GtfDict.c File Reference

Implementation of the GtfDict class. More...

#include "GtfDict.h"
#include <stdbool.h>
#include <stdlib.h>
#include "../formats/gtf.h"
#include <Python.h>

Include dependency graph for GtfDict.c:

Macros
#define	getGTFValue(dict, key)
	A macro that creates a string representation of a key in the GTF line.

Functions
static char *	PyUnicode_AsEncodedUTF8AndSize (PyObject *unicode, size_t *size)
	Returns the string representation of a Python string, with restricted characters percent encoded.
static int	GtfDict_init (GtfDict *restrict self, PyObject *restrict args, PyObject *restrict kwargs)
	GtfDict.__init__()
static PyObject *	GtfDict_getattro (GtfDict *restrict self, PyObject *restrict attr)
	A wrapper over the dict getattro that also acts as a getter for the 7 key GTF keys.
static int	GtfDict_setattro (GtfDict *restrict self, PyObject *restrict attr, PyObject *restrict value)
	A wrapper over the dict setattro that also acts as a setter for the 7 key GTF keys.
static PyObject *	GtfDict_richcompare (GtfDict *restrict self, PyObject *restrict other, const int op)
	A custom GtfDict richcompare.
static PyObject *	GtfDict_overlaps (GtfDict *restrict self, PyObject *restrict args)
	A custom method that determines if self overlaps with a different GtfDict.
int	GtfDict_containsValue (GtfDict *restrict self, PyObject *restrict other)
static PyObject *	GtfDict_contains (GtfDict *restrict self, PyObject *restrict args)
	Wrapper over GtfDict_containsValue() that allows for this method to be used as standalone.
static int	gtf_range_compare (const void *a, const void *b)
	Comparison function for sorting ranges by start, then end.
static PyObject *	GtfDict_coverage (GtfDict *restrict self, PyObject *restrict args)
	A custom method that returns the percentage of the gene that is covered by the other GtfDict or iterable of GtfDicts.
static Py_ssize_t	GtfDict_len (GtfDict *restrict self)
	Custom len method that returns actually the result of subtracting start from end.
static int	iterate_to_str (void *const context, struct hashmap_element_s *const e)
	Function to iterate over the attributes and append them to the result.
char *	GtfDictToGTF (GtfDict *restrict self, size_t *restrict len)
static PyObject *	GtfDict_str (GtfDict *restrict self)
	returns the GTF representation of the GtfDict
PyObject *	GtfDict_getitem (GtfDict *restrict self, PyObject *restrict key)
	A custom getitem that also checks the core attributes.
static int	GtfDict_setitem (GtfDict *restrict self, PyObject *restrict key, PyObject *restrict value)
	A custom setitem that also checks the core attributes.
static int	iterate_keys (void *const context, void *const e)
	A function to iterate over the keys of the GtfDict.
PyObject *	GtfDict_keys (GtfDict *restrict self)
	GtfDict.keys()
static int	iterate_values (void *const context, void *const held)
	A function to iterate over the values of the GtfDict.
static PyObject *	GtfDict_values (GtfDict *restrict self)
	A function that returns the values of the GtfDict.
static PyObject *	GtfDict_iter (GtfDict *restrict self)
	Returns the iterator for the GtfDict.
static PyObject *	GtfDict_pop (GtfDict *restrict self, PyObject *restrict args)
	A custom pop method that also checks the core attributes.
static PyObject *	GtfDict_get (GtfDict *restrict self, PyObject *restrict args)
	A custom get method that also allows for a default value to be provided.
static PyObject *	GtfDict_items (GtfDict *restrict self)
	A custom items method that also checks the core attributes.
static PyObject *	GtfDict_update (GtfDict *restrict self, PyObject *restrict args)
	A custom update method that also checks the core attributes.
static void	GtfDict_dealloc (GtfDict *restrict self)
	Custom deallocator that deallocates all the core attributes.
static int	iterate_hash (void *const context, void *const value)
	A custom hash function that XORs the hashes of the core attributes and the attributes.
static Py_hash_t	GtfDict_hash (GtfDict *restrict self)
	A GtfDict hash function that XORs the hashes of the core attributes and the attributes.
static PyObject *	GtfDict_repr (PyObject *restrict self)
	A custom repr method that returns a dict representation of the GtfDict.

Variables
static PyMethodDef	GtfDict_methods []
	All the methods of the GtfDict class.
static PySequenceMethods	GtfDictSeq
	The sequence methods of the GtfDict class.
static PyMappingMethods	GtfDictMap
	The mapping methods of the GtfDict class.
PyTypeObject	GtfDictType
	The Python type definition for the GtfDict object.

Detailed Description

Implementation of the GtfDict class.

Macro Definition Documentation

getGTFValue

#define getGTFValue	(		dict,
			key
	)

Value:

    PyObject *key##Str = NULL;                                                 \
    size_t key##Size;                                                          \
    char *restrict key;                                                        \
    if (Py_IsNone(dict->key)) {                                                \
        key = malloc(2);                                                       \
        key[0] = '.';                                                          \
        key[1] = '\0';                                                         \
        key##Size = 1;                                                         \
    } else {                                                                   \
        key##Str = PyObject_Str(dict->key);                                    \
        key = PyUnicode_AsEncodedUTF8AndSize(key##Str, &key##Size);            \
        Py_DECREF(key##Str);                                                   \
    }

A macro that creates a string representation of a key in the GTF line.

bit of a hack to avoid code duplication

Parameters

dict	the GtfDict instance
key	the key to get

Note

Creates keyStr, keySize and key variables

Function Documentation

gtf_range_compare()

static int gtf_range_compare ( const void *  a, const void *  b  )

static

Comparison function for sorting ranges by start, then end.

Parameters

a	pointer to the first range (long[2])
b	pointer to the second range (long[2])

Returns

negative if a < b, 0 if equal, positive if a > b

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GtfDict_containsValue()

int GtfDict_containsValue	(	GtfDict *restrict	self,
		PyObject *restrict	other
	)

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GtfDictToGTF()

char * GtfDictToGTF	(	GtfDict *restrict	self,
		size_t *restrict	len
	)

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iterate_hash()

static int iterate_hash ( void *const  context, void *const  value  )

static

A custom hash function that XORs the hashes of the core attributes and the attributes.

Parameters

context	the context to store the hash in
value	the current value

Returns

1 on success

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iterate_keys()

static int iterate_keys ( void *const  context, void *const  e  )

static

A function to iterate over the keys of the GtfDict.

Parameters

context	the list to append the keys to
e	the current element

Returns

1 on success

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iterate_to_str()

static int iterate_to_str ( void *const  context, struct hashmap_element_s *const  e  )

static

Function to iterate over the attributes and append them to the result.

Parameters

context	the iterateContext
e	the current element

Returns

0

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iterate_values()

static int iterate_values ( void *const  context, void *const  held  )

static

A function to iterate over the values of the GtfDict.

Parameters

context	the list to append the values to
held	the current element

Returns

1 on success

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PyUnicode_AsEncodedUTF8AndSize()

static char * PyUnicode_AsEncodedUTF8AndSize ( PyObject *  unicode, size_t *  size  )

inlinestatic

Returns the string representation of a Python string, with restricted characters percent encoded.

Parameters

unicode	the string to encode
size	the size of the string

Returns

a newly allocated string with percent encoded characters

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Variable Documentation

GtfDict_methods

PyMethodDef GtfDict_methods[]

static

Initial value:

= {
    {"overlaps", (PyCFunction)GtfDict_overlaps, METH_VARARGS,
     "Returns true if the provided GtfDict overlaps with this GtfDict"},
    {"contains", (PyCFunction)GtfDict_contains, METH_VARARGS,
     "Returns true if the provided GtfDict can be considered to be entirely "
     "contained within the range of this GtfDict"},
    {"keys", (PyCFunction)GtfDict_keys, METH_NOARGS, "Returns a list of keys"},
    {"values", (PyCFunction)GtfDict_values, METH_NOARGS,
     "Returns a list of values"},
    {"pop", (PyCFunction)GtfDict_pop, METH_VARARGS,
     "Pops the value of the provided key"},
    {"get", (PyCFunction)GtfDict_get, METH_VARARGS,
     "Gets the value of the provided key, or the default value if the key is "
     "not found"},
    {"items", (PyCFunction)GtfDict_items, METH_NOARGS,
     "Returns a list of tuples containing the key-value pairs"},
    {"update", (PyCFunction)GtfDict_update, METH_VARARGS,
     "Updates the GtfDict with the provided dict"},
    {"coverage", (PyCFunction)GtfDict_coverage, METH_VARARGS,
     "Returns the percentage of the gene that is covered by the other GtfDict "
     "or iterable of GtfDicts"},
    {NULL, NULL, 0, NULL} 
}

All the methods of the GtfDict class.

GtfDictMap

PyMappingMethods GtfDictMap

static

Initial value:

= {
    .mp_subscript = (binaryfunc)GtfDict_getitem,
    .mp_ass_subscript = (objobjargproc)GtfDict_setitem}

The mapping methods of the GtfDict class.

GtfDictSeq

PySequenceMethods GtfDictSeq

static

Initial value:

= {.sq_contains =
                                           (objobjproc)GtfDict_containsValue,
                                       .sq_length = (lenfunc)GtfDict_len}

The sequence methods of the GtfDict class.