void test_func_all(TIndex& index) {
const osmium::unsigned_object_id_type id1 = 12;
const osmium::unsigned_object_id_type id2 = 3;
const osmium::Location loc1{1.2, 4.5};
const osmium::Location loc2{3.5, -7.2};
REQUIRE_THROWS_AS(index.get(id1), const osmium::not_found&);
index.set(id1, loc1);
index.set(id2, loc2);
index.sort();
REQUIRE_THROWS_AS(index.get(0), const osmium::not_found&);
REQUIRE_THROWS_AS(index.get(1), const osmium::not_found&);
REQUIRE_THROWS_AS(index.get(5), const osmium::not_found&);
REQUIRE_THROWS_AS(index.get(100), const osmium::not_found&);
REQUIRE_THROWS_WITH(index.get(0), "id 0 not found");
REQUIRE_THROWS_WITH(index.get(1), "id 1 not found");
REQUIRE(index.get_noexcept(0) == osmium::Location{});
REQUIRE(index.get_noexcept(1) == osmium::Location{});
REQUIRE(index.get_noexcept(5) == osmium::Location{});
REQUIRE(index.get_noexcept(100) == osmium::Location{});
}
inline unsigned long long runTimePerIndexAF(CharString const dir, CharString const indexFolder, TText const & text, StringSet<TText> const & reads)
{
clock_t t, runningTimes[ITERATIONS];
unsigned long long sumTmp = 0;
typedef TSchnatt TIndex;
// prepare query sequences:
static unsigned char pattern[READCOUNT][READLENGTH + 1];
for (unsigned r = 0; r < READCOUNT; ++r)
{
CharString read(reads[r]);
strcpy(pattern[r], toCString(read));
}
TIndex::searchstate s;
// Load index
CharString tmp;
tmp = dir;
tmp += indexFolder;
tmp += "index";
TIndex index;
std::ifstream in(toCString(tmp));
index.load(in);
in.close();
for (unsigned i = 0; i < ITERATIONS; ++i)
{
t = clock();
for (int r = 0; r < READCOUNT; ++r)
{
index.init_search_state(s);
for (unsigned l = READLENGTH/2+1; l < READLENGTH; ++l)
{
index.backward_search(index.char2comp[pattern[r][l]], s);
}
for (signed l = READLENGTH/2; l >= 0; --l)
{
index.forward_search(index.char2comp[pattern[r][l]], s);
}
sumTmp += s.occ_begin;
#if _MY_DEBUG == 1
if (s.occ_end - s.occ_begin < 1)
std::cout << "AHHHHHHHHHHHHHHHHHHH6! " << (s.occ_end - s.occ_begin) << " " << reads[0] << std::endl;
#endif
}
runningTimes[i] = clock() - t;
}
std::cout << sumTmp << std::endl;
// Output: min, median, max
std::sort(runningTimes, runningTimes + ITERATIONS);
return runningTimes[(ITERATIONS-1)/2]; // return median
}
void test_func_all(TIndex& index) {
osmium::object_id_type id1 = 12;
osmium::object_id_type id2 = 3;
osmium::Location loc1(1.2, 4.5);
osmium::Location loc2(3.5, -7.2);
BOOST_CHECK_THROW(index.get(id1), osmium::not_found);
index.set(id1, loc1);
index.set(id2, loc2);
index.sort();
BOOST_CHECK_THROW(index.get(5), osmium::not_found);
BOOST_CHECK_THROW(index.get(100), osmium::not_found);
}
CDatedData::CDatedData(const CDatedData &right, const TIndex &selectedDim) :
date(right.date)
{
if ( selectedDim.Size() <= 0 )
data.CopyContent(right.data);
else
{
TIndex validDim;
for (int i=0; i<selectedDim.Size(); i++)
{
if (selectedDim[i] >=0 && selectedDim[i] < right.DataDimension())
validDim += selectedDim[i];
}
data = right.data.SubVector(validDim);
}
}
CDatedDataSeries::CDatedDataSeries(const TDenseMatrix &date_data_matrix, const TIndex &selectedTime, const TIndex &selectedDim)
{
if (selectedTime.Size() <= 0)
{
for (int i=0; i<date_data_matrix.rows; i++)
this->push_back(CDatedData(date_data_matrix.RowVector(i),selectedDim));
}
else
{
for (int i=0; i<selectedTime.Size(); i++)
{
if (selectedTime[i] >= 0 && selectedTime[i] < date_data_matrix.rows)
this->push_back(CDatedData(date_data_matrix.RowVector(selectedTime[i]), selectedDim));
}
}
}
CDatedDataSeries::CDatedDataSeries(const CDatedDataSeries &right, const TIndex &selectedTime, const TIndex &selectedDim)
{
if (selectedTime.Size() <= 0)
{
for (int i=0; i<right.ObservationLength(); i++)
this->push_back(CDatedData(right[i],selectedDim));
}
else
{
for (int i=0; i<selectedTime.Size(); i++)
{
if (selectedTime[i] >=0 && selectedTime[i] < (int)(right.size()) )
this->push_back(CDatedData(right[selectedTime[i]],selectedDim));
}
}
}
CDatedData::CDatedData(const CDate &_date, const TDenseVector &_data, const TIndex &selectedDim) :
date(_date)
{
if (selectedDim.Size() <= 0)
data.CopyContent(_data);
else
{
TIndex validDim;
for (int i=0; i<selectedDim.Size(); i++)
{
if (selectedDim[i] >=0 && selectedDim[i] < _data.Dimension())
validDim += selectedDim[i];
}
data = _data.SubVector(validDim);
}
}
CDatedDataSeries::CDatedDataSeries(const std::vector<CDate> &date_series, const TDenseMatrix &data_matrix, const TIndex &selectedTime, const TIndex &selectedDim)
{
int N = (int)date_series.size() <= data_matrix.rows ? (int)date_series.size() : data_matrix.rows;
if (selectedTime.Size() <= 0)
{
for (int i=0; i<N; i++)
this->push_back(CDatedData(date_series[i],data_matrix.RowVector(i,selectedDim)));
}
else
{
for (int i=0; i<selectedTime.Size(); i++)
{
if (selectedTime[i] >= 0 && selectedTime[i] < N)
this->push_back(CDatedData(date_series[selectedTime[i]],data_matrix.RowVector(selectedTime[i],selectedDim) ));
}
}
}
CDatedDataSeries::CDatedDataSeries(const std::vector<CDate> &date_series, const std::vector<TDenseVector> &data_series, const TIndex &selectedTime, const TIndex &selectedDim)
{
int N = (int)(date_series.size() <= data_series.size() ? date_series.size() : data_series.size());
if (selectedTime.Size() <= 0)
{
for (int i=0; i<N; i++)
this->push_back(CDatedData(date_series[i],data_series[i],selectedDim));
}
else
{
for (int i=0; i<selectedTime.Size(); i++)
{
if (selectedTime[i] >= 0 && selectedTime[i] < N)
this->push_back(CDatedData(date_series[selectedTime[i]], data_series[selectedTime[i]], selectedDim));
}
}
}
std::vector<CDate> CDatedDataSeries::GetDateSeries(const TIndex &selectedTime) const
{
std::vector<CDate> date_series;
if (selectedTime.Size() <= 0)
{
for (int i=0; i<ObservationLength(); i++)
date_series.push_back(this->operator[](i).GetDate());
}
else
{
for (int i=0; i<selectedTime.Size(); i++)
{
if (selectedTime[i] >= 0 || selectedTime[i] < ObservationLength())
date_series.push_back(this->operator[](selectedTime[i]).GetDate());
}
}
return date_series;
}
std::vector<TDenseVector> CDatedDataSeries::GetDataSeries_Vector(const TIndex &selectedTime, const TIndex &selectedDim) const
{
std::vector<TDenseVector> data_series;
if (selectedTime.Size() <= 0)
{
for (int i=0; i<ObservationLength(); i++)
data_series.push_back(this->operator[](i).GetData(selectedDim));
}
else
{
for (int i=0; i<selectedTime.Size(); i++)
{
if (selectedTime[i] >= 0 && selectedTime[i] < ObservationLength())
data_series.push_back(this->operator[](selectedTime[i]).GetData(selectedDim));
}
}
return data_series;
}
CDatedData::CDatedData(const TDenseVector &date_data, const TIndex &selectedDim) :
date(date_data)
{
if (date_data.Dimension() > 3) // there are data besides date
{
if (selectedDim.Size() <= 0)
data = date_data.SubVector(3,date_data.Dimension()-1);
else
{
TIndex validDim;
for (int i=0; i<selectedDim.Size(); i++)
{
if (selectedDim[i] >= 3 && selectedDim[i] < date_data.Dimension())
validDim += selectedDim[i];
}
data = date_data.SubVector(validDim);
}
}
}
