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/dports/devel/hyperscan/boost_1_75_0/libs/ptr_container/test/
H A Dptr_inserter.cpp43 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()
/dports/biology/bedtools/bedtools2-2.30.0/src/bamToFastq/
H A DbamToFastq.cpp115 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()
/dports/biology/jalview/jalview/test/jalview/analysis/
H A DAAFrequencyTest.java51 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()
/dports/security/sqlmap/sqlmap-1.3.12/sqlmap/lib/request/
H A Dcomparison.py129 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)
/dports/lang/nim/nim-1.6.2/tests/ccgbugs/
H A Dt10128.nim3 var seq2 = newSeq[char](data.len)
5 seq2[i] = data[i]
11 doAssert seq2[c.int] == 'y'
18 play(seq2)
/dports/databases/xapian-core/xapian-core-1.4.18/api/
H A Deditdistance.cc57 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()
/dports/devel/R-cran-rlang/rlang/man/
H A Dseq2.Rd3 \name{seq2}
4 \alias{seq2}
8 seq2(from, to)
31 seq2(2, 10)
32 seq2(10, 2)
/dports/net/libnids/libnids-1.24/src/
H A Dutil.h30 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()
/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/
H A Dgraph_align_tcoffee_io.h152 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 …]
/dports/math/pari/pari-2.13.3/src/functions/programming/
H A Dif5 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
/dports/biology/mafft/mafft-7.267-without-extensions/core/
H A DpartSalignmm.c179 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 …]
H A DDalignmm.c233 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 …]
H A Dgenalign11.c14 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 …]
H A DLalign11.c15 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 …]
/dports/textproc/p5-XML-STX/XML-STX-0.43/test/
H A Dstxpath-subsequence.stx9 <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))"/>
/dports/databases/xapian-core12/xapian-core-1.2.25/api/
H A Deditdistance.cc57 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()
/dports/biology/viennarna/ViennaRNA-2.4.18/src/RNAforester/src/
H A Drna_alignment.cpp124 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()
/dports/biology/viennarna/ViennaRNA-2.4.18/examples/
H A Dexample_old.c18 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()
/dports/lang/mono/mono-5.10.1.57/external/corefx/src/System.Private.Xml/src/System/Xml/Extensions/
H A DExtensionMethods.cs19 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()
/dports/math/clblas/clBLAS-2.10/src/library/blas/
H A Dxnrm2.c37 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()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_io.h169 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_io.h169 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 …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_io.h169 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 …]
/dports/japanese/scim-anthy/scim-anthy-1.2.7/src/
H A Dscim_anthy_table_editor.cpp396 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 …]
/dports/lang/spidermonkey60/firefox-60.9.0/third_party/rust/regex-0.2.2/examples/
H A Dshootout-regex-redux.rs50 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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