FastaBuffViews.c File Reference

#include "FastaBuffViews.h"
#include <stdbool.h>
#include <stdint.h>
#include <Python.h>
#include "../../formats/fasta.h"
#include "../../formats/gtf.h"

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Functions
void	FastaBuff_iterator_initialise (FastaBuff_iterator *iter, FastaBuff *buff, bool reverse)
static void	FastaBuff_iterator_dealloc (FastaBuff_iterator *self)
static PyObject *	FastaBuff_iterator_iter (FastaBuff_iterator *self)
static PyObject *	FastaBuff_iterator_next (FastaBuff_iterator *self)
PyObject *	FastaBuff_view_initialise (FastaBuff_view *view, FastaBuff *buff, Py_ssize_t start, Py_ssize_t stop, Py_ssize_t step, Py_ssize_t slicelength)
int	FastaBuff_view_init (FastaBuff_view *self, PyObject *args, PyObject *kwds)
static void	FastaBuff_view_dealloc (FastaBuff_view *self)
static PyObject *	FastaBuff_view_iter (FastaBuff_view *self)
static PyObject *	FastaBuff_view_reversed (FastaBuff_view *self)
static Py_ssize_t	FastaBuff_view_len (FastaBuff_view *self)
static PyObject *	FastaBuff_view_subscript (FastaBuff_view *self, PyObject *key)
static PyObject *	FastaBuff_view_richcompare (FastaBuff_view *restrict self, PyObject *restrict other, const int op)
static int64_t	view_index (FastaBuff_view *restrict self, PyObject *restrict other, size_t start, size_t end)
static PyObject *	FastaBuff_view_index (FastaBuff_view *self, PyObject *args, PyObject *kwargs)
static int	FastaBuff_view_contains (FastaBuff_view *self, PyObject *other)
static PyObject *	FastaBuff_view_count (FastaBuff_view *self, PyObject *other)
static PyObject *	FastaBuff_view_get_annotated (FastaBuff_view *restrict self, PyObject *restrict first)
static PyObject *	FastaBuff_view_str (FastaBuff_view *self)

Variables
PyTypeObject	FastaBuff_iteratorType
static PyMethodDef	FastaBuff_viewMethods []
static PyMappingMethods	FastaBuffMap
static PySequenceMethods	FastaBuffSeq
PyTypeObject	FastaBuff_viewType

Function Documentation

FastaBuff_iterator_dealloc()

static void FastaBuff_iterator_dealloc ( FastaBuff_iterator *  self )

static

FastaBuff_iterator_initialise()

void FastaBuff_iterator_initialise	(	FastaBuff_iterator *	iter,
		FastaBuff *	buff,
		bool	reverse
	)

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FastaBuff_iterator_iter()

static PyObject * FastaBuff_iterator_iter ( FastaBuff_iterator *  self )

static

FastaBuff_iterator_next()

static PyObject * FastaBuff_iterator_next ( FastaBuff_iterator *  self )

static

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FastaBuff_view_contains()

static int FastaBuff_view_contains ( FastaBuff_view *  self, PyObject *  other  )

static

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FastaBuff_view_count()

static PyObject * FastaBuff_view_count ( FastaBuff_view *  self, PyObject *  other  )

static

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FastaBuff_view_dealloc()

static void FastaBuff_view_dealloc ( FastaBuff_view *  self )

static

FastaBuff_view_get_annotated()

static PyObject * FastaBuff_view_get_annotated ( FastaBuff_view *restrict  self, PyObject *restrict  first  )

static

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FastaBuff_view_index()

static PyObject * FastaBuff_view_index ( FastaBuff_view *  self, PyObject *  args, PyObject *  kwargs  )

static

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FastaBuff_view_init()

int FastaBuff_view_init	(	FastaBuff_view *	self,
		PyObject *	args,
		PyObject *	kwds
	)

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FastaBuff_view_initialise()

PyObject * FastaBuff_view_initialise	(	FastaBuff_view *	view,
		FastaBuff *	buff,
		Py_ssize_t	start,
		Py_ssize_t	stop,
		Py_ssize_t	step,
		Py_ssize_t	slicelength
	)

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FastaBuff_view_iter()

static PyObject * FastaBuff_view_iter ( FastaBuff_view *  self )

static

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FastaBuff_view_len()

static Py_ssize_t FastaBuff_view_len ( FastaBuff_view *  self )

static

FastaBuff_view_reversed()

static PyObject * FastaBuff_view_reversed ( FastaBuff_view *  self )

static

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FastaBuff_view_richcompare()

static PyObject * FastaBuff_view_richcompare ( FastaBuff_view *restrict  self, PyObject *restrict  other, const int  op  )

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FastaBuff_view_str()

static PyObject * FastaBuff_view_str ( FastaBuff_view *  self )

static

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FastaBuff_view_subscript()

static PyObject * FastaBuff_view_subscript ( FastaBuff_view *  self, PyObject *  key  )

static

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view_index()

static int64_t view_index ( FastaBuff_view *restrict  self, PyObject *restrict  other, size_t  start, size_t  end  )

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Variable Documentation

FastaBuff_iteratorType

PyTypeObject FastaBuff_iteratorType

Initial value:

= {
    PyVarObject_HEAD_INIT(NULL, 0).tp_name = "eccLib.FastaBuff_iterator",
    .tp_basicsize = sizeof(FastaBuff_iterator),
    .tp_doc =
        PyDoc_STR("An iterator for a buffer for storing a FASTA sequence"),
    .tp_itemsize = 0,
    .tp_flags = Py_TPFLAGS_DEFAULT,
    .tp_new = PyType_GenericNew,
    .tp_getattro = PyObject_GenericGetAttr,
    .tp_iter = (getiterfunc)FastaBuff_iterator_iter,
    .tp_iternext = (iternextfunc)FastaBuff_iterator_next,
    .tp_dealloc = (destructor)FastaBuff_iterator_dealloc}

FastaBuff_viewMethods

PyMethodDef FastaBuff_viewMethods[]

static

Initial value:

= {
    {"get_annotated", (PyCFunction)FastaBuff_view_get_annotated, METH_O, ""},
    {"index", (PyCFunction)FastaBuff_view_index, METH_VARARGS | METH_KEYWORDS,
     "Returns the index of the first occurrence of a subsequence"},
    {"count", (PyCFunction)FastaBuff_view_count, METH_O,
     "Returns the number of occurrences of a subsequence"},
    {"__reversed__", (PyCFunction)FastaBuff_view_reversed, METH_NOARGS,
     "Returns the reverse of the sequence"},
    {NULL, NULL, 0, NULL} 
}

FastaBuff_viewType

PyTypeObject FastaBuff_viewType

Initial value:

= {
    PyVarObject_HEAD_INIT(NULL, 0).tp_name = "eccLib.FastaBuff_view",
    .tp_basicsize = sizeof(FastaBuff_view),
    .tp_doc = PyDoc_STR("An view into a buffer for storing a FASTA sequence"),
    .tp_itemsize = 0,
    .tp_flags = Py_TPFLAGS_DEFAULT,
    .tp_new = PyType_GenericNew,
    .tp_init = (initproc)FastaBuff_view_init,
    .tp_getattro = PyObject_GenericGetAttr,
    .tp_iter = (getiterfunc)FastaBuff_view_iter,
    .tp_dealloc = (destructor)FastaBuff_view_dealloc,
    .tp_str = (reprfunc)FastaBuff_view_str,
    .tp_as_mapping = &FastaBuffMap,
    .tp_as_sequence = &FastaBuffSeq,
    .tp_methods = FastaBuff_viewMethods,
    .tp_richcompare = (richcmpfunc)FastaBuff_view_richcompare,
}

FastaBuffMap

PyMappingMethods FastaBuffMap

static

Initial value:

= {
    .mp_subscript = (binaryfunc)FastaBuff_view_subscript}

FastaBuffSeq

PySequenceMethods FastaBuffSeq

static

Initial value:

= {
    .sq_length = (lenfunc)FastaBuff_view_len,
    .sq_contains = (objobjproc)FastaBuff_view_contains,
}