparseFoo);
  BOOST_LOG(rdInfoLog) << " Explicit ----------------------------------"
                       << std::endl;
  ExplicitBitVect explicitFoo(10);
  Test(explicitFoo);
  TaniTest(explicitFoo);
  BOOST_LOG(rdInfoLog) << " Done" << std::endl;

  BOOST_LOG(rdInfoLog)
      << " Test DiscreteValue Vectors 1 ----------------------------" << endl;
  test1DiscreteVect();
  BOOST_LOG(rdInfoLog)
      << " Test DiscreteValue Vectors 2 ------------------------------" << endl;
  test2DiscreteVectDists();
  BOOST_LOG(rdInfoLog)
      << " Test DiscreteValue Vectors 3 ---------------------------" << endl;
  test3DiscreteVectPickles();

  BOOST_LOG(rdInfoLog)
      << " Test DiscreteValue Operations -----------------------------" << endl;
  test4DiscreteVectOps1();

  BOOST_LOG(rdInfoLog)
      << " Test DiscreteValue Operations 2 -------------------------- " << endl;
  test5DiscreteVectOps2();

  BOOST_LOG(rdInfoLog)
      << " Test SparseIntVect  ------------------------------------"
      << std::endl;
  test6SparseIntVect();
  BOOST_LOG(rdInfoLog)
      << " Test SparseIntVect Serialization  --------------------------"
      << std::endl;
  test7SparseIntVectPickles();

  BOOST_LOG(rdInfoLog)
      << " Test BitVect Serialization  -------------------------------"
      << std::endl;
  test8BitVectPickles();

  BOOST_LOG(rdInfoLog)
      << " Test BitVect to FPS  -------------------------------" << std::endl;
  test9BitVectFPS();

  BOOST_LOG(rdInfoLog)
      << " Test BitVect to binary string  -------------------------------"
      << std::endl;
  test10BitVectBinaryText();

  BOOST_LOG(rdInfoLog)
      << " Test Similarity Measures BitVect -------------------------------"
      << std::endl;
  test11SimilaritiesBV();

  BOOST_LOG(rdInfoLog) << " Test Similarity Measures SparseBitVect "
                          "-------------------------------"
                       << std::endl;
  test12SimilaritiesSparseBV();

  BOOST_LOG(rdInfoLog)
      << " Test BitVect with all ones -------------------------------"
      << std::endl;
  test13BitVectAllOnes();

  BOOST_LOG(rdInfoLog) << " Test Explicit BitVects: Concatenation Operation  "
                          "-------------------------------"
                       << std::endl;
  test14BitVectConcatenation();

  BOOST_LOG(rdInfoLog) << " Test bitmap operations  "
                          "-------------------------------"
                       << std::endl;
  test15BitmapOps();

  BOOST_LOG(rdInfoLog) << " Test bitmaps as properties "
                          "-------------------------------"
                       << std::endl;
  test16BitVectProps();
  return 0;
}
