#include <Python.h>
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include "numpy/arrayobject.h"



static PyObject*
calculate(const char sequence[], int s, PyObject* matrix, npy_intp m)
{
    npy_intp n = s - m + 1;
    npy_intp i, j;
    char c;
    double score;
    int ok;
    PyObject* result;
    PyArrayObject* array;
    float* p;
    npy_intp shape = (npy_intp)n;
    float nan = 0.0;
    nan /= nan;
    if ((int)shape!=n)
    {
        PyErr_SetString(PyExc_ValueError, "integer overflow");
        return NULL;
    }
    result = PyArray_SimpleNew(1, &shape, NPY_FLOAT32);
    if (!result)
    {
        PyErr_SetString(PyExc_MemoryError, "failed to create output data");
        return NULL;
    }
    p = PyArray_DATA((PyArrayObject*)result);
    array = (PyArrayObject*)matrix;
    for (i = 0; i < n; i++)
    {
        score = 0.0;
        ok = 1;
        for (j = 0; j < m; j++)
        {
            c = sequence[i+j];
            switch (c)
            {
              /* Handling mixed case input here rather than converting it to
                 uppercase in Python code first, since doing so could use too
                 much memory if sequence is too long (e.g. chromosome or
                 plasmid). */
                case 'A':
                case 'a':
                    score += *((double*)PyArray_GETPTR2(array, j, 0)); break;
                case 'C':
                case 'c':
                    score += *((double*)PyArray_GETPTR2(array, j, 1)); break;
                case 'G':
                case 'g':
                    score += *((double*)PyArray_GETPTR2(array, j, 2)); break;
                case 'T':
                case 't':
                    score += *((double*)PyArray_GETPTR2(array, j, 3)); break;
                default:
                    ok = 0;
            }
        }
        if (ok) *p = (float)score;
        else *p = nan;
        p++;
    }
    return result;
}

static char calculate__doc__[] =
"    calculate(sequence, pwm) -> array of score values\n"
"\n"
"This function calculates the position-weight matrix scores for all\n"
"positions along the sequence, and returns them as a Numerical Python\n"
"array.\n";

static PyObject*
py_calculate(PyObject* self, PyObject* args, PyObject* keywords)
{
    const char* sequence;
    PyObject* matrix = NULL;
    static char* kwlist[] = {"sequence", "matrix", NULL};
    npy_intp m;
    int s;
    PyObject* result;
    PyArrayObject* array;
    if(!PyArg_ParseTupleAndKeywords(args, keywords, "s#O&", kwlist,
                                    &sequence,
                                    &s,
                                    PyArray_Converter,
                                    &matrix)) return NULL;

    array = (PyArrayObject*) matrix;
    if (PyArray_TYPE(array) != NPY_DOUBLE)
    {
        PyErr_SetString(PyExc_ValueError,
            "position-weight matrix should contain floating-point values");
        result = NULL;
    }
    else if (PyArray_NDIM(array) != 2) /* Checking number of dimensions */
    {
        result = PyErr_Format(PyExc_ValueError,
            "position-weight matrix has incorrect rank (%d expected 2)",
            PyArray_NDIM(array));
    }
    else if(PyArray_DIM(array, 1) != 4)
    {
        result = PyErr_Format(PyExc_ValueError,
            "position-weight matrix should have four columns (%" NPY_INTP_FMT
            " columns found)", PyArray_DIM(array, 1));
    }
    else
    {
        m = PyArray_DIM(array, 0);
        result = calculate(sequence, s, matrix, m);
    }
    Py_DECREF(matrix);
    return result;
}


static struct PyMethodDef methods[] = {
   {"calculate", (PyCFunction)py_calculate, METH_VARARGS | METH_KEYWORDS, calculate__doc__},
   {NULL,          NULL, 0, NULL} /* sentinel */
};


#if PY_MAJOR_VERSION >= 3

static struct PyModuleDef moduledef = {
        PyModuleDef_HEAD_INIT,
        "_pwm",
        "Fast calculations involving position-weight matrices",
        -1,
        methods,
        NULL,
        NULL,
        NULL,
        NULL
};

PyObject*
PyInit__pwm(void)

#else

void init_pwm(void)
#endif
{
  PyObject *m;

  import_array();

#if PY_MAJOR_VERSION >= 3
  m = PyModule_Create(&moduledef);
  if (m==NULL) return NULL;
#else
  m = Py_InitModule4("_pwm",
                     methods,
                     "Fast calculations involving position-weight matrices",
                     NULL,
                     PYTHON_API_VERSION);
  if (m==NULL) return;
#endif

  if (PyErr_Occurred()) Py_FatalError("can't initialize module _pwm");
#if PY_MAJOR_VERSION >= 3
    return m;
#endif
}