C++ (Cpp) getValueBegin示例

示例#1

文件： njn_dynprogproblim.cpp 项目： UCSantaCruzComputationalGenomicsLab/last

void DynProgProbLim::setValueBegin (Int4 valueBegin_)
// resets the offset d_valueBegin
// assert (offSet < getArrayCapacity ());
// if (getValueBegin () < valueBegin_) the caller must ensure consistency 
{
    if (valueBegin_ <= getValueBegin ()) 
    {
        DynProgProb::setValueBegin (valueBegin_);
        return;
    }

    assert (getValueBegin () < valueBegin_);
    size_t offSet = static_cast <size_t> (valueBegin_ - getValueBegin ());

    double *array = new double [getArrayCapacity ()];

    for (size_t i = 0; i < 2; i++) 
    {
        MemUtil::memCpy (array, getArray () [i], sizeof (double) * getArrayCapacity ());
        MemUtil::memZero (lgetArray () [i], sizeof (double) * getArrayCapacity ());
        
        if (offSet < getArrayCapacity ()) 
        {
            MemUtil::memCpy (lgetArray () [i], array + offSet, sizeof (double) * (getArrayCapacity () - offSet));
        }
    }

    delete [] array; array = 0;

    lgetValueBegin () = valueBegin_;
}

示例#2

文件： njn_dynprogprob.cpp 项目： atante/LAST-Plus

void DynProgProb::update () // updates dynamic prog probs 
{
    assert (getValueFct ());
    assert (getDimInputProb ());
    assert (getInputProb ());

    const size_t ARRAY_FAC = 2;
    assert (1 < ARRAY_FAC);

    Int4 i = 0;
    size_t j = 0;

    const double *oldArray = 0;
    double *array = 0;
    Int4 value = 0;
    Int4 valueBegin = 0;
    Int4 valueLower = 0;
    Int4 valueUpper = 0;
    size_t arrayPos = 0;

    oldArray = d_array_p [d_step % 2];
    array = d_array_p [(d_step + 1) % 2];
    valueLower = kMax_I4;
    valueUpper = kMin_I4;

    MemUtil::memZero (array, sizeof (double) * getArrayCapacity ());

    for (i = getValueLower (); i < getValueUpper (); i++) 
    {
        if (oldArray [getArrayPos (i)] == 0.0) continue;

        for (j = 0; j < getDimInputProb (); j++) 
        {
            if (getInputProb () [j] == 0.0) continue;

            // adjust the reserve, if necessary            
            value = getValueFct () (i, j);
            while (value < getValueBegin () || getValueEnd () <= value) {
            valueBegin = getValueBegin ();
            if (value < getValueBegin ()) valueBegin -= (ARRAY_FAC - 1) * getArrayCapacity ();
            reserve (ARRAY_FAC * getArrayCapacity ());
            setValueBegin (valueBegin);
            oldArray = d_array_p [d_step % 2];
            array = d_array_p [(d_step + 1) % 2];
            }

            if (value < valueLower) valueLower = value;
            if (valueUpper < value) valueUpper = value;

            // add the probability
            assert (getValueBegin () <= i);
            assert (i < getValueEnd ());
            array [getArrayPos (value)] += oldArray [getArrayPos (i)] * getInputProb () [j];
        }
    }

    d_valueLower = valueLower;
    d_valueUpper = valueUpper + 1;
    d_step++;
}

示例#3

文件： njn_dynprogproblim.cpp 项目： UCSantaCruzComputationalGenomicsLab/last

void DynProgProbLim::update () // updates dynamic prog probs 
    {
    assert (getValueFct ());
    assert (getDimInputProb ());
    assert (getInputProb ());
    assert (0 < getArrayCapacity ());

    Int4 i = 0;
    size_t j = 0;

    const double *oldArray = 0;
    double *array = 0;
    Int4 value = 0;
    Int4 valueLower = 0;
    Int4 valueUpper = 0;
    size_t arrayPos = 0;
    double prob = 0.0;

    oldArray = getArray () [getStep () % 2];
    array = lgetArray () [(getStep () + 1) % 2];
    valueLower = kMax_I4;
    valueUpper = kMin_I4;

    MemUtil::memZero (array, sizeof (double) * getArrayCapacity ());
    for (i = getValueLower (); i < getValueUpper (); i++) 
    {
        if (oldArray [getArrayPos (i)] == 0.0) continue;

        for (j = 0; j < getDimInputProb (); j++) 
        {
            if (getInputProb () [j] == 0.0) continue;

            value = getValueFct () (i, j);
            prob = oldArray [getArrayPos (i)] * getInputProb () [j];

            if (value < getValueBegin () || getValueEnd () <= value) 
            {
                d_probLost += prob;
            } 
            else 
            {
                if (value < valueLower) valueLower = value;
                if (valueUpper < value) valueUpper = value;

                // add the probability
                assert (getValueBegin () <= i);
                assert (i < getValueEnd ());
                array [getArrayPos (value)] += prob;
            }
        }
    }

    lgetValueLower () = valueLower;
    lgetValueUpper () = valueUpper + 1;
    lgetStep ()++;
}

示例#4

文件： njn_dynprogprob.cpp 项目： jackgopack4/pico-blast

void DynProgProb::setValueBegin (Int4 valueBegin_)
// resets the offset d_valueBegin
// assert (valueBegin_ <= getValueBegin ()) : enlarge the array only 
// assert (offSet < getArrayCapacity ());
{
    assert (valueBegin_ <= getValueBegin ());
    size_t offSet = static_cast <size_t> (getValueBegin () - valueBegin_);
    if (offSet == 0) return; // nothing to do

    assert (offSet < getArrayCapacity ());

    double *array = new double [getArrayCapacity ()];

    for (size_t i = 0; i < 2; i++) 
    {
        MemUtil::memCpy (array, d_array_p [i], sizeof (double) * getArrayCapacity ());
        MemUtil::memZero (d_array_p [i], sizeof (double) * getArrayCapacity ());
        MemUtil::memCpy (d_array_p [i] + offSet, array, sizeof (double) * (getArrayCapacity () - offSet));
    }

    delete [] array; array = 0;

    d_valueBegin = valueBegin_;
}