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parham-kparham-k
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Fix constructor types
1 parent 04bb1ef commit ed3979a

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4 files changed

+74
-60
lines changed

4 files changed

+74
-60
lines changed

‎include/btllib/nthash_kmer.hpp‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -247,8 +247,8 @@ class NtHash
247247
*/
248248
NtHash(const char* seq,
249249
size_t seq_len,
250-
unsigned num_hashes,
251-
unsigned k,
250+
hashing_internals::NUM_HASHES_TYPE num_hashes,
251+
hashing_internals::K_TYPE k,
252252
size_t pos = 0)
253253
: seq(seq)
254254
, seq_len(seq_len)
@@ -276,8 +276,8 @@ class NtHash
276276
* @param pos Position in sequence to start hashing from
277277
*/
278278
NtHash(const std::string& seq,
279-
unsigned num_hashes,
280-
unsigned k,
279+
hashing_internals::NUM_HASHES_TYPE num_hashes,
280+
hashing_internals::K_TYPE k,
281281
size_t pos = 0)
282282
: NtHash(seq.data(), seq.size(), num_hashes, k, pos)
283283
{
@@ -530,8 +530,8 @@ class BlindNtHash
530530
* @param pos Position in sequence to start hashing from
531531
*/
532532
BlindNtHash(const std::string& seq,
533-
unsigned num_hashes,
534-
unsigned k,
533+
hashing_internals::NUM_HASHES_TYPE num_hashes,
534+
hashing_internals::K_TYPE k,
535535
long pos = 0)
536536
: seq(seq.data() + pos, seq.data() + pos + k)
537537
, num_hashes(num_hashes)

‎include/btllib/nthash_seed.hpp‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -475,8 +475,8 @@ class SeedNtHash
475475
SeedNtHash(const char* seq,
476476
size_t seq_len,
477477
const std::vector<std::string>& seeds,
478-
unsigned num_hashes_per_seed,
479-
unsigned k,
478+
hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,
479+
hashing_internals::K_TYPE k,
480480
size_t pos = 0)
481481
: seq(seq)
482482
, seq_len(seq_len)
@@ -507,8 +507,8 @@ class SeedNtHash
507507
*/
508508
SeedNtHash(const std::string& seq,
509509
const std::vector<std::string>& seeds,
510-
unsigned num_hashes_per_seed,
511-
unsigned k,
510+
hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,
511+
hashing_internals::K_TYPE k,
512512
size_t pos = 0)
513513
: SeedNtHash(seq.data(), seq.size(), seeds, num_hashes_per_seed, k, pos)
514514
{
@@ -527,8 +527,8 @@ class SeedNtHash
527527
SeedNtHash(const char* seq,
528528
size_t seq_len,
529529
const std::vector<std::vector<unsigned>>& seeds,
530-
unsigned num_hashes_per_seed,
531-
unsigned k,
530+
hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,
531+
hashing_internals::K_TYPE k,
532532
size_t pos = 0)
533533
: seq(seq)
534534
, seq_len(seq_len)
@@ -556,8 +556,8 @@ class SeedNtHash
556556
*/
557557
SeedNtHash(const std::string& seq,
558558
const std::vector<std::vector<unsigned>>& seeds,
559-
unsigned num_hashes_per_seed,
560-
unsigned k,
559+
hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,
560+
hashing_internals::K_TYPE k,
561561
size_t pos = 0)
562562
: SeedNtHash(seq.data(), seq.size(), seeds, num_hashes_per_seed, k, pos)
563563
{
@@ -876,8 +876,8 @@ class BlindSeedNtHash
876876
*/
877877
BlindSeedNtHash(const char* seq,
878878
const std::vector<std::string>& seeds,
879-
unsigned num_hashes_per_seed,
880-
unsigned k,
879+
hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed,
880+
hashing_internals::K_TYPE k,
881881
long pos = 0)
882882
: seq(seq + pos, seq + pos + k)
883883
, num_hashes_per_seed(num_hashes_per_seed)

‎wrappers/extra_common.i‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -86,14 +86,14 @@ using SpacedSeed = std::vector<unsigned>;
8686
static std::map<void*, long> nthash_ids;
8787
%}
8888

89-
%ignore btllib::NtHash::NtHash(const char*, size_t, unsigned, unsigned, size_t pos = 0);
90-
%ignore btllib::BlindNtHash::BlindNtHash(const char*, size_t, unsigned, unsigned, size_t pos = 0);
91-
%ignore btllib::SeedNtHash::SeedNtHash(const char*, size_t, const std::vector<std::vector<unsigned>>&, unsigned, unsigned, size_t pos = 0);
92-
%ignore btllib::SeedNtHash::SeedNtHash(const char*, size_t, const std::vector<std::string>&, unsigned, unsigned, size_t pos = 0);
93-
%ignore btllib::NtHash::NtHash(const std::string&, unsigned, unsigned, size_t pos = 0);
94-
%ignore btllib::BlindNtHash::BlindNtHash(const std::string&, unsigned, unsigned, size_t pos = 0);
95-
%ignore btllib::SeedNtHash::SeedNtHash(const std::string&, const std::vector<std::vector<unsigned>>&, unsigned, unsigned, size_t pos = 0);
96-
%ignore btllib::SeedNtHash::SeedNtHash(const std::string&, const std::vector<std::string>&, unsigned, unsigned, size_t pos = 0);
89+
%ignore btllib::NtHash::NtHash(const char*, size_t, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
90+
%ignore btllib::BlindNtHash::BlindNtHash(const char*, size_t, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
91+
%ignore btllib::SeedNtHash::SeedNtHash(const char*, size_t, const std::vector<std::vector<unsigned>>&, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
92+
%ignore btllib::SeedNtHash::SeedNtHash(const char*, size_t, const std::vector<std::string>&, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
93+
%ignore btllib::NtHash::NtHash(const std::string&, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
94+
%ignore btllib::BlindNtHash::BlindNtHash(const std::string&, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
95+
%ignore btllib::SeedNtHash::SeedNtHash(const std::string&, const std::vector<std::vector<unsigned>>&, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
96+
%ignore btllib::SeedNtHash::SeedNtHash(const std::string&, const std::vector<std::string>&, hashing_internals::NUM_HASHES_TYPE, hashing_internals::K_TYPE, size_t pos = 0);
9797
%ignore btllib::AAHash::AAHash(const std::string&, unsigned, unsigned, unsigned, size_t pos = 0);
9898

9999
%ignore btllib::NtHash::NtHash(NtHash&&);

‎wrappers/python/btllib_wrap.cxx‎

Lines changed: 50 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -38591,16 +38591,16 @@ SWIGINTERN int _wrap_new_BlindSeedNtHash__SWIG_0(PyObject *self, Py_ssize_t nobj
3859138591
PyObject *resultobj = 0;
3859238592
char *arg1 = (char *) 0 ;
3859338593
std::vector< std::string,std::allocator< std::string > > *arg2 = 0 ;
38594-
unsigned int arg3 ;
38595-
unsigned int arg4 ;
38594+
btllib::hashing_internals::NUM_HASHES_TYPE arg3 ;
38595+
btllib::hashing_internals::K_TYPE arg4 ;
3859638596
long arg5 ;
3859738597
int res1 ;
3859838598
char *buf1 = 0 ;
3859938599
int alloc1 = 0 ;
3860038600
int res2 = SWIG_OLDOBJ ;
38601-
unsigned int val3 ;
38601+
unsigned char val3 ;
3860238602
int ecode3 = 0 ;
38603-
unsigned int val4 ;
38603+
unsigned short val4 ;
3860438604
int ecode4 = 0 ;
3860538605
long val5 ;
3860638606
int ecode5 = 0 ;
@@ -38624,16 +38624,16 @@ SWIGINTERN int _wrap_new_BlindSeedNtHash__SWIG_0(PyObject *self, Py_ssize_t nobj
3862438624
}
3862538625
arg2 = ptr;
3862638626
}
38627-
ecode3 = SWIG_AsVal_unsigned_SS_int(swig_obj[2], &val3);
38627+
ecode3 = SWIG_AsVal_unsigned_SS_char(swig_obj[2], &val3);
3862838628
if (!SWIG_IsOK(ecode3)) {
38629-
SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_BlindSeedNtHash" "', argument " "3"" of type '" "unsigned int""'");
38629+
SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_BlindSeedNtHash" "', argument " "3"" of type '" "btllib::hashing_internals::NUM_HASHES_TYPE""'");
3863038630
}
38631-
arg3 = static_cast< unsigned int >(val3);
38632-
ecode4 = SWIG_AsVal_unsigned_SS_int(swig_obj[3], &val4);
38631+
arg3 = static_cast< btllib::hashing_internals::NUM_HASHES_TYPE >(val3);
38632+
ecode4 = SWIG_AsVal_unsigned_SS_short(swig_obj[3], &val4);
3863338633
if (!SWIG_IsOK(ecode4)) {
38634-
SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "new_BlindSeedNtHash" "', argument " "4"" of type '" "unsigned int""'");
38634+
SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "new_BlindSeedNtHash" "', argument " "4"" of type '" "btllib::hashing_internals::K_TYPE""'");
3863538635
}
38636-
arg4 = static_cast< unsigned int >(val4);
38636+
arg4 = static_cast< btllib::hashing_internals::K_TYPE >(val4);
3863738637
ecode5 = SWIG_AsVal_long(swig_obj[4], &val5);
3863838638
if (!SWIG_IsOK(ecode5)) {
3863938639
SWIG_exception_fail(SWIG_ArgError(ecode5), "in method '" "new_BlindSeedNtHash" "', argument " "5"" of type '" "long""'");
@@ -38655,15 +38655,15 @@ SWIGINTERN int _wrap_new_BlindSeedNtHash__SWIG_1(PyObject *self, Py_ssize_t nobj
3865538655
PyObject *resultobj = 0;
3865638656
char *arg1 = (char *) 0 ;
3865738657
std::vector< std::string,std::allocator< std::string > > *arg2 = 0 ;
38658-
unsigned int arg3 ;
38659-
unsigned int arg4 ;
38658+
btllib::hashing_internals::NUM_HASHES_TYPE arg3 ;
38659+
btllib::hashing_internals::K_TYPE arg4 ;
3866038660
int res1 ;
3866138661
char *buf1 = 0 ;
3866238662
int alloc1 = 0 ;
3866338663
int res2 = SWIG_OLDOBJ ;
38664-
unsigned int val3 ;
38664+
unsigned char val3 ;
3866538665
int ecode3 = 0 ;
38666-
unsigned int val4 ;
38666+
unsigned short val4 ;
3866738667
int ecode4 = 0 ;
3866838668
btllib::BlindSeedNtHash *result = 0 ;
3866938669

@@ -38685,16 +38685,16 @@ SWIGINTERN int _wrap_new_BlindSeedNtHash__SWIG_1(PyObject *self, Py_ssize_t nobj
3868538685
}
3868638686
arg2 = ptr;
3868738687
}
38688-
ecode3 = SWIG_AsVal_unsigned_SS_int(swig_obj[2], &val3);
38688+
ecode3 = SWIG_AsVal_unsigned_SS_char(swig_obj[2], &val3);
3868938689
if (!SWIG_IsOK(ecode3)) {
38690-
SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_BlindSeedNtHash" "', argument " "3"" of type '" "unsigned int""'");
38690+
SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_BlindSeedNtHash" "', argument " "3"" of type '" "btllib::hashing_internals::NUM_HASHES_TYPE""'");
3869138691
}
38692-
arg3 = static_cast< unsigned int >(val3);
38693-
ecode4 = SWIG_AsVal_unsigned_SS_int(swig_obj[3], &val4);
38692+
arg3 = static_cast< btllib::hashing_internals::NUM_HASHES_TYPE >(val3);
38693+
ecode4 = SWIG_AsVal_unsigned_SS_short(swig_obj[3], &val4);
3869438694
if (!SWIG_IsOK(ecode4)) {
38695-
SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "new_BlindSeedNtHash" "', argument " "4"" of type '" "unsigned int""'");
38695+
SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "new_BlindSeedNtHash" "', argument " "4"" of type '" "btllib::hashing_internals::K_TYPE""'");
3869638696
}
38697-
arg4 = static_cast< unsigned int >(val4);
38697+
arg4 = static_cast< btllib::hashing_internals::K_TYPE >(val4);
3869838698
result = (btllib::BlindSeedNtHash *)new btllib::BlindSeedNtHash((char const *)arg1,(std::vector< std::string,std::allocator< std::string > > const &)*arg2,arg3,arg4);
3869938699
resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_btllib__BlindSeedNtHash, SWIG_BUILTIN_INIT | 0 );
3870038700
if (alloc1 == SWIG_NEWOBJ) delete[] buf1;
@@ -38803,8 +38803,8 @@ SWIGINTERN int _wrap_new_BlindSeedNtHash(PyObject *self, PyObject *args, PyObjec
3880338803
fail:
3880438804
SWIG_Python_RaiseOrModifyTypeError("Wrong number or type of arguments for overloaded function 'new_BlindSeedNtHash'.\n"
3880538805
" Possible C/C++ prototypes are:\n"
38806-
" btllib::BlindSeedNtHash::BlindSeedNtHash(char const *,std::vector< std::string,std::allocator< std::string > > const &,unsigned int,unsigned int,long)\n"
38807-
" btllib::BlindSeedNtHash::BlindSeedNtHash(char const *,std::vector< std::string,std::allocator< std::string > > const &,unsigned int,unsigned int)\n"
38806+
" btllib::BlindSeedNtHash::BlindSeedNtHash(char const *,std::vector< std::string,std::allocator< std::string > > const &,btllib::hashing_internals::NUM_HASHES_TYPE,btllib::hashing_internals::K_TYPE,long)\n"
38807+
" btllib::BlindSeedNtHash::BlindSeedNtHash(char const *,std::vector< std::string,std::allocator< std::string > > const &,btllib::hashing_internals::NUM_HASHES_TYPE,btllib::hashing_internals::K_TYPE)\n"
3880838808
" btllib::BlindSeedNtHash::BlindSeedNtHash(btllib::BlindSeedNtHash const &)\n"
3880938809
" btllib::BlindSeedNtHash::BlindSeedNtHash(btllib::BlindSeedNtHash &&)\n");
3881038810
return -1;
@@ -42891,13 +42891,13 @@ SWIGPY_DESTRUCTOR_CLOSURE(_wrap_delete_NtHash) /* defines _wrap_delete_NtHash_de
4289142891
SWIGINTERN int _wrap_new_BlindNtHash__SWIG_0(PyObject *self, Py_ssize_t nobjs, PyObject **swig_obj) {
4289242892
PyObject *resultobj = 0;
4289342893
std::string *arg1 = 0 ;
42894-
unsigned int arg2 ;
42895-
unsigned int arg3 ;
42894+
btllib::hashing_internals::NUM_HASHES_TYPE arg2 ;
42895+
btllib::hashing_internals::K_TYPE arg3 ;
4289642896
long arg4 ;
4289742897
int res1 = SWIG_OLDOBJ ;
42898-
unsigned int val2 ;
42898+
unsigned char val2 ;
4289942899
int ecode2 = 0 ;
42900-
unsigned int val3 ;
42900+
unsigned short val3 ;
4290142901
int ecode3 = 0 ;
4290242902
long val4 ;
4290342903
int ecode4 = 0 ;
@@ -42916,16 +42916,16 @@ SWIGINTERN int _wrap_new_BlindNtHash__SWIG_0(PyObject *self, Py_ssize_t nobjs, P
4291642916
}
4291742917
arg1 = ptr;
4291842918
}
42919-
ecode2 = SWIG_AsVal_unsigned_SS_int(swig_obj[1], &val2);
42919+
ecode2 = SWIG_AsVal_unsigned_SS_char(swig_obj[1], &val2);
4292042920
if (!SWIG_IsOK(ecode2)) {
42921-
SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "new_BlindNtHash" "', argument " "2"" of type '" "unsigned int""'");
42921+
SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "new_BlindNtHash" "', argument " "2"" of type '" "btllib::hashing_internals::NUM_HASHES_TYPE""'");
4292242922
}
42923-
arg2 = static_cast< unsigned int >(val2);
42924-
ecode3 = SWIG_AsVal_unsigned_SS_int(swig_obj[2], &val3);
42923+
arg2 = static_cast< btllib::hashing_internals::NUM_HASHES_TYPE >(val2);
42924+
ecode3 = SWIG_AsVal_unsigned_SS_short(swig_obj[2], &val3);
4292542925
if (!SWIG_IsOK(ecode3)) {
42926-
SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_BlindNtHash" "', argument " "3"" of type '" "unsigned int""'");
42926+
SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_BlindNtHash" "', argument " "3"" of type '" "btllib::hashing_internals::K_TYPE""'");
4292742927
}
42928-
arg3 = static_cast< unsigned int >(val3);
42928+
arg3 = static_cast< btllib::hashing_internals::K_TYPE >(val3);
4292942929
ecode4 = SWIG_AsVal_long(swig_obj[3], &val4);
4293042930
if (!SWIG_IsOK(ecode4)) {
4293142931
SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "new_BlindNtHash" "', argument " "4"" of type '" "long""'");
@@ -43309,25 +43309,39 @@ SWIGINTERN int _wrap_new_BlindNtHash(PyObject *self, PyObject *args, PyObject *k
4330943309
int _v = 0;
4331043310
{
4331143311
{
43312-
int res = SWIG_AsVal_size_t(argv[3], NULL);
43312+
int res = SWIG_AsVal_unsigned_SS_char(argv[1], NULL);
43313+
_v = SWIG_CheckState(res);
43314+
}
43315+
}
43316+
if (!_v) goto check_2;
43317+
{
43318+
{
43319+
int res = SWIG_AsVal_unsigned_SS_short(argv[2], NULL);
43320+
_v = SWIG_CheckState(res);
43321+
}
43322+
}
43323+
if (!_v) goto check_2;
43324+
{
43325+
{
43326+
int res = SWIG_AsVal_long(argv[3], NULL);
4331343327
_v = SWIG_CheckState(res);
4331443328
}
4331543329
}
4331643330
if (!_v) goto check_2;
43317-
return _wrap_new_BlindNtHash__SWIG_1(self, argc, argv);
43331+
return _wrap_new_BlindNtHash__SWIG_0(self, argc, argv);
4331843332
}
4331943333
check_2:
4332043334

4332143335
if (argc == 4) {
43322-
int retval = _wrap_new_BlindNtHash__SWIG_0(self, argc, argv);
43336+
int retval = _wrap_new_BlindNtHash__SWIG_1(self, argc, argv);
4332343337
if (retval == 0 || !SWIG_Python_TypeErrorOccurred(NULL)) return retval;
4332443338
SWIG_fail;
4332543339
}
4332643340

4332743341
fail:
4332843342
SWIG_Python_RaiseOrModifyTypeError("Wrong number or type of arguments for overloaded function 'new_BlindNtHash'.\n"
4332943343
" Possible C/C++ prototypes are:\n"
43330-
" btllib::BlindNtHash::BlindNtHash(std::string const &,unsigned int,unsigned int,long)\n"
43344+
" btllib::BlindNtHash::BlindNtHash(std::string const &,btllib::hashing_internals::NUM_HASHES_TYPE,btllib::hashing_internals::K_TYPE,long)\n"
4333143345
" btllib::BlindNtHash::BlindNtHash(std::string,unsigned int,unsigned int,size_t)\n"
4333243346
" btllib::BlindNtHash::BlindNtHash(std::string,unsigned int,unsigned int)\n");
4333343347
return -1;

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