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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dseqsrc_multiseq.c59 Uint4 num_seqs; /**< Number of sequences. */ member
70 Uint4 num_seqs = ValNodeLen((ValNode*)seqloc_list); in s_MultiSeqInfoNew() local
75 retval->num_seqs = num_seqs; in s_MultiSeqInfoNew()
80 calloc(retval->num_seqs, sizeof(BLAST_SequenceBlk*)); in s_MultiSeqInfoNew()
83 index < num_seqs; ++index, seqloc_ptr = seqloc_ptr->next) { in s_MultiSeqInfoNew()
129 for (index=0; index<seq_info->num_seqs; ++index) in s_MultiSeqGetMaxLength()
153 for (index=0; index<seq_info->num_seqs; ++index) in s_MultiSeqGetAvgLength()
171 return seq_info->num_seqs; in s_MultiSeqGetNumSeqs()
241 if (seq_info->num_seqs == 0 || !seq_args) in s_MultiSeqGetSequence()
246 if (index >= (Int4) seq_info->num_seqs) in s_MultiSeqGetSequence()
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H A Drepeats_filter.c95 Int4 num_seqs = 0; in s_FillMaskLocFromBlastHSPResults() local
111 num_seqs = ValNodeLen(query_seqloc); in s_FillMaskLocFromBlastHSPResults()
112 mask = BlastMaskLocNew(num_seqs*kNumContexts); in s_FillMaskLocFromBlastHSPResults()
/dports/misc/thrill/thrill-12c5b59bca66df93b66628b3829027bd0f110dd9/extlib/tlx/tlx/algorithm/
H A Dmultiway_merge_splitting.hpp119 const DiffType num_seqs = seqs_end - seqs_begin; in multiway_merge_sampling_splitting() local
124 simple_vector<value_type> samples(num_seqs * num_samples); in multiway_merge_sampling_splitting()
126 for (DiffType s = 0; s < num_seqs; ++s) in multiway_merge_sampling_splitting()
147 for (DiffType seq = 0; seq < num_seqs; ++seq) in multiway_merge_sampling_splitting()
153 samples[num_samples * num_seqs * slab / num_threads], in multiway_merge_sampling_splitting()
163 samples[num_samples * num_seqs * (slab + 1) / num_threads], in multiway_merge_sampling_splitting()
214 const size_t num_seqs = static_cast<size_t>(seqs_end - seqs_begin); in multiway_merge_exact_splitting() local
224 offsets[s].resize(num_seqs); in multiway_merge_exact_splitting()
231 offsets[num_threads - 1].resize(num_seqs); in multiway_merge_exact_splitting()
242 for (size_t s = 0; s < num_seqs; ++s) in multiway_merge_exact_splitting()
H A Dparallel_multiway_merge.hpp102 size_t num_seqs = seqs_ne.size(); in parallel_multiway_merge_base() local
104 if (total_size == 0 || num_seqs == 0) in parallel_multiway_merge_base()
115 chunks[s].resize(num_seqs); in parallel_multiway_merge_base()
140 for (size_t s = 0; s < num_seqs; ++s) in parallel_multiway_merge_base()
160 for (size_t s = 0; s < num_seqs; ++s) in parallel_multiway_merge_base()
/dports/devel/tlx/tlx-0.5.20200222-5-g8982a9d/tlx/algorithm/
H A Dmultiway_merge_splitting.hpp119 const DiffType num_seqs = seqs_end - seqs_begin; in multiway_merge_sampling_splitting() local
124 simple_vector<value_type> samples(num_seqs * num_samples); in multiway_merge_sampling_splitting()
126 for (DiffType s = 0; s < num_seqs; ++s) in multiway_merge_sampling_splitting()
147 for (DiffType seq = 0; seq < num_seqs; ++seq) in multiway_merge_sampling_splitting()
153 samples[num_samples * num_seqs * slab / num_threads], in multiway_merge_sampling_splitting()
163 samples[num_samples * num_seqs * (slab + 1) / num_threads], in multiway_merge_sampling_splitting()
214 const size_t num_seqs = static_cast<size_t>(seqs_end - seqs_begin); in multiway_merge_exact_splitting() local
224 offsets[s].resize(num_seqs); in multiway_merge_exact_splitting()
231 offsets[num_threads - 1].resize(num_seqs); in multiway_merge_exact_splitting()
242 for (size_t s = 0; s < num_seqs; ++s) in multiway_merge_exact_splitting()
H A Dparallel_multiway_merge.hpp102 size_t num_seqs = seqs_ne.size(); in parallel_multiway_merge_base() local
104 if (total_size == 0 || num_seqs == 0) in parallel_multiway_merge_base()
115 chunks[s].resize(num_seqs); in parallel_multiway_merge_base()
140 for (size_t s = 0; s < num_seqs; ++s) in parallel_multiway_merge_base()
160 for (size_t s = 0; s < num_seqs; ++s) in parallel_multiway_merge_base()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/
H A Dseq.cpp238 int num_seqs = index_list.size(); in CompressSequences() local
245 for (j = 0; j < num_seqs; j++) { in CompressSequences()
253 if (j < num_seqs) { in CompressSequences()
254 for (j = 0; j < num_seqs; j++) { in CompressSequences()
269 for (int i = 0; i < num_seqs; i++) { in CompressSequences()
284 int num_seqs = denseg.GetDim(); in CreateMsa() local
291 msa.resize(num_seqs); in CreateMsa()
300 seq_vectors.reserve(num_seqs); in CreateMsa()
320 for (int i=0;i < num_seqs;i++) { in CreateMsa()
323 if (starts[seg_index * num_seqs + i] < 0) { in CreateMsa()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/blast_mt/
H A Dblast_mt_unit_test.cpp78 int num_seqs = seqdb->GetNumSeqs(); in BOOST_AUTO_TEST_SUITE() local
79 int kNumTestOids = MIN(5000, num_seqs/4); in BOOST_AUTO_TEST_SUITE()
81 int oid = rand() % num_seqs; in BOOST_AUTO_TEST_SUITE()
96 int num_seqs = seqdb->GetNumSeqs(); in s_GenerateAccsList() local
97 int kNumTestOids = MIN(5000, num_seqs/4); in s_GenerateAccsList()
99 int oid = rand() % num_seqs; in s_GenerateAccsList()
275 int num_seqs = seqdb->GetNumSeqs(); in s_MTSeqDBTest() local
344 int num_seqs = seqdb->GetNumSeqs(); in s_MTSeqDBTest2() local
346 int oid = rand() % num_seqs; in s_MTSeqDBTest2()
401 int num_seqs = seqdb->GetNumSeqs(); in s_MTSeqDBTest3() local
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/blast_mt/
H A Dblast_mt_unit_test.cpp78 int num_seqs = seqdb->GetNumSeqs(); in BOOST_AUTO_TEST_SUITE() local
79 int kNumTestOids = MIN(5000, num_seqs/4); in BOOST_AUTO_TEST_SUITE()
81 int oid = rand() % num_seqs; in BOOST_AUTO_TEST_SUITE()
96 int num_seqs = seqdb->GetNumSeqs(); in s_GenerateAccsList() local
97 int kNumTestOids = MIN(5000, num_seqs/4); in s_GenerateAccsList()
99 int oid = rand() % num_seqs; in s_GenerateAccsList()
275 int num_seqs = seqdb->GetNumSeqs(); in s_MTSeqDBTest() local
344 int num_seqs = seqdb->GetNumSeqs(); in s_MTSeqDBTest2() local
346 int oid = rand() % num_seqs; in s_MTSeqDBTest2()
401 int num_seqs = seqdb->GetNumSeqs(); in s_MTSeqDBTest3() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/
H A Dwritedb.cpp363 int num_seqs = 0; in s_CreateAliasFilePriv() local
390 if (!s_ComputeNumSequencesAndDbLength(file_name, is_prot, &dbsize, &num_seqs)){ in s_CreateAliasFilePriv()
396 if (num_seqs == 0) { in s_CreateAliasFilePriv()
407 out << "NSEQ " << num_seqs << "\n"; in s_CreateAliasFilePriv()
411 s_PrintAliasFileCreationLog(file_name, is_prot, num_seqs); in s_CreateAliasFilePriv()
432 int num_seqs = 0; in CWriteDB_CreateAliasFile() local
434 &dbsize, &num_seqs); in CWriteDB_CreateAliasFile()
451 out << "NSEQ " << num_seqs << "\n"; in CWriteDB_CreateAliasFile()
454 s_PrintAliasFileCreationLog(concatenated_blastdb_name, is_prot, num_seqs); in CWriteDB_CreateAliasFile()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/
H A Dwritedb.cpp363 int num_seqs = 0; in s_CreateAliasFilePriv() local
390 if (!s_ComputeNumSequencesAndDbLength(file_name, is_prot, &dbsize, &num_seqs)){ in s_CreateAliasFilePriv()
396 if (num_seqs == 0) { in s_CreateAliasFilePriv()
407 out << "NSEQ " << num_seqs << "\n"; in s_CreateAliasFilePriv()
411 s_PrintAliasFileCreationLog(file_name, is_prot, num_seqs); in s_CreateAliasFilePriv()
432 int num_seqs = 0; in CWriteDB_CreateAliasFile() local
434 &dbsize, &num_seqs); in CWriteDB_CreateAliasFile()
451 out << "NSEQ " << num_seqs << "\n"; in CWriteDB_CreateAliasFile()
454 s_PrintAliasFileCreationLog(concatenated_blastdb_name, is_prot, num_seqs); in CWriteDB_CreateAliasFile()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_setup.c855 Int4* num_seqs) in BLAST_GetSubjectTotals() argument
857 ASSERT(total_length && num_seqs); in BLAST_GetSubjectTotals()
860 *num_seqs = -1; in BLAST_GetSubjectTotals()
872 if (*num_seqs <= 0) in BLAST_GetSubjectTotals()
873 *num_seqs = BlastSeqSrcGetNumSeqs(seqsrc); in BLAST_GetSubjectTotals()
880 *num_seqs = -1; in BLAST_GetSubjectTotals()
883 *num_seqs = 1; in BLAST_GetSubjectTotals()
906 Int4 num_seqs = -1; in BLAST_GapAlignSetUp() local
927 if (num_seqs <= 0) in BLAST_GapAlignSetUp()
935 num_seqs = -1; in BLAST_GapAlignSetUp()
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H A Dblast_psi_priv.c153 _PSIAllocateMatrix(msa->dimensions->num_seqs + 1, in DEFINE_COPY_MATRIX_FUNCTION()
160 for (s = 0; s < msa->dimensions->num_seqs + 1; s++) { in DEFINE_COPY_MATRIX_FUNCTION()
175 for (s = 0; s < msa->dimensions->num_seqs + 1; s++) { in DEFINE_COPY_MATRIX_FUNCTION()
218 for (i = 0; i < msa->dimensions->num_seqs + 1; i++) { in _PSIPackedMsaGetNumberOfAlignedSeqs()
253 for (i = 0; i < msa->dimensions->num_seqs + 1; i++) { in PrintMsaFP()
1001 kNumberOfSeqs = msa->dimensions->num_seqs + 1; in _PSIUpdatePositionCounts()
1327 ASSERT(seq_index < msa->dimensions->num_seqs + 1); in _PSIGetLeftExtents()
1361 ASSERT(seq_index < msa->dimensions->num_seqs + 1); in _PSIGetRightExtents()
1399 ASSERT(seq_index < msa->dimensions->num_seqs + 1);
1668 if (cd_msa->dimensions->num_seqs == 0) {
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_setup.c855 Int4* num_seqs) in BLAST_GetSubjectTotals() argument
857 ASSERT(total_length && num_seqs); in BLAST_GetSubjectTotals()
860 *num_seqs = -1; in BLAST_GetSubjectTotals()
872 if (*num_seqs <= 0) in BLAST_GetSubjectTotals()
873 *num_seqs = BlastSeqSrcGetNumSeqs(seqsrc); in BLAST_GetSubjectTotals()
880 *num_seqs = -1; in BLAST_GetSubjectTotals()
883 *num_seqs = 1; in BLAST_GetSubjectTotals()
906 Int4 num_seqs = -1; in BLAST_GapAlignSetUp() local
927 if (num_seqs <= 0) in BLAST_GapAlignSetUp()
935 num_seqs = -1; in BLAST_GapAlignSetUp()
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H A Dblast_psi_priv.c153 _PSIAllocateMatrix(msa->dimensions->num_seqs + 1, in DEFINE_COPY_MATRIX_FUNCTION()
160 for (s = 0; s < msa->dimensions->num_seqs + 1; s++) { in DEFINE_COPY_MATRIX_FUNCTION()
175 for (s = 0; s < msa->dimensions->num_seqs + 1; s++) { in DEFINE_COPY_MATRIX_FUNCTION()
218 for (i = 0; i < msa->dimensions->num_seqs + 1; i++) { in _PSIPackedMsaGetNumberOfAlignedSeqs()
253 for (i = 0; i < msa->dimensions->num_seqs + 1; i++) { in PrintMsaFP()
1001 kNumberOfSeqs = msa->dimensions->num_seqs + 1; in _PSIUpdatePositionCounts()
1327 ASSERT(seq_index < msa->dimensions->num_seqs + 1); in _PSIGetLeftExtents()
1361 ASSERT(seq_index < msa->dimensions->num_seqs + 1); in _PSIGetRightExtents()
1399 ASSERT(seq_index < msa->dimensions->num_seqs + 1);
1668 if (cd_msa->dimensions->num_seqs == 0) {
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_setup.c855 Int4* num_seqs) in BLAST_GetSubjectTotals() argument
857 ASSERT(total_length && num_seqs); in BLAST_GetSubjectTotals()
860 *num_seqs = -1; in BLAST_GetSubjectTotals()
872 if (*num_seqs <= 0) in BLAST_GetSubjectTotals()
873 *num_seqs = BlastSeqSrcGetNumSeqs(seqsrc); in BLAST_GetSubjectTotals()
880 *num_seqs = -1; in BLAST_GetSubjectTotals()
883 *num_seqs = 1; in BLAST_GetSubjectTotals()
906 Int4 num_seqs = -1; in BLAST_GapAlignSetUp() local
927 if (num_seqs <= 0) in BLAST_GapAlignSetUp()
935 num_seqs = -1; in BLAST_GapAlignSetUp()
[all …]
H A Dblast_psi_priv.c153 _PSIAllocateMatrix(msa->dimensions->num_seqs + 1, in DEFINE_COPY_MATRIX_FUNCTION()
160 for (s = 0; s < msa->dimensions->num_seqs + 1; s++) { in DEFINE_COPY_MATRIX_FUNCTION()
175 for (s = 0; s < msa->dimensions->num_seqs + 1; s++) { in DEFINE_COPY_MATRIX_FUNCTION()
218 for (i = 0; i < msa->dimensions->num_seqs + 1; i++) { in _PSIPackedMsaGetNumberOfAlignedSeqs()
253 for (i = 0; i < msa->dimensions->num_seqs + 1; i++) { in PrintMsaFP()
1001 kNumberOfSeqs = msa->dimensions->num_seqs + 1; in _PSIUpdatePositionCounts()
1327 ASSERT(seq_index < msa->dimensions->num_seqs + 1); in _PSIGetLeftExtents()
1361 ASSERT(seq_index < msa->dimensions->num_seqs + 1); in _PSIGetRightExtents()
1399 ASSERT(seq_index < msa->dimensions->num_seqs + 1);
1668 if (cd_msa->dimensions->num_seqs == 0) {
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/dports/www/h2o-devel/h2o-dcc7134/deps/quicly/t/
H A Dretire_cid.c31 …tic int verify(const quicly_retire_cid_set_t *set, const uint64_t expected_seqs[], size_t num_seqs) in verify() argument
35 if (set->_num_pending != num_seqs) in verify()
38 for (i = 0; i < num_seqs && i < PTLS_ELEMENTSOF(set->sequences); i++) { in verify()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/proteinkmer/
H A Dblastkmerindex.cpp559 int num_seqs = 0; in x_BuildIndex() local
561 num_seqs = stop - start; in x_BuildIndex()
563 num_seqs = m_SeqDB->GetNumSeqs(); in x_BuildIndex()
567 index_file.write((char *) &(num_seqs), 4); in x_BuildIndex()
583 uint32_t* dead = new uint32_t[3*num_seqs]; in x_BuildIndex()
585 for(int q_oid=0;q_oid<3*num_seqs;q_oid++) in x_BuildIndex()
592 vector < vector < vector < uint32_t > > > seq_hash(num_seqs); in x_BuildIndex()
595 for(int q_oid=0;q_oid<num_seqs;q_oid++) in x_BuildIndex()
638 for(int q_oid=0;q_oid<num_seqs;q_oid++) in x_BuildIndex()
750 x_WriteDataFile(seq_hash, num_seqs, data_file); in x_BuildIndex()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/proteinkmer/
H A Dblastkmerindex.cpp559 int num_seqs = 0; in x_BuildIndex() local
561 num_seqs = stop - start; in x_BuildIndex()
563 num_seqs = m_SeqDB->GetNumSeqs(); in x_BuildIndex()
567 index_file.write((char *) &(num_seqs), 4); in x_BuildIndex()
583 uint32_t* dead = new uint32_t[3*num_seqs]; in x_BuildIndex()
585 for(int q_oid=0;q_oid<3*num_seqs;q_oid++) in x_BuildIndex()
592 vector < vector < vector < uint32_t > > > seq_hash(num_seqs); in x_BuildIndex()
595 for(int q_oid=0;q_oid<num_seqs;q_oid++) in x_BuildIndex()
638 for(int q_oid=0;q_oid<num_seqs;q_oid++) in x_BuildIndex()
750 x_WriteDataFile(seq_hash, num_seqs, data_file); in x_BuildIndex()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/
H A Dunit_test_gap_analysis.cpp69 << "\tnum seqs: " << one_summary.num_seqs in s_PrintSummary()
168 size_t num_seqs; member
173 return 0 == (gap_length | num_seqs | num_gaps); } in empty()
183 << ", num_seqs: " << expected_result.num_seqs in operator <<()
221 one_gap_summary.num_seqs, one_expected_result.num_seqs); in CheckExpectedResults()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/
H A DcuPssmMaker.cpp60 int startRow = msa->dimensions->num_seqs + 1 - seqIds.size(); in BEGIN_SCOPE()
63 for (i = startRow; i < msa->dimensions->num_seqs + 1; i++) { in BEGIN_SCOPE()
109 m_msaDimensions.num_seqs = m_profiles.getNumRows(); in CdPssmInput()
116 m_msaDimensions.num_seqs = m_profiles.getNumRows() - 1; in CdPssmInput()
211 for (unsigned int row = 1; row <= m_msaDimensions.num_seqs; row++) in unalignLeadingTrailingGaps()
236 for (int row = 2; row <= (int) m_msaDimensions.num_seqs; row++) in moveUpLongestRow()
602 nRows = msa.dimensions->num_seqs; in printAlignmentByColumn()
640 nRows = msa.dimensions->num_seqs; in getPssmColumnResidues()
/dports/misc/frugally-deep/frugally-deep-0.15.13-p0/test/stateful_test/
H A Dstateful_recurrent_tests.py187 num_seqs = 8
189 x_train = np.random.normal(0, 1, num_seqs * train_seq_length * feature_dim)
190 x_train = x_train.reshape(num_seqs, train_seq_length, feature_dim)
191 y_train = np.random.normal(0, 1, num_seqs * train_seq_length)
192 y_train = y_train.reshape(num_seqs, train_seq_length, 1)
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dmsa2pssm_unit_test.cpp75 BOOST_REQUIRE_EQUAL((Uint4)24, msa->dimensions->num_seqs); in BOOST_AUTO_TEST_CASE()
106 BOOST_REQUIRE_EQUAL((Uint4)24, msa->dimensions->num_seqs); in BOOST_AUTO_TEST_CASE()
131 BOOST_REQUIRE_EQUAL((Uint4)13, msa->dimensions->num_seqs); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dmsa2pssm_unit_test.cpp75 BOOST_REQUIRE_EQUAL((Uint4)24, msa->dimensions->num_seqs); in BOOST_AUTO_TEST_CASE()
106 BOOST_REQUIRE_EQUAL((Uint4)24, msa->dimensions->num_seqs); in BOOST_AUTO_TEST_CASE()
131 BOOST_REQUIRE_EQUAL((Uint4)13, msa->dimensions->num_seqs); in BOOST_AUTO_TEST_CASE()

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