/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | seqsrc_multiseq.c | 59 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() [all …]
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H A D | repeats_filter.c | 95 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()
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/dports/misc/thrill/thrill-12c5b59bca66df93b66628b3829027bd0f110dd9/extlib/tlx/tlx/algorithm/ |
H A D | multiway_merge_splitting.hpp | 119 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()
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H A D | parallel_multiway_merge.hpp | 102 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()
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/dports/devel/tlx/tlx-0.5.20200222-5-g8982a9d/tlx/algorithm/ |
H A D | multiway_merge_splitting.hpp | 119 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()
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H A D | parallel_multiway_merge.hpp | 102 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/ |
H A D | seq.cpp | 238 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/blast_mt/ |
H A D | blast_mt_unit_test.cpp | 78 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/blast_mt/ |
H A D | blast_mt_unit_test.cpp | 78 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/ |
H A D | writedb.cpp | 363 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/ |
H A D | writedb.cpp | 363 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()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_setup.c | 855 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 …]
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H A D | blast_psi_priv.c | 153 _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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_setup.c | 855 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 …]
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H A D | blast_psi_priv.c | 153 _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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_setup.c | 855 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 …]
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H A D | blast_psi_priv.c | 153 _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 …]
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/dports/www/h2o-devel/h2o-dcc7134/deps/quicly/t/ |
H A D | retire_cid.c | 31 …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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/proteinkmer/ |
H A D | blastkmerindex.cpp | 559 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/proteinkmer/ |
H A D | blastkmerindex.cpp | 559 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/ |
H A D | unit_test_gap_analysis.cpp | 69 << "\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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
H A D | cuPssmMaker.cpp | 60 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()
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/dports/misc/frugally-deep/frugally-deep-0.15.13-p0/test/stateful_test/ |
H A D | stateful_recurrent_tests.py | 187 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)
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | msa2pssm_unit_test.cpp | 75 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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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | msa2pssm_unit_test.cpp | 75 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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