/dports/lang/erlang/otp-OTP-24.1.7/lib/asn1/test/ |
H A D | testSeqDefault.erl | 31 -record('SeqDef2',{seq2 = asn1_DEFAULT, bool2 = asn1_DEFAULT, int2}). 32 -record('SeqDef2Imp',{seq2 = asn1_DEFAULT, bool2 = asn1_DEFAULT, int2}). 33 -record('SeqDef2Exp',{seq2 = asn1_DEFAULT, bool2, int2}). 48 #'SeqDef2'{seq2=asn1_DEFAULT,bool2=asn1_DEFAULT,int2=15}, 49 #'SeqDef2'{seq2=#'SeqIn'{},bool2=true,int2=15}), 62 roundtrip('SeqDef2Imp', #'SeqDef2Imp'{seq2=#'SeqIn'{boolIn=true,intIn=66}, 65 #'SeqDef2Imp'{seq2=asn1_DEFAULT,bool2=asn1_DEFAULT,int2=15}, 66 #'SeqDef2Imp'{seq2=#'SeqIn'{},bool2=true,int2=15}), 80 roundtrip('SeqDef2Exp', #'SeqDef2Exp'{seq2=#'SeqIn'{boolIn=true,intIn=66}, 83 #'SeqDef2Exp'{seq2=asn1_DEFAULT,bool2=true,int2=15}, [all …]
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/dports/lang/erlang-java/otp-OTP-24.1.7/lib/asn1/test/ |
H A D | testSeqDefault.erl | 31 -record('SeqDef2',{seq2 = asn1_DEFAULT, bool2 = asn1_DEFAULT, int2}). 32 -record('SeqDef2Imp',{seq2 = asn1_DEFAULT, bool2 = asn1_DEFAULT, int2}). 33 -record('SeqDef2Exp',{seq2 = asn1_DEFAULT, bool2, int2}). 48 #'SeqDef2'{seq2=asn1_DEFAULT,bool2=asn1_DEFAULT,int2=15}, 49 #'SeqDef2'{seq2=#'SeqIn'{},bool2=true,int2=15}), 62 roundtrip('SeqDef2Imp', #'SeqDef2Imp'{seq2=#'SeqIn'{boolIn=true,intIn=66}, 65 #'SeqDef2Imp'{seq2=asn1_DEFAULT,bool2=asn1_DEFAULT,int2=15}, 66 #'SeqDef2Imp'{seq2=#'SeqIn'{},bool2=true,int2=15}), 80 roundtrip('SeqDef2Exp', #'SeqDef2Exp'{seq2=#'SeqIn'{boolIn=true,intIn=66}, 83 #'SeqDef2Exp'{seq2=asn1_DEFAULT,bool2=true,int2=15}, [all …]
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/dports/lang/erlang-runtime21/otp-OTP-21.3.8.24/lib/asn1/test/ |
H A D | testSeqDefault.erl | 31 -record('SeqDef2',{seq2 = asn1_DEFAULT, bool2 = asn1_DEFAULT, int2}). 32 -record('SeqDef2Imp',{seq2 = asn1_DEFAULT, bool2 = asn1_DEFAULT, int2}). 33 -record('SeqDef2Exp',{seq2 = asn1_DEFAULT, bool2, int2}). 48 #'SeqDef2'{seq2=asn1_DEFAULT,bool2=asn1_DEFAULT,int2=15}, 49 #'SeqDef2'{seq2=#'SeqIn'{},bool2=true,int2=15}), 62 roundtrip('SeqDef2Imp', #'SeqDef2Imp'{seq2=#'SeqIn'{boolIn=true,intIn=66}, 65 #'SeqDef2Imp'{seq2=asn1_DEFAULT,bool2=asn1_DEFAULT,int2=15}, 66 #'SeqDef2Imp'{seq2=#'SeqIn'{},bool2=true,int2=15}), 80 roundtrip('SeqDef2Exp', #'SeqDef2Exp'{seq2=#'SeqIn'{boolIn=true,intIn=66}, 83 #'SeqDef2Exp'{seq2=asn1_DEFAULT,bool2=true,int2=15}, [all …]
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/dports/biology/sim4/sim4.2003-09-21/ |
H A D | prnt.c | 25 static void print_align_header_n(SEQ *seq1, SEQ *seq2, argv_scores_t *ds, int n) in print_align_header_n() argument 42 offset2 = SEQ_FROM(seq2) - F; in print_align_header_n() 45 F = SEQ_FROM(seq2); T = SEQ_TO(seq2); in print_align_header_n() 50 SEQ_NAME(seq2), revflag(seq2), F, T); in print_align_header_n() 54 SEQ_HEAD(seq2), in print_align_header_n() 55 revlabel(seq2), in print_align_header_n() 60 void print_align_header(SEQ *seq1, SEQ *seq2, argv_scores_t *ds) in print_align_header() argument 62 print_align_header_n(seq1, seq2, ds, 0); in print_align_header() 85 void print_align(int score, uchar *seq1, uchar *seq2, int beg1, int end1, int beg2, int end2,int *S) in print_align() argument 104 q = seq2 + beg2 + j - 1; in print_align()
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H A D | sim4.init.c | 124 uchar *seq1, *seq2; in main() local 154 seq2 = SEQ_CHARS(sf2); in main() 157 if (!is_DNA(seq2, len2)) in main() 159 seq_toupper(seq2, len2, argv[2]); in main() 204 seq2 = SEQ_CHARS(sf2); in main() 208 if (!is_DNA(seq2, len2)) { in main() 213 seq_toupper(seq2, len2, argv[2]); in main() 264 seq2 = SEQ_CHARS(sf2); in main() 279 seq2 = SEQ_CHARS(sf2); in main() 427 seq2 = SEQ_CHARS(sf2); in main() [all …]
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/kalign2/ |
H A D | kalign2_hirschberg_dna.h | 26 int* hirsch_dna_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hir… 27 int* hirsch_align_two_dna_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* … 28 struct states* foward_hirsch_dna_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_m… 29 struct states* backward_hirsch_dna_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch… 31 int* hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path,i… 32 int* hirsch_align_two_dna_ps_vector(const float* prof1,const int* seq2,struct hirsch_mem* hm,int* h… 33 struct states* foward_hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,in… 34 struct states* backward_hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,…
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H A D | kalign2_hirschberg.h | 35 int* hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path,int s… 36 struct states* foward_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int si… 37 struct states* backward_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int … 38 int* hirsch_align_two_ps_vector(const float* prof1,const int* seq2,struct hirsch_mem* hm,int* hirsc… 41 int* hirsch_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hirsch_… 42 struct states* foward_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* … 43 struct states* backward_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem… 44 int* hirsch_align_two_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm,i…
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/unittests/ |
H A D | test_whole_sequence_parser.cc | 29 static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT"; in TEST() local 38 << seq2 << "\n\n\n" in TEST() 59 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size()); in TEST() 60 EXPECT_STREQ(seq2, j->data[0].seq.substr(0, strlen(seq2)).c_str()); in TEST() 61 EXPECT_STREQ(seq1, j->data[0].seq.substr(strlen(seq2)).c_str()); in TEST() 74 static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT"; in TEST() local 85 << seq2 << "\n\n\n" in TEST() 89 << seq2 << "\n"; in TEST() 110 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size()); in TEST() 111 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].qual.size()); in TEST() [all …]
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/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/unit_tests/ |
H A D | test_whole_sequence_parser.cc | 28 static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT"; in TEST() local 37 << seq2 << "\n\n\n" in TEST() 58 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size()); in TEST() 59 EXPECT_STREQ(seq2, j->data[0].seq.substr(0, strlen(seq2)).c_str()); in TEST() 60 EXPECT_STREQ(seq1, j->data[0].seq.substr(strlen(seq2)).c_str()); in TEST() 73 static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT"; in TEST() local 84 << seq2 << "\n\n\n" in TEST() 88 << seq2 << "\n"; in TEST() 109 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size()); in TEST() 110 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].qual.size()); in TEST() [all …]
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/dports/biology/jellyfish/jellyfish-2.3.0/unit_tests/ |
H A D | test_whole_sequence_parser.cc | 28 static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT"; in TEST() local 37 << seq2 << "\n\n\n" in TEST() 58 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size()); in TEST() 59 EXPECT_STREQ(seq2, j->data[0].seq.substr(0, strlen(seq2)).c_str()); in TEST() 60 EXPECT_STREQ(seq1, j->data[0].seq.substr(strlen(seq2)).c_str()); in TEST() 73 static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT"; in TEST() local 84 << seq2 << "\n\n\n" in TEST() 88 << seq2 << "\n"; in TEST() 109 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size()); in TEST() 110 EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].qual.size()); in TEST() [all …]
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/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/ |
H A D | _pairwise.py | 183 for seq in seq1, seq2: 254 for seq in seq1, seq2: 268 def local_pairwise_align(seq1, seq2, gap_open_penalty, argument 323 for seq in seq1, seq2: 329 if type(seq1) is not type(seq2): 335 seq2 = _coerce_alignment_input_type(seq2) 426 for seq in seq1, seq2: 514 for seq in seq1, seq2: 601 for seq in seq1, seq2: 611 seq2 = _coerce_alignment_input_type(seq2) [all …]
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/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/gpu/command_buffer/service/ |
H A D | scheduler_unittest.cc | 544 seq2->AddWaitFence(sync_token1, 1, seq_id1, seq1); in TEST_F() 549 seq2->AddWaitFence(sync_token1, 1, seq_id1, seq1); in TEST_F() 554 seq3->AddWaitFence(sync_token2, 2, seq_id2, seq2); in TEST_F() 560 seq2->RemoveWaitFence(sync_token1, 1, seq_id1); in TEST_F() 565 seq2->RemoveWaitFence(sync_token1, 1, seq_id1); in TEST_F() 602 seq2->AddWaitFence(sync_token1, 1, seq_id1, seq1); in TEST_F() 603 seq2->AddWaitFence(sync_token1, 1, seq_id1, seq1); in TEST_F() 604 seq3->AddWaitFence(sync_token2, 2, seq_id2, seq2); in TEST_F() 652 seq2->AddWaitFence(sync_token1, 1, seq_id1, seq1); in TEST_F() 660 seq2->RemoveWaitFence(sync_token1, 1, seq_id1); in TEST_F() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/pairwise_alignment/ |
H A D | NWAligner.cpp | 34 NWAligner::NWAligner(const QByteArray &seq1, const QByteArray &seq2) in NWAligner() argument 35 : PairwiseAligner(seq1, seq2), fMatrix(nullptr) { in NWAligner() 84 fMatrix->calculate(seq1, seq2); in align() 89 int j = seq2.size(); in align() 100 aligned2.prepend(seq2[j - 1]); in align() 110 aligned2.prepend(seq2[j - 1]); in align() 123 aligned2.prepend(seq2[j - 1]); in align() 147 void FMatrix::calculate(const QByteArray &seq1, const QByteArray &seq2) { in calculate() argument 149 init(seq1, seq2); in calculate() 178 void FMatrix::init(const QByteArray &seq1, const QByteArray &seq2) { in init() argument [all …]
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | sywise.c | 100 char seq2[20]; in show_score_sequence() local 110 seq2[0] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+1])); in show_score_sequence() 111 seq2[1] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+2])); in show_score_sequence() 112 seq2[2] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+3])); in show_score_sequence() 115 seq2[3] = '\0'; in show_score_sequence() 137 seq2[0] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start-3])); in show_score_sequence() 138 seq2[1] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start-2])); in show_score_sequence() 139 seq2[2] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start-1])); in show_score_sequence() 140 seq2[3] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start])); in show_score_sequence() 150 seq2[11] = '\0'; in show_score_sequence() [all …]
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/dports/biology/cd-hit/cdhit-4.8.1/usecases/Miseq-16S/ |
H A D | 16S-ref-db-PE-splice.pl | 206 my $seq2 = ""; 219 $seq2 = substr($seq, 0, $p2); 228 $seq2 = "N" x $pad; 232 $seq2.= $seq; 238 $seq2 = reverse_complement($seq2); 241 print OUT2 "$des loc=$p2 len=", length($seq2), "\n$seq2\n"; 268 my $seq2 = ""; 290 $seq2 = "N" x $pad; 294 $seq2.= $seq; 300 $seq2 = reverse_complement($seq2); [all …]
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/dports/textproc/p5-XML-STX/XML-STX-0.43/STX/ |
H A D | Functions.pm | 338 my ($self, $seq1, $seq2) = @_; 346 ? $seq2->[0] : $self->F_string($seq2->[0]); 354 my ($self, $seq1, $seq2) = @_; 362 ? $seq2->[0] : $self->F_string($seq2->[0]); 372 my ($self, $seq1, $seq2) = @_; 380 ? $seq2->[0] : $self->F_string($seq2->[0]); 396 ? $seq2->[0] : $self->F_number($seq2->[0]); 416 my ($self, $seq1, $seq2) = @_; 424 ? $seq2->[0] : $self->F_string($seq2->[0]); 433 my ($self, $seq1, $seq2) = @_; [all …]
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/dports/databases/db5/db-5.3.28/lang/cxx/stl/ |
H A D | dbstl_utility.h | 174 return inst_->seqncmp_(seq1, seq2, cnt); in START_NS() 176 for (; 0 < cnt; --cnt, ++seq1, ++seq2) in START_NS() 177 if (!eq(*seq1, *seq2)) in START_NS() 178 return (lt(*seq1, *seq2) ? -1 : +1); in START_NS() 197 inst_->seqcpy_(seq1, seq2, cnt); in START_NS() 200 for (; 0 < cnt; --cnt, ++pnext, ++seq2) in START_NS() 201 assign(*pnext, *seq2); in START_NS() 223 if (seq2 < pnext && pnext < seq2 + cnt) in START_NS() 225 assign(*--pnext, *--seq2); in START_NS() 227 for (; 0 < cnt; --cnt, ++pnext, ++seq2) in START_NS() [all …]
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/dports/databases/db18/db-18.1.40/lang/cxx/stl/ |
H A D | dbstl_utility.h | 174 return inst_->seqncmp_(seq1, seq2, cnt); in START_NS() 176 for (; 0 < cnt; --cnt, ++seq1, ++seq2) in START_NS() 177 if (!eq(*seq1, *seq2)) in START_NS() 178 return (lt(*seq1, *seq2) ? -1 : +1); in START_NS() 197 inst_->seqcpy_(seq1, seq2, cnt); in START_NS() 200 for (; 0 < cnt; --cnt, ++pnext, ++seq2) in START_NS() 201 assign(*pnext, *seq2); in START_NS() 223 if (seq2 < pnext && pnext < seq2 + cnt) in START_NS() 225 assign(*--pnext, *--seq2); in START_NS() 227 for (; 0 < cnt; --cnt, ++pnext, ++seq2) in START_NS() [all …]
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/dports/devel/poco/poco-1.10.1-all/Encodings/testsuite/src/ |
H A D | DoubleByteEncodingTest.cpp | 40 unsigned char seq2[] = { 0xF9 }; // 0x0173 LATIN SMALL LETTER U WITH OGONEK in testSingleByte() local 41 assertTrue (enc.convert(seq2) == 0x0173); in testSingleByte() 42 assertTrue (enc.queryConvert(seq2, 1) == 0x0173); in testSingleByte() 43 assertTrue (enc.sequenceLength(seq2, 1) == 1); in testSingleByte() 76 unsigned char seq2[] = { 0xA1, 0x40 }; // 0x3000 IDEOGRAPHIC SPACE in testDoubleByte() local 77 assertTrue (enc.convert(seq2) == 0x3000); in testDoubleByte() 78 assertTrue (enc.queryConvert(seq2, 1) == -2); in testDoubleByte() 79 assertTrue (enc.queryConvert(seq2, 2) == 0x3000); in testDoubleByte() 80 assertTrue (enc.sequenceLength(seq2, 1) == 2); in testDoubleByte() 81 assertTrue (enc.sequenceLength(seq2, 2) == 2); in testDoubleByte()
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/dports/biology/jalview/jalview/test/jalview/datamodel/ |
H A D | SequenceGroupTest.java | 46 sg.addSequence(seq2, false); in testAddSequence() 47 sg.addSequence(seq2, false); in testAddSequence() 67 sg.addOrRemove(seq2, false); in testAddOrRemove() 183 assertFalse(sg1.contains(seq2)); in testContains() 203 sg2.addSequence(seq2, false); in testContains() 218 assertTrue(sg2.contains(seq2, 4)); in testContains() 219 assertTrue(sg2.contains(seq2, 5)); in testContains() 220 assertTrue(sg2.contains(seq2, 6)); in testContains() 221 assertTrue(sg2.contains(seq2, 7)); in testContains() 226 sg2.deleteSequence(seq2, false); in testContains() [all …]
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/dports/textproc/datamash/datamash-1.7/tests/ |
H A D | datamash-stats.pl | 84 my $seq2 = c( 1,2,3 ); 285 ['mean2', 'mean 1' , {IN_PIPE=>$seq2}, {OUT => "2\n"}], 335 ['med2', 'median 1' , {IN_PIPE=>$seq2}, {OUT => "2\n"}], 351 ['q1_2', 'q1 1' , {IN_PIPE=>$seq2}, {OUT => "1.5\n"}], 367 ['q3_2', 'q3 1' , {IN_PIPE=>$seq2}, {OUT => "2.5\n"}], 383 ['range_2', 'range 1' , {IN_PIPE=>$seq2}, {OUT => "2\n"}], 539 ['iqr_2', 'iqr 1' , {IN_PIPE=>$seq2}, {OUT => "1\n"}], 578 ['svar_2', 'svar 1' , {IN_PIPE=>$seq2}, {OUT => "1\n"}], 605 ['mad_2', 'mad 1' , {IN_PIPE=>$seq2}, {OUT => "1.482\n"}], 639 ['pskew_2', 'pskew 1' , {IN_PIPE=>$seq2}, {OUT => "0\n"}], [all …]
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/dports/biology/avida/avida-2.12.4-src/avida-core/source/core/ |
H A D | Sequence.cc | 381 assert(-offset < seq2.GetSize()); in FindOverlap() 385 return Min(seq2.GetSize() + offset, seq1.GetSize()); in FindOverlap() 393 const int overlap = FindOverlap(seq1, seq2, offset); in FindHammingDistance() 411 const int size2 = seq2.GetSize(); in FindBestOffset() 414 int cur_distance = FindHammingDistance(seq1, seq2); in FindBestOffset() 420 cur_distance = FindHammingDistance(seq1, seq2, i); in FindBestOffset() 430 cur_distance = FindHammingDistance(seq1, seq2, -i); in FindBestOffset() 443 const int offset = FindBestOffset(seq1, seq2); in FindSlidingDistance() 444 return FindHammingDistance(seq1, seq2, offset); in FindSlidingDistance() 451 const int size2 = seq2.GetSize(); in FindEditDistance() [all …]
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/dports/print/py-reportlab/reportlab-3.5.68/tests/ |
H A D | test_pyfiles.py | 22 seq2 = seq[:] 23 if cnvt: seq2 = list(seq2) 24 seq2.sort() 28 while i < len(seq2)-1: 29 elem = seq2[i] 31 while elem == seq2[i+1]: 32 del seq2[i+1] 39 return seq[0:0].join(seq2) 41 return seq2
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/ |
H A D | tinyseq.t | 40 my $seq2 = $reread->next_seq; 42 ok($seq2); 43 ok($seq2->seq); 44 is($seq2->length, 5830); 45 is($seq2->accession_number, 'NM_002253'); 46 ok($seq2->species); 47 is($seq2->species->binomial, 'Homo sapiens'); 48 is($seq2->species->ncbi_taxid, 9606);
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | diffseq.c | 144 AjPSeq seq2; in main() local 176 ajSeqTrim(seq2); in main() 201 seq1, seq2); in main() 233 ajSeqDel(&seq2); in main() 307 len2 = ajSeqGetLen(seq2); in diffseq_Diff() 310 s2 = ajSeqGetSeqS(seq2); in diffseq_Diff() 313 feat2 = ajSeqGetFeatCopy(seq2); in diffseq_Diff() 324 ajSeqGetBegin(seq2), ajSeqGetEnd(seq2)); in diffseq_Diff() 526 len2 = ajSeqGetLen(seq2); in diffseq_WordMatchListConvDiffToFeat() 791 seqc2 = ajSeqGetSeqC(seq2); in diffseq_DiffList() [all …]
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