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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqFeature/
H A DSubSeq.t20 is $subseq->length, undef;
28 is $subseq->length, 20;
29 ok $subseq_seq = $subseq->seq;
39 is $subseq->length, 20;
40 ok $subseq_seq = $subseq->seq;
53 is $subseq->length, 30;
54 ok $subseq_seq = $subseq->seq;
68 is $subseq->length, 20;
71 ok $subseq_seq = $subseq->seq;
86 is $subseq->length, 20;
[all …]
/dports/lang/eisl/eisl-2.35/verify/
H A Dseq.lsp168 ($argc subseq 3 0 0)
177 ($test (subseq "" 0 0) "" string=)
186 ($test (subseq "abc" 0 0) "" string=)
187 ($test (subseq "abc" 0 1) "a" string=)
192 ($test (subseq "abc" 1 1) "" string=)
193 ($test (subseq "abc" 1 2) "b" string=)
198 ($test (subseq "abc" 2 2) "" string=)
199 ($test (subseq "abc" 2 3) "c" string=)
204 ($test (subseq "abc" 3 3) "" string=)
214 ($test (subseq #() 0 0) #() equal)
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dorigsplitter.c47 AjPSeq subseq = NULL; in main() local
63 subseq = ajSeqNew(); in main()
78 ajSeqAssignSeqS(subseq, str); in main()
84 ajSeqAssignSeqS(subseq, str); in main()
92 ajSeqAssignSeqS(subseq,str); in main()
98 ajSeqAssignSeqS(subseq, str); in main()
106 ajSeqDel(&subseq); in main()
150 ajSeqAssignNameS(subseq, name); in origsplitter_write()
153 ajSeqAssignDescS(subseq, ajSeqGetDescS(seq)); in origsplitter_write()
156 ajSeqType(subseq); in origsplitter_write()
[all …]
H A Dsplitter.c137 AjPSeq subseq, const AjPSeq seq) in splitter_write() argument
140 ajSeqAssignDescS(subseq, ajSeqGetDescS(seq)); in splitter_write()
143 ajSeqType(subseq); in splitter_write()
145 ajSeqoutWriteSeq(default_seqout, subseq); in splitter_write()
205 AjPSeq subseq; in splitter_ProcessChunk() local
211 subseq = ajSeqNew(); in splitter_ProcessChunk()
215 subseq->Fttable = new_feattable; in splitter_ProcessChunk()
219 ajSeqAssignSeqS(subseq,str); in splitter_ProcessChunk()
224 ajSeqAssignNameS(subseq, name); in splitter_ProcessChunk()
225 splitter_write(seqout,subseq,seq); in splitter_ProcessChunk()
[all …]
H A Dsplitsource.c29 static void splitsource_write(AjPSeqout seqout, AjPSeq subseq,
127 ajSeqAssignDescS(subseq, desc); in splitsource_write()
130 ajSeqType(subseq); in splitsource_write()
132 ajSeqoutWriteSeq(default_seqout, subseq); in splitsource_write()
199 AjPSeq subseq = ajSeqNew (); in splitsource_ProcessChunk() local
215 subseq->Fttable = new_feattable; in splitsource_ProcessChunk()
219 ajSeqAssignSeqS(subseq,str); in splitsource_ProcessChunk()
221 splitsource_AddSubSeqFeat(subseq->Fttable,gf,seq); in splitsource_ProcessChunk()
222 ajSeqAssignNameS(subseq, name); in splitsource_ProcessChunk()
233 splitsource_write(seqout,subseq,desc); in splitsource_ProcessChunk()
[all …]
H A Dsirna.c617 AjPStr subseq; in sirna_output() local
626 subseq = ajStrNew(); in sirna_output()
656 ajStrAssignC(&subseq, "("); in sirna_output()
659 ajStrAppendC(&subseq, ")"); in sirna_output()
664 ajStrFmtUpper(&subseq); in sirna_output()
666 ajStrAppendC(&subseq, "dTdT"); in sirna_output()
672 ajStrFmtUpper(&subseq); in sirna_output()
673 ajSeqstrReverse(&subseq); in sirna_output()
675 ajStrAppendC(&subseq, "dTdT"); in sirna_output()
709 ajStrSetClear(&subseq); in sirna_output()
[all …]
/dports/net/tcpdump/tcpdump-4.99.1/tests/
H A Dmptcp-v0.out11 …TS val 4294943168 ecr 4294943474,mptcp dss ack 3518592185 seq 3576348403 subseq 42 len 848 csum 0x…
14 …TS val 4294943474 ecr 4294943168,mptcp dss ack 3576349251 seq 3518592185 subseq 1 len 784 csum 0x5…
16 …TS val 4294943170 ecr 4294943474,mptcp dss ack 3518592969 seq 3576349251 subseq 1 len 24 csum 0xec…
18 …TS val 4294943474 ecr 4294943170,mptcp dss ack 3576349275 seq 3518592969 subseq 785 len 152 csum 0…
19 …TS val 4294943170 ecr 4294943474,mptcp dss ack 3518593121 seq 3576349275 subseq 25 len 144 csum 0x…
21 …TS val 4294943172 ecr 4294943474,mptcp dss ack 3518593841 seq 3576349419 subseq 890 len 16 csum 0x…
23 …TS val 4294943172 ecr 4294943474,mptcp dss ack 3518593841 seq 3576349435 subseq 906 len 48 csum 0x…
27 …TS val 4294943172 ecr 4294943474,mptcp dss ack 3518593889 seq 3576349483 subseq 954 len 64 csum 0x…
40 …TS val 4294943611 ecr 4294943301,mptcp dss ack 3576350699 seq 3518594337 subseq 42 len 32 csum 0x2…
259 …al 4294944064 ecr 4294944372,mptcp dss fin ack 3518600705 seq 3576353483 subseq 0 len 1 csum 0xa51…
[all …]
H A Dmptcp-aa-v1.out8 …r 2070300963,mptcp dss ack 17186763219675866581 seq 12148165319181844526 subseq 1 len 16,nop,nop],…
10 …r 2070300964,mptcp dss ack 17186763219675866581 seq 12148165319181844526 subseq 17 len 16,nop,nop]…
12 …cr 938670368,mptcp dss ack 12148165319181844542 seq 17186763219675866581 subseq 17 len 16,nop,nop]…
14 …r 2070301967,mptcp dss ack 17186763219675866597 seq 12148165319181844542 subseq 33 len 16,nop,nop]…
16 …r 2070301969,mptcp dss ack 17186763219675866597 seq 12148165319181844542 subseq 49 len 16,nop,nop]…
18 …cr 938671376,mptcp dss ack 12148165319181844558 seq 17186763219675866597 subseq 33 len 16,nop,nop]…
20 …r 2070302969,mptcp dss ack 17186763219675866613 seq 12148165319181844558 subseq 65 len 16,nop,nop]…
22 …38672169,mptcp dss fin ack 12148165319181844574 seq 17186763219675866613 subseq 0 len 1,nop,nop], …
23 …70302970,mptcp dss fin ack 17186763219675866613 seq 12148165319181844574 subseq 0 len 1,nop,nop], …
/dports/math/maxima/maxima-5.43.2/share/stringproc/
H A Dprintf.lisp92 spec (subseq ctrls (1- pos2) pos2) )
104 ch (subseq params p (1+ p)) ))
168 (concatenate 'string (subseq ctrls 0 pos1) arg (subseq ctrls pos2)) )
203 (subseq params (1- p))
204 (subseq params p) )))
299 spec (subseq ctrls (1- pos2) pos2) )
348 spec (subseq ctrls (1- pos2) pos2) )
367 ((string= (subseq params p (1+ p)) "'")
392 (string= (subseq smarap 0 1) "@")
467 (part1 (subseq s 0 1))
[all …]
/dports/biology/pbbam/pbbam-0.18.0/src/
H A DIndexedFastaReader.cpp108 std::string subseq = Subsequence(bamRecord.ReferenceName(), bamRecord.ReferenceStart(), in ReferenceSubsequence() local
126 subseq.reserve(subseq.size() + opLength); in ReferenceSubsequence()
127 subseq.insert(seqIndex, opLength, '-'); in ReferenceSubsequence()
137 subseq.reserve(subseq.size() + opLength); in ReferenceSubsequence()
138 subseq.insert(seqIndex, opLength, '-'); in ReferenceSubsequence()
140 subseq.reserve(subseq.size() + opLength); in ReferenceSubsequence()
141 subseq.insert(seqIndex, opLength, '*'); in ReferenceSubsequence()
151 if (reverse) internal::ReverseComplementCaseSens(subseq); in ReferenceSubsequence()
153 return subseq; in ReferenceSubsequence()
/dports/biology/wise/wise2.4.1/src/dnaindex/
H A Dmake_shotgun.pl39 my $subseq = $seq->trunc($start+1,$start+$seq_size);
40 $subseq->id(($seq->id.".".$start.".".($start+$seq_size)));
44 my $seqstr = $subseq->seq();
48 …t STDERR "[$i] Randomising a position $j... ",substr($seqstr,$j,1)," to $new on ".$subseq->id,"\n";
53 $subseq->seq($seqstr);
62 $seqout->write_seq($subseq);
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Seq/
H A DPrimarySeq.t72 # Test subseq
73 is $seq->subseq(2, 5), 'TGGT';
82 is $seq->subseq($location), 'ACCA';
101 is $seq->subseq($splitlocation), 'TTGGTGACGC';
109 is $seq->subseq($fuzzy), 'GGTGGC';
113 is $seq->subseq(2, 5, 'nogap'), 'TGT';
507 is $seq->subseq($loc1_strand), 'AAAAA';
508 is $seq->subseq($loc1_no_strand), 'AAAAA';
513 is $seq->subseq($loc1_strand), 'TTTTT';
514 is $seq->subseq($loc1_no_strand), 'TTTTT';
[all …]
H A DLargePSeq.t28 is $pseq->subseq(3,7), 'GGGGT', "Subseq is ".$pseq->subseq(3,7);
31 is($pseq->subseq($location), 'GGGTG');
43 is( $pseq->subseq($splitlocation), 'ATGGGGTGGGGTGAACCCCCAA');
49 is( $pseq->subseq($fuzzy), 'GGTGAAACC');
79 is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7);
92 is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7);
/dports/biology/p5-BioPerl/BioPerl-1.7.7/examples/
H A Dmake_primers.pl85 $upprimer = $seq->subseq($start-$oligolength-$upgap, $start-1-$upgap);
86 $downprimer = $seq->subseq($stop+1+$downgap,$stop+$oligolength+$downgap);
90 $uppcr = $seq->subseq($start-$oligolength-$upgap-20,$start-1-$upgap-$oligolength);
91 $downpcr = $seq->subseq($stop+1+$downgap+$oligolength,$stop+$oligolength+$downgap+20);
97 $upprimer = $seq->subseq($start+$upgap+1,$start+$oligolength+$upgap);
98 $downprimer = $seq->subseq($stop-$oligolength-$downgap, $stop-1-$downgap);
102 $uppcr = $seq->subseq($start+$oligolength+$upgap+1,$start+$oligolength+$upgap+20);
103 $downpcr = $seq->subseq($stop-$oligolength-$downgap-20,$stop-1-$downgap-$oligolength);
/dports/textproc/py-textdistance/textdistance-4.2.2/textdistance/algorithms/
H A Dsequence_based.py104 for subseq in find_ngrams(short, n):
105 subseq = ''.join(subseq)
107 if subseq not in seq:
110 return subseq
152 subseq = LCSStr()(*sequences)
153 length = len(subseq)
156 before = [s[:s.find(subseq)] for s in sequences]
157 after = [s[s.find(subseq) + length:] for s in sequences]
/dports/biology/py-biopython/biopython-1.79/Scripts/xbbtools/
H A Dxbb_translations.py80 subseq = seq[i : i + 60]
86 res += subseq.lower() + "%5d %%\n" % int(self.gc(subseq)) + "\n"
90 res += subseq.lower() + "%5d %%\n" % int(self.gc(subseq))
112 subseq = seq[i : i + 60]
122 res += subseq.lower() + "%5d %%\n" % int(self.gc(subseq))
/dports/lang/abcl/abcl-src-1.8.0/contrib/abcl-introspect/
H A Dstacktrace.lisp118 (append (subseq sequence 0 from) (subseq sequence to)))
125 (append (subseq stacktrace 0 extra-java-frames-pos)
128 (subseq stacktrace
140 (coerce (subseq exception-stack-trace
146 (subseq exception-stack-trace
172 (subseq stacktrace 0 (1+ error-position))
216 …(splice-out-java-stack-duplicating-lisp-stack (subseq lisp-stacktrace invoke-pos (and repl-loop-po…
222 (subseq narrowed-lisp-stacktrace 0 swank-start)
233 (subseq narrowed-lisp-stacktrace (length exception-frames)))))
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tools/
H A DPrositeScan.t26 { seq_id => 'roa1_drome', coords => [253, 256], psac => 'PS00001', subseq => 'NNSF' },
27 { seq_id => 'roa1_drome', coords => [270, 273], psac => 'PS00001', subseq => 'NNSW' },
28 { seq_id => 'roa2_drome', coords => [344, 349], psac => 'PS00008', subseq => 'GNNQGF' },
29 … { seq_id => 'roa2_drome', coords => [217, 355], psac => 'PS50321', subseq => re(qr/NR.{135}NN/) },
38 subseq => $match->feature1->seq->seq,
/dports/biology/exonerate/exonerate-2.4.0/src/util/
H A Dfastasubseq.c21 register Sequence *subseq; in Argument_main() local
47 subseq = Sequence_subseq(fdbs->seq, subseq_start, subseq_length); in Argument_main()
48 Sequence_print_fasta(subseq, stdout, FALSE); in Argument_main()
49 Sequence_destroy(subseq); in Argument_main()
/dports/databases/pgloader3/cl+ssl-20210124-git/src/
H A Dverify-hostname.lisp41 (let ((after-wildcard (subseq identifier (1+ wildcard-pos)))
42 (before-wildcard (subseq identifier 0 wildcard-pos)))
53 (not (search "xn--" (subseq after-wildcard 0 after-w-dot-pos))))))
66 (subseq pattern first-hostname-dot-post)
74 (case-insensitive-match before-wildcard (subseq pattern 0 (length before-wildcard)))
75 (case-insensitive-match after-wildcard (subseq pattern
/dports/biology/exonerate/exonerate-2.4.0/src/sequence/
H A Dsequence.c257 g_free(subseq); in Sequence_Subseq_data_destroy()
263 return Sequence_get_symbol(subseq->sequence, subseq->start+pos); in Sequence_Subseq_get_symbol()
268 register Sequence_Subseq *subseq; in Sequence_subseq() local
281 subseq->start = start; in Sequence_subseq()
284 ns->data = subseq; in Sequence_subseq()
550 register Sequence_Subseq *subseq;
565 subseq = s->data;
618 subseq = s->data; in Sequence_strncpy()
619 Sequence_strncpy(subseq->sequence, start+subseq->start, length, dst); in Sequence_strncpy()
824 subseq = s->data; in Sequence_lock()
[all …]
/dports/databases/pgloader3/ironclad-v0.54/src/public-key/
H A Dpkcs1.lisp20 finally (return (subseq result 0 num-bytes))))
54 (masked-seed (subseq message 1 (1+ digest-len)))
55 (masked-db (subseq message (1+ digest-len)))
61 (l-hash2 (subseq db 0 digest-len))
69 (subseq db (+ digest-len padding-len 1)))))
99 (masked-db (subseq encoded-message 0 (- em-len digest-len 1)))
100 (h (subseq encoded-message (- em-len digest-len 1) (- em-len 1)))
104 (let* ((ps (subseq db 0 (- em-len (* 2 digest-len) 2)))
106 (salt (subseq db (- (length db) digest-len)))
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/angle/third_party/vulkan-validation-layers/src/scripts/
H A Dsync_val_gen.py310 def BubbleInsertStages(stage_order, prior, subseq): argument
335 if stages[i] in subseq[stage]:
400 subseq = { stage:set() for stage in all_stages }
414 subseq[fdp_stage] = set([fdp_before])
415 subseq[fdp_stage].update(subseq[fdp_before])
416 for stage in subseq[fdp_stage]:
424 subseq[cr_stage] = set()
433 subseq[top_stage].add(stage)
434 for stage, subseq_stages in subseq.items():
445 subseq_sets = subseq
[all …]
/dports/devel/llvm-cheri/llvm-project-37c49ff00e3eadce5d8703fdc4497f28458c64a8/llvm/test/MC/ARM/
H A Darm-arithmetic-aliases.s68 subseq r2, r2, #6 label
69 subseq r2, #6 label
70 subseq r2, r2, r3 label
71 subseq r2, r3 label
73 @ CHECK: subseq r2, r2, #6 @ encoding: [0x06,0x20,0x52,0x02]
74 @ CHECK: subseq r2, r2, #6 @ encoding: [0x06,0x20,0x52,0x02]
75 @ CHECK: subseq r2, r2, r3 @ encoding: [0x03,0x20,0x52,0x00]
76 @ CHECK: subseq r2, r2, r3 @ encoding: [0x03,0x20,0x52,0x00]
/dports/devel/llvm11/llvm-11.0.1.src/test/MC/ARM/
H A Darm-arithmetic-aliases.s68 subseq r2, r2, #6 label
69 subseq r2, #6 label
70 subseq r2, r2, r3 label
71 subseq r2, r3 label
73 @ CHECK: subseq r2, r2, #6 @ encoding: [0x06,0x20,0x52,0x02]
74 @ CHECK: subseq r2, r2, #6 @ encoding: [0x06,0x20,0x52,0x02]
75 @ CHECK: subseq r2, r2, r3 @ encoding: [0x03,0x20,0x52,0x00]
76 @ CHECK: subseq r2, r2, r3 @ encoding: [0x03,0x20,0x52,0x00]

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