FastaBuff.c File Reference

Implementations for the FastaBuff object. More...

#include "FastaBuff.h"
#include <stdbool.h>
#include <stdint.h>
#include <Python.h>
#include "../../formats/fasta.h"
#include "../../formats/gtf.h"
#include "../../modules/eccLib.h"
#include "../GtfDict/GtfDict.h"
#include "FastaBuffViews.h"

Include dependency graph for FastaBuff.c:

Functions
static FastaBuff *	FastaBuff_new (PyTypeObject *type, PyObject *args, PyObject *kwargs)
	Allocates a new FastaBuff object.
static int	FastaBuff_init (FastaBuff *self, PyObject *restrict args, PyObject *restrict kwds)
	Initializes a FastaBuff object. Equivalent to the constructor in Python.
static Py_ssize_t	FastaBuff_len (FastaBuff *self)
	Returns the length of the FastaBuff.
static PyObject *	FastaBuff_str (FastaBuff *self)
	Converts the FastaBuff to a string.
uint8_t	FastaBuff_getItem (FastaBuff *self, Py_ssize_t index)
	Gets an item from the FastaBuff.
static int	FastaBuff_setItem (FastaBuff *self, Py_ssize_t index, PyObject *value)
	Sets a part of the sequence.
static int	FastaBuff_strindex (FastaBuff *self, size_t offset, size_t end, const char *value, size_t len)
	Returns the index of the first occurrence of the specified sequence in this FastaBuff, or -1 if this FastaBuff does not contain the sequence.
static int	FastaBuff_buffindex (FastaBuff *self, size_t offset, size_t end, FastaBuff *restrict other)
	Returns the index of the first occurrence of the specified sequence in this FastaBuff.
static int	FastaBuff_viewindex (FastaBuff *self, size_t offset, size_t end, FastaBuff_view *restrict other)
static int	FastaBuff_contains (FastaBuff *restrict self, PyObject *restrict value)
	Checks if the FastaBuff contains the specified value.
static PyObject *	FastaBuff_index (FastaBuff *restrict self, PyObject *restrict args)
	Returns the index of the first occurrence of the specified value in this FastaBuff.
static PyObject *	FastaBuff_count (FastaBuff *restrict self, PyObject *restrict value)
	Counts the number of occurrences of the specified value in this FastaBuff.
static PyObject *	FastaBuff_dump (FastaBuff *restrict self)
	Converts the FastaBuff to a bytes object.
static PyObject *	FastaBuff_get_annotated (FastaBuff *restrict self, PyObject *restrict first)
	Returns the annotated sequence.
static PyObject *	FastaBuff_richcompare (FastaBuff *restrict self, PyObject *restrict other, const int op)
	FastaBuff comparison function.
PyObject *	FastaBuff_getSubscript (FastaBuff *restrict self, PyObject *restrict key)
	Gets a subsequence of the FastaBuff.
static PyObject *	FastaBuff_find (FastaBuff *restrict self, PyObject *restrict firstArg)
	Finds occurrences of the specified sequence in this FastaBuff.
static PyObject *	FastaBuff_iter (FastaBuff *self)
static PyObject *	FastaBuff_reversed (FastaBuff *self)
static void	FastaBuff_dealloc (FastaBuff *self)
	Deallocates the FastaBuff.
FastaBuff *	FastaBuff_New (uint8_t *restrict buff, size_t buffSize, size_t buffLen, bool RNA)
	Creates a new FastaBuff object.
static PyObject *	FastaBuff_getstate (FastaBuff *self)
static PyObject *	FastaBuff_setstate (FastaBuff *self, PyObject *state)
	Sets the state of the FastaBuff from a tuple.
int	FastaBuff_getbuffer (FastaBuff *self, Py_buffer *view, int flags)

Variables
static PyMethodDef	FastaBuffMethods []
	The FastaBuff methods.
static PyMappingMethods	FastaBuffMap
	The FastaBuff mapping methods.
static PySequenceMethods	FastaBuffSeq
	The FastaBuff sequence methods.
static PyBufferProcs	FastaBuffBuffer
PyTypeObject	FastaBuffType
	The Python type definition for the FastaBuff object.

Detailed Description

Implementations for the FastaBuff object.

Function Documentation

FastaBuff_buffindex()

static int FastaBuff_buffindex ( FastaBuff * self, size_t offset, size_t end, FastaBuff *restrict other )

static

Returns the index of the first occurrence of the specified sequence in this FastaBuff.

Parameters

self	the FastaBuff to search in
offset	the offset to start searching from
end	the end offset to stop searching at
other	the other FastaBuff to search for

Returns

The index of the first occurrence of the specified sequence, or -1 on error.

Here is the call graph for this function:

Here is the caller graph for this function:

FastaBuff_getbuffer()

int FastaBuff_getbuffer	(	FastaBuff *	self,
		Py_buffer *	view,
		int	flags )

FastaBuff_getstate()

static PyObject * FastaBuff_getstate ( FastaBuff * self )

static

Here is the call graph for this function:

FastaBuff_iter()

static PyObject * FastaBuff_iter ( FastaBuff * self )

static

Here is the call graph for this function:

FastaBuff_reversed()

static PyObject * FastaBuff_reversed ( FastaBuff * self )

static

Here is the call graph for this function:

FastaBuff_setstate()

static PyObject * FastaBuff_setstate ( FastaBuff * self, PyObject * state )

static

Sets the state of the FastaBuff from a tuple.

Parameters

self	the FastaBuff to set the state of
state	the tuple to set the state from

Returns

NULL on error, otherwise the state tuple

FastaBuff_strindex()

static int FastaBuff_strindex ( FastaBuff * self, size_t offset, size_t end, const char * value, size_t len )

static

Returns the index of the first occurrence of the specified sequence in this FastaBuff, or -1 if this FastaBuff does not contain the sequence.

Parameters

self	the FastaBuff to search in
offset	the offset to start searching from
end	the end offset to stop searching at
value	substring
len	length of substring

Returns

The index of the first occurrence of the specified sequence, or -1 on error.

Here is the call graph for this function:

Here is the caller graph for this function:

FastaBuff_viewindex()

static int FastaBuff_viewindex ( FastaBuff * self, size_t offset, size_t end, FastaBuff_view *restrict other )

static

Here is the call graph for this function:

Here is the caller graph for this function:

Variable Documentation

FastaBuffBuffer

PyBufferProcs FastaBuffBuffer

static

Initial value:

= {.bf_getbuffer =
                                            (getbufferproc)FastaBuff_getbuffer,
                                        .bf_releasebuffer = NULL}

FastaBuffMap

PyMappingMethods FastaBuffMap

static

Initial value:

= {.mp_subscript =
                                            (binaryfunc)FastaBuff_getSubscript}

The FastaBuff mapping methods.

FastaBuffMethods

PyMethodDef FastaBuffMethods[]

static

Initial value:

= {
    {"dump", (PyCFunction)FastaBuff_dump, METH_NOARGS,
     "Dumps the buffer as bytes"},
    {"index", (PyCFunction)FastaBuff_index, METH_VARARGS,
     "Returns the index of the first occurrence of the specified "
     "sequence "
     "in this FastaBuff."},
    {"get_annotated", (PyCFunction)FastaBuff_get_annotated, METH_O,
     "Returns the annotated sequence based on the GtfDict"},
    {"count", (PyCFunction)FastaBuff_count, METH_O,
     "Returns the number of occurrences of the specified sequence in "
     "this "
     "FastaBuff."},
    {"find", (PyCFunction)FastaBuff_find, METH_O,
     "Returns the indices of the first occurrence of the specified "
     "sequence in this FastaBuff."},
    {"__reversed__", (PyCFunction)FastaBuff_reversed, METH_NOARGS,
     "Returns the reverse of the sequence"},
    {"__getstate__", (PyCFunction)FastaBuff_getstate, METH_NOARGS, ""},
    {"__setstate__", (PyCFunction)FastaBuff_setstate, METH_O, ""},
    {NULL, NULL, 0, NULL} 
}

The FastaBuff methods.

FastaBuffSeq

PySequenceMethods FastaBuffSeq

static

Initial value:

= {
    .sq_length = (lenfunc)FastaBuff_len,
    .sq_ass_item = (ssizeobjargproc)FastaBuff_setItem,
    .sq_contains = (objobjproc)FastaBuff_contains,
}

The FastaBuff sequence methods.