#include <Python.h>
#include <structmember.h>
#include "gtf.h"

typedef struct {
    PyObject_HEAD
    GTFtree *t;
} pyGTFtree_t;

/* 
  Remove all asserts and ensure that the new return values are honoured.

  Profile the code with a test to eliminate unneeded cruft.
*/

static PyObject *pyGTFinit(PyObject *self, PyObject *args);
static PyObject *pyAddEntry(pyGTFtree_t *self, PyObject *args);
static PyObject *pyAddEnrichmentEntry(pyGTFtree_t *self, PyObject *args);
static PyObject *pyVine2Tree(pyGTFtree_t *self, PyObject *args);
static PyObject *pyPrintGTFtree(pyGTFtree_t *self, PyObject *args);
static PyObject *pyCountEntries(pyGTFtree_t *self, PyObject *args);
static PyObject *pyFindOverlaps(pyGTFtree_t *self, PyObject *args);
static PyObject *pyFindOverlappingFeatures(pyGTFtree_t *self, PyObject *args);
static PyObject *pyIsTree(pyGTFtree_t *self, PyObject *args);
static void pyGTFDealloc(pyGTFtree_t *self);

static PyMethodDef treeMethods[] = {
    {"initTree", (PyCFunction) pyGTFinit, METH_VARARGS,
"Initialize the tree\n"},
    {"addEntry", (PyCFunction) pyAddEntry, METH_VARARGS,
"Some documentation for pyAddEntry\n"},
    {"addEnrichmentEntry", (PyCFunction) pyAddEnrichmentEntry, METH_VARARGS,
"Some documentation for pyAddEnrichmentEntry\n"},
    {"finish", (PyCFunction) pyVine2Tree, METH_VARARGS,
"This must be called after ALL entries from ALL files have been added.\n"},
    {"printGTFtree", (PyCFunction) pyPrintGTFtree, METH_VARARGS,
"Prints a text representation in dot format.\n"},
    {"countEntries", (PyCFunction) pyCountEntries, METH_VARARGS,
"Count the number of entries in a GTFtree\n"},
    {"isTree", (PyCFunction) pyIsTree, METH_VARARGS,
"Return True if the object is a tree\n"},
    {"findOverlaps", (PyCFunction) pyFindOverlaps, METH_VARARGS,
"Find overlapping intervals\n"},
    {"findOverlappingFeatures", (PyCFunction) pyFindOverlappingFeatures, METH_VARARGS,
"Find overlapping intervals, returning a list of features\n"},
    {NULL, NULL, 0, NULL}
};

#if PY_MAJOR_VERSION >= 3
struct treemodule_state {
    PyObject *error;
};

#define GETSTATE(m) ((struct treemodule_state*)PyModule_GetState(m))

static PyModuleDef treemodule = {
    PyModuleDef_HEAD_INIT,
    "tree",
    "A python module creating/accessing GTF-based interval trees with associated meta-data",
    -1,
    treeMethods,
    NULL, NULL, NULL, NULL
};
#endif


//Should set tp_dealloc, tp_print, tp_repr, tp_str, tp_members
static PyTypeObject pyGTFtree = {
#if PY_MAJOR_VERSION >= 3
    PyVarObject_HEAD_INIT(NULL, 0)
#else
    PyObject_HEAD_INIT(NULL)
    0,              /*ob_size*/
#endif
    "pyGTFtree",          /*tp_name*/
    sizeof(pyGTFtree_t),           /*tp_basicsize*/
    0,                         /*tp_itemsize*/
    (destructor)pyGTFDealloc,  /*tp_dealloc*/
    0,                         /*tp_print*/
    0,                         /*tp_getattr*/
    0,                         /*tp_setattr*/
    0,                         /*tp_compare*/
    0,                         /*tp_repr*/
    0,                         /*tp_as_number*/
    0,                         /*tp_as_sequence*/
    0,                         /*tp_as_mapping*/
    0,                         /*tp_hash*/
    0,                         /*tp_call*/
    0,                         /*tp_str*/
    PyObject_GenericGetAttr,   /*tp_getattro*/
    PyObject_GenericSetAttr,   /*tp_setattro*/
    0,                         /*tp_as_buffer*/
#if PY_MAJOR_VERSION >= 3
    Py_TPFLAGS_DEFAULT,        /*tp_flags*/
#else
    Py_TPFLAGS_HAVE_CLASS,     /*tp_flags*/
#endif
    "GTF tree",                /*tp_doc*/
    0,                         /*tp_traverse*/
    0,                         /*tp_clear*/
    0,                         /*tp_richcompare*/
    0,                         /*tp_weaklistoffset*/
    0,                         /*tp_iter*/
    0,                         /*tp_iternext*/
    treeMethods,               /*tp_methods*/
    0,                         /*tp_members*/
    0,                         /*tp_getset*/
    0,                         /*tp_base*/
    0,                         /*tp_dict*/
    0,                         /*tp_descr_get*/
    0,                         /*tp_descr_set*/
    0,                         /*tp_dictoffset*/
    0,                         /*tp_init*/
    0,                         /*tp_alloc*/
    0,                         /*tp_new*/
    0,0,0,0,0,0
};