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Searched refs:kAlphabetSize (Results 1 – 25 of 40) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/
H A Dseq.cpp113 m_Freqs.Resize(seq_length, kAlphabetSize); in Reset()
147 TFreqMatrix new_freq(new_size, kAlphabetSize, 0.0); in PropagateGaps()
158 for (int k = 0; k < kAlphabetSize; k++) in PropagateGaps()
186 new_freq.Resize(new_size, kAlphabetSize, 0.0); in InsertGaps()
206 for (int k = 0; k < kAlphabetSize; k++) in InsertGaps()
257 for (int k = 0; k < kAlphabetSize; k++) { in CompressSequences()
271 seq[index_list[i]].m_Freqs.Resize(new_length, kAlphabetSize); in CompressSequences()
294 it->m_Freqs.Resize(seq_length, kAlphabetSize); in CreateMsa()
H A Dresfreq.cpp80 m_PssmRows[i] = pssm_start + kAlphabetSize * i; in BEGIN_SCOPE()
103 m_ResFreqRows[i] = resfreq_start + kAlphabetSize * i; in BEGIN_SCOPE()
H A Dprog.cpp172 for (int k = 0; k < kAlphabetSize; k++) { in x_FillResidueFrequencies()
194 for (int j = 0; j < kAlphabetSize; j++) { in x_NormalizeResidueFrequencies()
201 for (int j = 0; j < kAlphabetSize; j++) { in x_NormalizeResidueFrequencies()
820 freq1_data[0] = new double[kAlphabetSize * freq1_size]; in x_AlignProfileProfile()
823 freq1_data[i] = freq1_data[0] + kAlphabetSize * i; in x_AlignProfileProfile()
833 freq2_data[0] = new double[kAlphabetSize * freq2_size]; in x_AlignProfileProfile()
836 freq2_data[i] = freq2_data[0] + kAlphabetSize * i; in x_AlignProfileProfile()
986 freq1_data[0] = new double[kAlphabetSize * freq1_size]; in x_ComputeProfileRangeAlignment()
989 freq1_data[i] = freq1_data[0] + kAlphabetSize * i; in x_ComputeProfileRangeAlignment()
1001 freq2_data[i] = freq2_data[0] + kAlphabetSize * i; in x_ComputeProfileRangeAlignment()
[all …]
H A Dkmercounts.cpp55 unsigned int CSparseKmerCounts::sm_AlphabetSize = kAlphabetSize;
62 unsigned int CBinaryKmerCounts::sm_AlphabetSize = kAlphabetSize;
H A Drps.cpp580 for (int m = 0; m < kAlphabetSize; m++) { in x_AssignRPSResFreqs()
620 for (int k = 0; k < kAlphabetSize; k++) { in x_AssignDefaultResFreqs()
640 for (int k = 0; k < kAlphabetSize; k++) { in x_AssignDefaultResFreqs()
/dports/lang/v8/v8-9.6.180.12/test/unittests/base/platform/
H A Dsemaphore-unittest.cc18 static const size_t kAlphabetSize = sizeof(kAlphabet) - 1; variable
20 static const size_t kDataSize = kBufferSize * kAlphabetSize * 10;
34 buffer_[n % kBufferSize] = kAlphabet[n % kAlphabetSize]; in Run()
58 EXPECT_EQ(kAlphabet[n % kAlphabetSize], buffer_[n % kBufferSize]); in Run()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dcdd_pssm_input.cpp319 for (int k=0;k < kAlphabetSize;k++) { in x_ValidateMsa()
778 _ASSERT((int)m_WFreqsData.size() == kSubjectLength * kAlphabetSize); in Validate()
820 const TFreqs* counts = db_counts + db_seq_offsets[db_oid] * kAlphabetSize; in x_FillResidueCounts()
830 m_WFreqsData.resize(num_columns * kAlphabetSize); in x_FillResidueCounts()
832 m_MsaData[i].wfreqs = &m_WFreqsData[i * kAlphabetSize]; in x_FillResidueCounts()
838 for (int j=0;j < kAlphabetSize;j++) { in x_FillResidueCounts()
840 counts[(m_SubjectRange.GetFrom() + i) * kAlphabetSize + j]; in x_FillResidueCounts()
843 for (int j=0;j < kAlphabetSize;j++) { in x_FillResidueCounts()
845 (double)counts[(m_SubjectRange.GetFrom() + i) * kAlphabetSize + j] in x_FillResidueCounts()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dcdd_pssm_input.cpp319 for (int k=0;k < kAlphabetSize;k++) { in x_ValidateMsa()
778 _ASSERT((int)m_WFreqsData.size() == kSubjectLength * kAlphabetSize); in Validate()
820 const TFreqs* counts = db_counts + db_seq_offsets[db_oid] * kAlphabetSize; in x_FillResidueCounts()
830 m_WFreqsData.resize(num_columns * kAlphabetSize); in x_FillResidueCounts()
832 m_MsaData[i].wfreqs = &m_WFreqsData[i * kAlphabetSize]; in x_FillResidueCounts()
838 for (int j=0;j < kAlphabetSize;j++) { in x_FillResidueCounts()
840 counts[(m_SubjectRange.GetFrom() + i) * kAlphabetSize + j]; in x_FillResidueCounts()
843 for (int j=0;j < kAlphabetSize;j++) { in x_FillResidueCounts()
845 (double)counts[(m_SubjectRange.GetFrom() + i) * kAlphabetSize + j] in x_FillResidueCounts()
/dports/textproc/regex2dfa/regex2dfa-0.1.6/third_party/openfst/src/include/fst/
H A Drandom-weight.h163 v.push_back(rand() % kAlphabetSize + 1); in operator()
169 static const int kAlphabetSize = 5;
177 const int StringWeightGenerator<L, S>::kAlphabetSize;
/dports/net/ooni-probe-cli/probe-cli-3.10.1/vendor/github.com/ooni/psiphon/oopsi/github.com/redjack/marionette/third_party/openfst/src/include/fst/
H A Drandom-weight.h163 v.push_back(rand() % kAlphabetSize + 1); in operator()
169 static const int kAlphabetSize = 5;
177 const int StringWeightGenerator<L, S>::kAlphabetSize;
/dports/net/ooni-mini/probe-engine-0.23.0/vendor/github.com/ooni/psiphon/oopsi/github.com/redjack/marionette/third_party/openfst/src/include/fst/
H A Drandom-weight.h163 v.push_back(rand() % kAlphabetSize + 1); in operator()
169 static const int kAlphabetSize = 5;
177 const int StringWeightGenerator<L, S>::kAlphabetSize;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/cobalt/
H A Dbase.hpp119 static const int kAlphabetSize = 28; variable
H A Dkmercounts.hpp524 TKmerCounts::SetAlphabetSize(kAlphabetSize); in SetParams()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/unit_test/
H A Dkmer_unit_test.cpp194 const int kAlphabetSize = 28; in BOOST_AUTO_TEST_CASE() local
217 TKMethods::SetParams(kKmerLen, kAlphabetSize); in BOOST_AUTO_TEST_CASE()
H A Dseq_unit_test.cpp108 BOOST_REQUIRE_EQUAL((int)it->GetFreqs().GetCols(), kAlphabetSize); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dpssmcreate_cdd_unit_test.cpp598 const int kAlphabetSize = CPssmCddInputTest::GetAlphabetSize(); in BOOST_AUTO_TEST_CASE() local
616 freq_start + freq_offsets[db_oid] * kAlphabetSize; in BOOST_AUTO_TEST_CASE()
695 for (int j=0;j < kAlphabetSize;j++) { in BOOST_AUTO_TEST_CASE()
704 * kAlphabetSize + j] == 0); in BOOST_AUTO_TEST_CASE()
1175 return CCddInputData::kAlphabetSize; in GetAlphabetSize()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dpssmcreate_cdd_unit_test.cpp598 const int kAlphabetSize = CPssmCddInputTest::GetAlphabetSize(); in BOOST_AUTO_TEST_CASE() local
616 freq_start + freq_offsets[db_oid] * kAlphabetSize; in BOOST_AUTO_TEST_CASE()
695 for (int j=0;j < kAlphabetSize;j++) { in BOOST_AUTO_TEST_CASE()
704 * kAlphabetSize + j] == 0); in BOOST_AUTO_TEST_CASE()
1175 return CCddInputData::kAlphabetSize; in GetAlphabetSize()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/
H A Dcdd_pssm_input.hpp487 static const int kAlphabetSize = 28; member in CCddInputData
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/
H A Dcdd_pssm_input.hpp487 static const int kAlphabetSize = 28; member in CCddInputData
/dports/security/keybase/client-v5.7.1/shared/ios/Pods/libwebp/src/dec/
H A Dvp8l_dec.c49 static const uint16_t kAlphabetSize[HUFFMAN_CODES_PER_META_CODE] = { variable
426 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
452 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
470 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/libwebp/src/dec/
H A Dvp8l_dec.c49 static const uint16_t kAlphabetSize[HUFFMAN_CODES_PER_META_CODE] = { variable
426 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
452 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
470 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
/dports/multimedia/gstreamer1-plugins-rust/gst-plugins-rs-d0466b3eee114207f851b37cae0015c0e718f021/cargo-crates/libwebp-sys2-0.1.2/c_src/src/dec/
H A Dvp8l_dec.c49 static const uint16_t kAlphabetSize[HUFFMAN_CODES_PER_META_CODE] = { variable
426 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
452 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
470 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
/dports/www/firefox-esr/firefox-91.8.0/media/libwebp/src/dec/
H A Dvp8l_dec.c49 static const uint16_t kAlphabetSize[HUFFMAN_CODES_PER_META_CODE] = { variable
426 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
452 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
470 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
/dports/devel/godot/godot-3.2.3-stable/thirdparty/libwebp/src/dec/
H A Dvp8l_dec.c49 static const uint16_t kAlphabetSize[HUFFMAN_CODES_PER_META_CODE] = { variable
426 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
452 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
470 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
/dports/devel/godot-tools/godot-3.2.3-stable/thirdparty/libwebp/src/dec/
H A Dvp8l_dec.c49 static const uint16_t kAlphabetSize[HUFFMAN_CODES_PER_META_CODE] = { variable
426 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
452 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()
470 int alphabet_size = kAlphabetSize[j]; in ReadHuffmanCodes()

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