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/dports/lang/erlang/otp-OTP-24.1.7/lib/asn1/test/
H A DtestSeqDefault.erl31 -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 …]
/dports/lang/erlang-java/otp-OTP-24.1.7/lib/asn1/test/
H A DtestSeqDefault.erl31 -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 …]
/dports/lang/erlang-runtime21/otp-OTP-21.3.8.24/lib/asn1/test/
H A DtestSeqDefault.erl31 -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 …]
/dports/biology/sim4/sim4.2003-09-21/
H A Dprnt.c25 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()
H A Dsim4.init.c124 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 …]
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/kalign2/
H A Dkalign2_hirschberg_dna.h26 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,…
H A Dkalign2_hirschberg.h35 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…
/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/unittests/
H A Dtest_whole_sequence_parser.cc29 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 …]
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/jellyfish/unit_tests/
H A Dtest_whole_sequence_parser.cc28 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 …]
/dports/biology/jellyfish/jellyfish-2.3.0/unit_tests/
H A Dtest_whole_sequence_parser.cc28 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 …]
/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/
H A D_pairwise.py183 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 …]
/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/gpu/command_buffer/service/
H A Dscheduler_unittest.cc544 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 …]
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/pairwise_alignment/
H A DNWAligner.cpp34 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 …]
/dports/biology/wise/wise2.4.1/src/models/
H A Dsywise.c100 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 …]
/dports/biology/cd-hit/cdhit-4.8.1/usecases/Miseq-16S/
H A D16S-ref-db-PE-splice.pl206 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 …]
/dports/textproc/p5-XML-STX/XML-STX-0.43/STX/
H A DFunctions.pm338 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 …]
/dports/databases/db5/db-5.3.28/lang/cxx/stl/
H A Ddbstl_utility.h174 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 …]
/dports/databases/db18/db-18.1.40/lang/cxx/stl/
H A Ddbstl_utility.h174 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 …]
/dports/devel/poco/poco-1.10.1-all/Encodings/testsuite/src/
H A DDoubleByteEncodingTest.cpp40 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()
/dports/biology/jalview/jalview/test/jalview/datamodel/
H A DSequenceGroupTest.java46 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 …]
/dports/textproc/datamash/datamash-1.7/tests/
H A Ddatamash-stats.pl84 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 …]
/dports/biology/avida/avida-2.12.4-src/avida-core/source/core/
H A DSequence.cc381 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 …]
/dports/print/py-reportlab/reportlab-3.5.68/tests/
H A Dtest_pyfiles.py22 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
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/
H A Dtinyseq.t40 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);
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Ddiffseq.c144 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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