/dports/devel/hyperscan/boost_1_75_0/libs/ptr_container/test/ |
H A D | ptr_inserter.cpp | 43 PtrSequence seq2; in test_ptr_inserter_helper() local 50 ptr_container::ptr_back_inserter( seq2 ) ); in test_ptr_inserter_helper() 54 ptr_container::ptr_front_inserter( seq2 ) ); in test_ptr_inserter_helper() 55 BOOST_CHECK_EQUAL( seq.size()*2, seq2.size() ); in test_ptr_inserter_helper() 67 BOOST_CHECK_EQUAL( seq.size(), seq2.size() ); in test_ptr_inserter_helper()
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/dports/biology/bedtools/bedtools2-2.30.0/src/bamToFastq/ |
H A D | bamToFastq.cpp | 115 string seq1, seq2; in WritePairs() local 133 seq2 = alignments[1].QueryBases; in WritePairs() 140 reverseComplement(seq2); in WritePairs() 148 seq2 = alignments[0].QueryBases; in WritePairs() 155 reverseComplement(seq2); in WritePairs() 184 seq2 = alignments[mateIndex].QueryBases; in WritePairs() 191 reverseComplement(seq2); in WritePairs() 214 seq2 = alignments[0].QueryBases; in WritePairs() 223 reverseComplement(seq2); in WritePairs() 247 *_fq2 << seq2 << endl; in WritePairs()
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/dports/biology/jalview/jalview/test/jalview/analysis/ |
H A D | AAFrequencyTest.java | 51 SequenceI seq2 = new Sequence("Seq2", "CAC-T"); in testCalculate_noProfile() local 54 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCalculate_noProfile() 100 SequenceI seq2 = new Sequence("Seq2", "CACT"); in testCalculate_withProfile() local 103 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCalculate_withProfile() 135 SequenceI seq2 = new Sequence("Seq2", "CACT"); in testCalculate_withProfileTiming() local 138 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCalculate_withProfileTiming() 166 SequenceI seq2 = new Sequence("Seq2", "CAC-T"); in testCompleteConsensus_includeGaps_showLogo() local 169 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCompleteConsensus_includeGaps_showLogo() 207 SequenceI seq2 = new Sequence("Seq2", "CAC-T"); in testCompleteConsensus_ignoreGaps_noLogo() local 210 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCompleteConsensus_ignoreGaps_noLogo()
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/dports/security/sqlmap/sqlmap-1.3.12/sqlmap/lib/request/ |
H A D | comparison.py | 129 seq1, seq2 = None, None 133 seq2 = extractRegexResult(HTML_TITLE_REGEX, page) 136 seq2 = getFilteredPageContent(page, True) if conf.textOnly else page 138 if seq1 is None or seq2 is None: 142 seq2 = seq2.replace(REFLECTED_VALUE_MARKER, "") 146 seq2 = seq2.split("\n") 149 seqMatcher.set_seq2(seq2)
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/dports/lang/nim/nim-1.6.2/tests/ccgbugs/ |
H A D | t10128.nim | 3 var seq2 = newSeq[char](data.len) 5 seq2[i] = data[i] 11 doAssert seq2[c.int] == 'y' 18 play(seq2)
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/dports/databases/xapian-core/xapian-core-1.4.18/api/ |
H A D | editdistance.cc | 57 edist_seq<CHR> seq2; member in edist_state 90 if (pos1 <= 0 || pos2 <= 0 || pos1 >= seq1.len || pos2 >= seq2.len) return false; in is_transposed() 91 return (seq1.ptr[pos1 - 1] == seq2.ptr[pos2] && in is_transposed() 92 seq1.ptr[pos1] == seq2.ptr[pos2 - 1]); in is_transposed() 130 maxlen + k < seq2.len && in edist_calc_f_kp() 131 seq1.ptr[maxlen] == seq2.ptr[maxlen + k]) { in edist_calc_f_kp() 141 : seq1(ptr1, len1), seq2(ptr2, len2), maxdist(len2) in edist_state()
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/dports/devel/R-cran-rlang/rlang/man/ |
H A D | seq2.Rd | 3 \name{seq2} 4 \alias{seq2} 8 seq2(from, to) 31 seq2(2, 10) 32 seq2(10, 2)
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/dports/net/libnids/libnids-1.24/src/ |
H A D | util.h | 30 before(u_int seq1, u_int seq2) in before() argument 32 return ((int)(seq1 - seq2) < 0); in before() 36 after(u_int seq1, u_int seq2) in after() argument 38 return ((int)(seq2 - seq1) < 0); in after()
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/ |
H A D | graph_align_tcoffee_io.h | 152 TSize seq2 = 0; in read() local 169 --seq2; in read() 172 seq2 = value(posMap, seq2); in read() 183 if (seq1 < seq2) { in read() 195 TSize seq2 = i % nseq; in read() local 320 TSize seq2 = i % nseq; in write() local 408 for(TSize seq2 = seq1 + 1; seq2 < nseq; ++seq2) { in _collectSegmentMatches() local 574 TName seq2; in read() local 577 clear(seq2); in read() 582 if (seq1 == seq2) { in read() [all …]
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/dports/math/pari/pari-2.13.3/src/functions/programming/ |
H A D | if | 5 Help: if(a,{seq1},{seq2}): if a is nonzero, seq1 is evaluated, otherwise seq2. 6 seq1 and seq2 are optional, and if seq2 is omitted, the preceding comma can 9 the expression \var{seq2}. Of course, \var{seq1} or \var{seq2} may be empty: 29 test2, seq2, 36 , if (test2, seq2
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/dports/biology/mafft/mafft-7.267-without-extensions/core/ |
H A D | partSalignmm.c | 179 pt = seq2[j]; in part_imp_match_init_strict() 215 pt2 = seq2[j] + k2; in part_imp_match_init_strict() 348 pt = seq2[j]; in part_imp_match_init() 355 start2 = pt - seq2[j] - 1; in part_imp_match_init() 361 end2 = pt - seq2[j] - 1; in part_imp_match_init() 681 lgth2 = strlen( seq2[0] ); in Atracking_localhom() 827 lgth2 = strlen( seq2[0] ); in Atracking() 1075 lgth2 = strlen( seq2[0] ); in partA__align() 1100 seq2[i][j] = 0; in partA__align() 1788 lgth2 = strlen( seq2[0] ); in partA__align_variousdist() [all …]
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H A D | Dalignmm.c | 233 pt = seq2[j]; in imp_match_init_strictD() 250 end2 = pt - seq2[j] - 0; in imp_match_init_strictD() 257 end2 = pt - seq2[j] - 1; in imp_match_init_strictD() 270 pt2 = seq2[j] + k2; in imp_match_init_strictD() 644 lgth2 = strlen( seq2[0] ); in Atracking_localhom() 784 lgth2 = strlen( seq2[0] ); in Atracking() 2887 seq2[i][j] = 0; in D__align() 3216 seq2[j][lgth2] = 0; in D__align() 4514 v2 = gapvariety( jcyc, strlen( seq2[0] ), seq2 ); in D__align_ls() 4757 seq2[i][j] = 0; in D__align_variousdist() [all …]
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H A D | genalign11.c | 14 char *seq2 = s2[0]; in match_calc_mtx() local 18 *match++ = doubleptr[(int)*seq2++]; in match_calc_mtx() 31 char **seq1, char **seq2, in gentracking() argument 42 lgth2 = strlen( seq2[0] ); in gentracking() 90 *--mseq2[0] = seq2[0][jfi+l]; in gentracking() 96 *--mseq2[0] = seq2[0][jfi]; in gentracking() 208 lgth2 = strlen( seq2[0] ); in genL__align11() 322 match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 ); in genL__align11() 353 fprintf( stderr, "%c ", seq2[0][j] ); in genL__align11() 578 strcpy( seq2[0], "" ); in genL__align11() [all …]
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H A D | Lalign11.c | 15 char *seq2 = s2[0]; in match_calc_mtx() local 19 *match++ = doubleptr[(int)*seq2++]; in match_calc_mtx() 92 char **seq1, char **seq2, in Ltracking() argument 103 lgth2 = strlen( seq2[0] ); in Ltracking() 163 *--mseq2[0] = seq2[0][l]; in Ltracking() 190 *--mseq2[0] = seq2[0][jfi]; in Ltracking() 300 lgth2 = strlen( seq2[0] ); in L__align11() 711 strcpy( seq2[0], "" ); in L__align11() 731 strcpy( seq2[0], mseq2[0] ); in L__align11() 822 lgth2 = strlen( seq2[0] ); in L__align11_noalign() [all …]
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/dports/textproc/p5-XML-STX/XML-STX-0.43/test/ |
H A D | stxpath-subsequence.stx | 9 <stx:variable name="seq2" select="subsequence($seq1, 3)"/> 12 <stx:value-of select="count($seq2)"/> 14 <stx:value-of select="item-at($seq2, 1)"/> 16 <stx:value-of select="item-at($seq2, count($seq2))"/>
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/dports/databases/xapian-core12/xapian-core-1.2.25/api/ |
H A D | editdistance.cc | 57 edist_seq<CHR> seq2; member in edist_state 90 if (pos1 <= 0 || pos2 <= 0 || pos1 >= seq1.len || pos2 >= seq2.len) return false; in is_transposed() 91 return (seq1.ptr[pos1 - 1] == seq2.ptr[pos2] && in is_transposed() 92 seq1.ptr[pos1] == seq2.ptr[pos2 - 1]); in is_transposed() 130 maxlen + k < seq2.len && in edist_calc_f_kp() 131 seq1.ptr[maxlen] == seq2.ptr[maxlen + k]) { in edist_calc_f_kp() 141 : seq1(ptr1, len1), seq2(ptr2, len2), maxdist(len2) in edist_state()
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/RNAforester/src/ |
H A D | rna_alignment.cpp | 124 std::string str1,str2,seq1,seq2; in squigglePlot() local 129 getSequenceAlignments(seq1,seq2); in squigglePlot() 132 RNAFuncs::drawRNAAlignment(str1,str2,seq1,seq2,strname1_,strname2_,filename,true,options); in squigglePlot() 134 RNAFuncs::drawRNAAlignment(str2,str1,seq1,seq2,strname1_,strname2_,filename,false,options); in squigglePlot() 146 std::string str1,str2,seq1,seq2; in generateXML() local 150 getSequenceAlignments(seq1,seq2); in generateXML() 152 RNAFuncs::generateRNAAlignmentXML(str1,str2,seq1,seq2,strname1_,strname2_,s); in generateXML()
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/dports/biology/viennarna/ViennaRNA-2.4.18/examples/ |
H A D | example_old.c | 18 char *seq1 = "CGCAGGGAUACCCGCG", *seq2 = "GCGCCCAUAGGGACGC", in main() local 33 struct2 = (char *)space(sizeof(char) * (strlen(seq2) + 1)); in main() 34 e2 = fold(seq2, struct2); in main() 75 e2 = pf_fold(seq2, struct2); in main() 78 pf2 = Make_bp_profile_bppm(bppm, strlen(seq2)); in main()
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/dports/lang/mono/mono-5.10.1.57/external/corefx/src/System.Private.Xml/src/System/Xml/Extensions/ |
H A D | ExtensionMethods.cs | 19 private static bool TypeSequenceEqual(Type[] seq1, Type[] seq2) in TypeSequenceEqual() argument 21 if (seq1 == null || seq2 == null || seq1.Length != seq2.Length) in TypeSequenceEqual() 25 if (!seq1[i].Equals(seq2[i]) && !seq1[i].IsAssignableFrom(seq2[i])) in TypeSequenceEqual()
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/dports/math/clblas/clBLAS-2.10/src/library/blas/ |
H A D | xnrm2.c | 37 ListHead seq, seq2; in doNrm2_hypot() local 70 listInitHead(&seq2); in doNrm2_hypot() 72 1, &firstNrmCall, events, &seq2); in doNrm2_hypot() 76 err = executeSolutionSeq(&seq2); in doNrm2_hypot() 78 freeSolutionSeq(&seq2); in doNrm2_hypot() 95 ListHead seq, seq2; in doNrm2_ssq() local 128 listInitHead(&seq2); in doNrm2_ssq() 130 1, &firstNrmCall, events, &seq2); in doNrm2_ssq() 134 err = executeSolutionSeq(&seq2); in doNrm2_ssq() 136 freeSolutionSeq(&seq2); in doNrm2_ssq()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_io.h | 169 TSize seq2 = 0; in read() local 192 --seq2; in read() 195 seq2 = value(posMap, seq2); in read() 212 if (seq1 < seq2) { in read() 224 TSize seq2 = i % nseq; in read() local 457 for(TSize seq2 = seq1 + 1; seq2 < nseq; ++seq2) { in _collectSegmentMatches() local 627 TName seq2; in read() local 631 clear(seq2); in read() 639 if (seq1 == seq2) in read() 844 TName seq2; in read() local [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_io.h | 169 TSize seq2 = 0; in read() local 192 --seq2; in read() 195 seq2 = value(posMap, seq2); in read() 212 if (seq1 < seq2) { in read() 224 TSize seq2 = i % nseq; in read() local 457 for(TSize seq2 = seq1 + 1; seq2 < nseq; ++seq2) { in _collectSegmentMatches() local 627 TName seq2; in read() local 631 clear(seq2); in read() 639 if (seq1 == seq2) in read() 844 TName seq2; in read() local [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_io.h | 169 TSize seq2 = 0; in read() local 192 --seq2; in read() 195 seq2 = value(posMap, seq2); in read() 212 if (seq1 < seq2) { in read() 224 TSize seq2 = i % nseq; in read() local 460 for(TSize seq2 = seq1 + 1; seq2 < nseq; ++seq2) { in _collectSegmentMatches() local 634 TName seq2; in read() local 638 clear(seq2); in read() 646 if (seq1 == seq2) in read() 854 TName seq2; in read() local [all …]
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/dports/japanese/scim-anthy/scim-anthy-1.2.7/src/ |
H A D | scim_anthy_table_editor.cpp | 396 gchar *seq1 = NULL, *seq2 = NULL; in compare_string() local 403 if (!seq1 && seq2) { in compare_string() 405 } else if (seq1 && !seq2) { in compare_string() 407 } else if (seq1 && seq2) { in compare_string() 408 ret = strcmp (seq1, seq2); in compare_string() 413 g_free (seq2); in compare_string() 428 if (!seq1 && seq2) { in compare_string() 430 } else if (seq1 && !seq2) { in compare_string() 432 } else if (!seq1 && !seq2) { in compare_string() 433 ret = strcmp (seq1, seq2); in compare_string() [all …]
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/dports/lang/spidermonkey60/firefox-60.9.0/third_party/rust/regex-0.2.2/examples/ |
H A D | shootout-regex-redux.rs | 50 let mut seq2 = read().unwrap(); in main() localVariable 51 let ilen = seq2.len(); in main() 55 let seq = Arc::new(squash.replace_all(&seq2, &b""[..]).into_owned()); in main() 97 replace(&re, &seq1, replacement, &mut seq2); in main() 98 ::std::mem::swap(&mut seq1, &mut seq2); in main()
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