-
Notifications
You must be signed in to change notification settings - Fork 295
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
More consolidation of Hashtable derived types. #1504
Changes from 31 commits
8295782
9991ecc
bf9f899
7371492
7132983
a6040c4
30e1ba4
d28d38b
ac0cc3a
29e42ed
22942f6
d021c05
a681366
c9fc7c9
a7213b1
c52c88a
bc48a6f
8a171d4
5a532e3
4ebc47f
6c33e2d
6096ab5
12fc7b4
95ed9f6
c4e2318
a6f896d
651519a
07fc51d
e2f58f1
ad1d7b9
b9ff3fc
e112c9e
cda6c5f
6303cb8
File filter
Filter by extension
Conversations
Jump to
Diff view
Diff view
There are no files selected for viewing
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,132 @@ | ||
/* | ||
This file is part of khmer, https://github.com/dib-lab/khmer/, and is | ||
Copyright (C) 2010-2015, Michigan State University. | ||
Copyright (C) 2015-2016, The Regents of the University of California. | ||
|
||
Redistribution and use in source and binary forms, with or without | ||
modification, are permitted provided that the following conditions are | ||
met: | ||
|
||
* Redistributions of source code must retain the above copyright | ||
notice, this list of conditions and the following disclaimer. | ||
|
||
* Redistributions in binary form must reproduce the above | ||
copyright notice, this list of conditions and the following | ||
disclaimer in the documentation and/or other materials provided | ||
with the distribution. | ||
|
||
* Neither the name of the Michigan State University nor the names | ||
of its contributors may be used to endorse or promote products | ||
derived from this software without specific prior written | ||
permission. | ||
|
||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS | ||
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT | ||
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | ||
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | ||
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, | ||
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT | ||
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | ||
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | ||
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
LICENSE (END) | ||
|
||
Contact: khmer-project@idyll.org | ||
*/ | ||
|
||
typedef struct { | ||
khmer_KHashtable_Object khashtable; | ||
Counttable * counttable; | ||
} khmer_KCounttable_Object; | ||
|
||
static PyMethodDef khmer_counttable_methods[] = { | ||
{NULL, NULL, 0, NULL} /* sentinel */ | ||
}; | ||
|
||
static PyObject* khmer_counttable_new(PyTypeObject * type, PyObject * args, | ||
PyObject * kwds); | ||
|
||
static PyTypeObject khmer_KCounttable_Type | ||
CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KCounttable_Object") | ||
= { | ||
PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */ | ||
"_khmer.Counttable", /* tp_name */ | ||
sizeof(khmer_KCounttable_Object), /* tp_basicsize */ | ||
0, /* tp_itemsize */ | ||
0, /*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*/ | ||
0, /*tp_getattro*/ | ||
0, /*tp_setattro*/ | ||
0, /*tp_as_buffer*/ | ||
Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ | ||
"counttable object", /* tp_doc */ | ||
0, /* tp_traverse */ | ||
0, /* tp_clear */ | ||
0, /* tp_richcompare */ | ||
0, /* tp_weaklistoffset */ | ||
0, /* tp_iter */ | ||
0, /* tp_iternext */ | ||
khmer_counttable_methods, /* 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 */ | ||
khmer_counttable_new, /* tp_new */ | ||
}; | ||
|
||
|
||
// | ||
// khmer_counttable_new | ||
// | ||
|
||
static PyObject* khmer_counttable_new(PyTypeObject * type, PyObject * args, | ||
PyObject * kwds) | ||
{ | ||
khmer_KCounttable_Object * self; | ||
|
||
self = (khmer_KCounttable_Object *)type->tp_alloc(type, 0); | ||
|
||
if (self != NULL) { | ||
WordLength k = 0; | ||
PyListObject * sizes_list_o = NULL; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Do you know who owns the reference to the list that comes from PyArg_ParseTuple? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. PyArg_ParseTuple doesn't increase the reference count, and presumably the ref count can't decrease to zero while we are using an argument to this function. There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Yep (or at least not with the GIL held). |
||
|
||
if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) { | ||
Py_DECREF(self); | ||
return NULL; | ||
} | ||
|
||
std::vector<uint64_t> sizes; | ||
if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) { | ||
Py_DECREF(self); | ||
return NULL; | ||
} | ||
|
||
try { | ||
self->counttable = new Counttable(k, sizes); | ||
} catch (std::bad_alloc &e) { | ||
Py_DECREF(self); | ||
return PyErr_NoMemory(); | ||
} | ||
self->khashtable.hashtable = | ||
dynamic_cast<Hashtable*>(self->counttable); | ||
} | ||
|
||
return (PyObject *) self; | ||
} |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Do we need this here if it is just empty?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I went both ways on this - it's nice to have it there for if/when we add methods... but yeah, I guess no need.