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/dports/math/jts/jts-jts-1.18.1/modules/core/src/test/java/org/locationtech/jts/geom/impl/
H A DCoordinateArraySequenceTest.java94 CoordinateSequence copy; in testDimensionAndMeasure() local
109 copy = factory.create(array); in testDimensionAndMeasure()
110 assertTrue(isEqual(copy,array)); in testDimensionAndMeasure()
111 copy = factory.create(seq); in testDimensionAndMeasure()
112 assertTrue(isEqual(copy,array)); in testDimensionAndMeasure()
127 copy = factory.create(array); in testDimensionAndMeasure()
129 copy = factory.create(seq); in testDimensionAndMeasure()
145 copy = factory.create(array); in testDimensionAndMeasure()
147 copy = factory.create(seq); in testDimensionAndMeasure()
164 copy = factory.create(array); in testDimensionAndMeasure()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/
H A DA3MReader.cpp39 kseq_t *seq = kseq_init(&buffer); in KSEQ_INIT() local
40 while (kseq_read(seq) >= 0) { in KSEQ_INIT()
41 std::string header = seq->name.s; in KSEQ_INIT()
43 header.append(seq->comment.s); in KSEQ_INIT()
46 std::string sequence = seq->seq.s; in KSEQ_INIT() local
47 addSequence(sequence); in KSEQ_INIT()
49 kseq_destroy(seq); in KSEQ_INIT()
106 sequence.insert(sequence.begin() + col, '.'); in addInsert()
138 if (sequence.empty()) { in addSequence()
145 std::vector<char> copy(sequence.begin(), sequence.end()); in addSequence() local
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/dports/biology/primer3/primer3-2.3.6/test/
H A Dprimer_position_penalty_output55 …ER_RIGHT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
56 …ER_PAIR_0_LIBRARY_MISPRIMING=16.00, L1 Human L1 interspersed repetitive sequence - full length copy
91 …ER_RIGHT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
163 …ER_RIGHT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
236 …ER_PAIR_0_LIBRARY_MISPRIMING=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
270 …MER_LEFT_0_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
306 …ER_LEFT_0_LIBRARY_MISPRIMING=10.00, L1 Human L1 interspersed repetitive sequence - full length copy
307 …ER_RIGHT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
308 …ER_PAIR_0_LIBRARY_MISPRIMING=19.00, L1 Human L1 interspersed repetitive sequence - full length copy
450 …MER_LEFT_0_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
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H A Dprimer_mispriming_output41 …ER_RIGHT_0_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
63 …MER_LEFT_1_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
64 …ER_RIGHT_1_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
65 …ER_PAIR_1_LIBRARY_MISPRIMING=16.00, L1 Human L1 interspersed repetitive sequence - full length copy
87 …ER_RIGHT_2_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
110 …ER_RIGHT_3_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
133 …ER_RIGHT_4_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
166 …MER_LEFT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
275 …XPLAIN=considered 3079, GC content failed 316, low tm 517, high tm 178, long poly-x seq 23, ok 2045
614 …XPLAIN=considered 3079, GC content failed 316, low tm 517, high tm 178, long poly-x seq 23, ok 2045
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H A Dprimer_mispriming_th_output49 …MER_LEFT_0_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
50 …ER_RIGHT_0_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
51 …ER_PAIR_0_LIBRARY_MISPRIMING=16.00, L1 Human L1 interspersed repetitive sequence - full length copy
74 …MER_LEFT_1_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
75 …ER_RIGHT_1_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
76 …ER_PAIR_1_LIBRARY_MISPRIMING=16.00, L1 Human L1 interspersed repetitive sequence - full length copy
99 …MER_LEFT_2_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
100 …ER_RIGHT_2_LIBRARY_MISPRIMING=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
304 PRIMER_INTERNAL_EXPLAIN=considered 3079, GC content failed 316, low tm 1417, long poly-x seq 23, ok…
675 PRIMER_INTERNAL_EXPLAIN=considered 3079, GC content failed 316, low tm 1417, long poly-x seq 23, ok…
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/dports/biology/jalview/jalview/src/jalview/util/
H A DMappingUtils.java119 final SequenceI copy = new Sequence(seq); in mapEditCommand() local
785 if (sequence == null || mappings == null)
791 if (mapping.involvesSequence(sequence))
798 if (otherseq == sequence
801 || otherDataset == sequence
913 cdspos += Math.abs(copy[x + 1] - copy[x]) + 1;
924 if (copy[x] <= copy[x + 1])
926 copy[x] = copy[x + 1] - cdspos + removeCount + 1;
930 copy[x] = copy[x + 1] + cdspos - removeCount - 1;
942 System.arraycopy(copy, sxpos, nxon, 0, copy.length - sxpos);
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/dports/x11-toolkits/gtk30/gtk+-3.24.31/gtk/compose/
H A Dcompose-parse.py18 from copy import copy
136 def all_permutations(seq): argument
139 if len(seq) <=1:
140 yield seq
420 for ks in seq:
524 seq = seq.strip() variable
578 original_sequence = copy(sequence)
579 stats_sequence = copy(sequence)
736 xorg_compose_sequences = copy(xorg_compose_sequences_uniqued)
773 def num_of_keysyms(seq): argument
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/dports/math/jts/jts-jts-1.18.1/modules/core/src/test/java/org/locationtech/jts/geom/
H A DCoordinateSequencesTest.java192 CoordinateSequence reversed = sequence.copy(); in doTestReverse()
216 CoordinateSequences.copy(sequence, 0, fullCopy, 0, sequence.size()); in doTestCopy()
217 CoordinateSequences.copy(sequence, 2, partialCopy, 0, partialCopy.size()); in doTestCopy()
297 CoordinateSequence scrolled = sequence.copy(); in doTestScroll()
316 CoordinateSequence scrolled = sequence.copy(); in doTestScrollRing()
372 if (seq.getDimension() < 3) in fillNonPlanarDimensions()
373 return seq; in fillNonPlanarDimensions()
375 for (int i = 0; i < seq.size(); i++) in fillNonPlanarDimensions()
376 for (int j = 2; j < seq.getDimension(); j++) in fillNonPlanarDimensions()
377 seq.setOrdinate(i, j, i* Math.pow(10, j-1)); in fillNonPlanarDimensions()
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/dports/devel/swig/swig-4.0.2/Lib/python/
H A Dstd_array.i25 if (swigpyseq.size() < seq->size())
27 else if (swigpyseq.size() > seq->size())
29 std::copy(swigpyseq.begin(), swigpyseq.end(), seq->begin());
49 Sequence *sequence = new Sequence();
50 std::copy(self->begin(), self->end(), sequence->begin());
51 return sequence;
53 Sequence *sequence = new Sequence();
54 std::copy(self->rbegin(), self->rend(), sequence->begin());
55 return sequence;
71 std::copy(is.begin(), is.end(), self->begin());
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/dports/lang/kawa/kawa-3.1.1/gnu/lists/
H A DSeqPosition.java48 public SeqPosition(ESEQ seq) in SeqPosition() argument
50 this.sequence = seq; in SeqPosition()
55 this.sequence = seq; in SeqPosition()
61 this.sequence = seq; in SeqPosition()
70 return new SeqPosition<E,ESEQ>(seq, seq.copyPos(ipos)); in make()
73 public SeqPosition<E,ESEQ> copy () in copy() method in SeqPosition
80 setPos(seq, seq.startPos()); in gotoStart()
83 public final void gotoEnd(ESEQ seq) in gotoEnd() argument
85 setPos(seq, seq.endPos()); in gotoEnd()
313 this.sequence = seq; in setPos()
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H A DLListPosition.java33 sequence = old.sequence; in LListPosition()
38 public LListPosition copy() in copy() method in LListPosition
43 public LListPosition (LList seq, int index, boolean isAfter) in LListPosition() argument
45 set(seq, index, isAfter); in LListPosition()
48 public void set (LList seq, int index, boolean isAfter) in set() argument
50 sequence = seq; in set()
63 Object p = seq; in set()
104 next = sequence; in getNextPair()
114 next = sequence; in getNextPair()
189 if (sequence == LList.Empty) in gotoNext()
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/dports/databases/pgloader3/alexandria-20200925-git/alexandria-1/
H A Dsequences.lisp383 (defun map-combinations (function sequence &key (start 0) end length (copy t))
400 (funcall function (if copy
435 (defun map-permutations (function sequence &key (start 0) end length (copy t))
443 (labels ((permute (seq n)
446 (funcall function (if copy
452 (rotatef (elt seq 0) (elt seq n-1))
453 (rotatef (elt seq i) (elt seq n-1)))))))
454 (permute-sequence (seq)
455 (permute seq length)))
474 (defun map-derangements (function sequence &key (start 0) end (copy t))
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/dports/devel/cl-alexandria/alexandria-f35e232ceb2ada8d10e7fdf27ccac07f781eea0e/alexandria-1/
H A Dsequences.lisp383 (defun map-combinations (function sequence &key (start 0) end length (copy t))
400 (funcall function (if copy
435 (defun map-permutations (function sequence &key (start 0) end length (copy t))
443 (labels ((permute (seq n)
446 (funcall function (if copy
452 (rotatef (elt seq 0) (elt seq n-1))
453 (rotatef (elt seq i) (elt seq n-1)))))))
454 (permute-sequence (seq)
455 (permute seq length)))
474 (defun map-derangements (function sequence &key (start 0) end (copy t))
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/dports/textproc/ibus/ibus-1.5.24/src/
H A Dcompose-parse.py18 from copy import copy
143 def all_permutations(seq): argument
146 if len(seq) <=1:
147 yield seq
427 for ks in seq:
520 seq = seq.strip() variable
574 original_sequence = copy(sequence)
575 stats_sequence = copy(sequence)
709 def num_of_keysyms(seq): argument
710 value_length = seq[-1]
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/dports/editors/emacs/emacs-27.2/doc/lispref/
H A Dsequences.texi157 @defun copy-sequence seqr
160 sequence or a record. The copy is the same type of object as the
194 (setq y (copy-sequence x))
323 (setq x (copy-sequence [1 2 3 4]))
368 original, copy it first with @code{copy-sequence} and then sort.
774 This function returns a copy of @var{sequence} that is sorted
1246 ;; @r{@code{copy-sequence} copies the string to be modified later.}
1247 (setq x (copy-sequence "asdfasfd"))
1269 (setq a (copy-sequence [a b c d e f g]))
1277 (setq s (copy-sequence "When in the course"))
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/dports/editors/emacs-devel/emacs-4d1968b/doc/lispref/
H A Dsequences.texi172 @defun copy-sequence seqr
175 sequence or a record. The copy is the same type of object as the
209 (setq y (copy-sequence x))
338 (setq x (copy-sequence [1 2 3 4]))
383 original, copy it first with @code{copy-sequence} and then sort.
789 This function returns a copy of @var{sequence} that is sorted
1296 ;; @r{@code{copy-sequence} copies the string to be modified later.}
1297 (setq x (copy-sequence "asdfasfd"))
1319 (setq a (copy-sequence [a b c d e f g]))
1327 (setq s (copy-sequence "When in the course"))
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/dports/net-mgmt/adcli/adcli-0.9.1/library/
H A Dseq.c70 void **seq = sequence; in seq_count() local
98 void **seq = sequence; in seq_push() local
162 void **seq = sequence; in seq_insert() local
200 void **seq = sequence; in seq_remove_int() local
250 void **seq = sequence; in seq_filter() local
281 void **seq = sequence; in seq_lookup() local
302 seq_copy copy) in seq_dup() argument
304 void **seq = sequence; in seq_dup() local
320 if (copy == NULL) { in seq_dup()
323 copied[at] = copy (seq[at]); in seq_dup()
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/dports/lang/kawa/kawa-3.1.1/gnu/kawa/xml/
H A DKNode.java24 super(seq, ipos); in KNode()
65 index = seq.gapEnd; in make()
72 return new KElement(seq, ipos); in make()
74 return new KAttr(seq, ipos); in make()
76 return new KDocument(seq, ipos); in make()
80 return new KComment(seq, ipos); in make()
84 if (! seq.isEmpty()) in make()
88 return new KText(seq, ipos); in make()
93 public KNode copy () in copy() method in KNode
106 return make(seq, 0); in make()
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/
H A Dstring_utils.c77 va_list copy; in vrna_strdup_vprintf() local
78 va_copy(copy, argp); in vrna_strdup_vprintf()
148 va_list copy; in vrna_strcat_vprintf() local
149 va_copy(copy, args); in vrna_strcat_vprintf()
388 char *pos, *copy = NULL; in vrna_cut_point_remove() local
395 copy = strdup(string); in vrna_cut_point_remove()
397 *cp = (int)(pos - copy) + 1; in vrna_cut_point_remove()
409 return copy; in vrna_cut_point_remove()
570 vrna_seq_ungapped(const char *seq) in vrna_seq_ungapped() argument
577 if (seq) { in vrna_seq_ungapped()
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/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/sequence/
H A D_sequence.py540 for seq in seqs:
557 for seq in seqs:
923 sequence=seq,
943 seq = self._bytes[indexable]
951 sequence=seq,
1174 seq=self,
1241 bytes_ = np.copy(self._bytes)
1306 outbytes = self._bytes.copy()
1420 seq_bytes = self._bytes.copy()
1963 freqs = dict(collections.Counter((str(seq) for seq in kmers)))
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/dports/games/py-pysol-cards/pysol_cards-0.14.2/pysol_cards/
H A Drandom_base.py28 def shuffle(self, seq): argument
29 for n in range(len(seq) - 1, 0, -1):
31 seq[n], seq[j] = seq[j], seq[n]
32 return seq
42 def choice(self, sequence): argument
44 return sequence[self.randrange(0, len(sequence))]
68 def copy(self): member in RandomBase
/dports/math/gecode/gecode-0916a1a/gecode/int/ldsb/
H A Dsym-imp.hpp112 VariableSymmetryImp<View>::copy(Space& home) const { in copy() function in Gecode::Int::LDSB::VariableSymmetryImp
165 ValueSymmetryImp<View>::copy(Space& home) const { in copy() function in Gecode::Int::LDSB::ValueSymmetryImp
174 ::getVal(unsigned int sequence, unsigned int position) const { in getVal() argument
175 return indices[sequence*seq_size + position]; in getVal()
236 for (unsigned int seq = 0 ; seq < n_seqs ; seq++) { in symmetric() local
278 ::copy(Space& home) const { in copy() function in Gecode::Int::LDSB::VariableSequenceSymmetryImp
287 ::getVal(unsigned int sequence, unsigned int position) const { in getVal() argument
288 return values[sequence*seq_size + position]; in getVal()
327 unsigned int seq = 0; in update() local
341 seq++; in update()
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/dports/devel/swig/swig-4.0.2/Lib/ruby/
H A Dstd_array.i24 assign(const RubySeq& rubyseq, std::array<T, N>* seq) {
25 if (rubyseq.size() < seq->size())
27 else if (rubyseq.size() > seq->size())
29 std::copy(rubyseq.begin(), rubyseq.end(), seq->begin());
34 …resize(std::array<T, N> *seq, typename std::array<T, N>::size_type n, typename std::array<T, N>::v…
48 Sequence *sequence = new Sequence();
49 std::copy(self->begin(), self->end(), sequence->begin());
50 return sequence;
65 std::copy(v.begin(), v.end(), self->begin());
/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/
H A D_tabular_msa.py10 import copy
18 from skbio.sequence import Sequence
825 sequences = [copy.copy(s) for s in sequences]
1134 seqs = (copy.deepcopy(seq, memo) for seq in self._seqs)
1209 return seq
1212 seqs = self._seqs.apply(lambda seq: seq[i])
1638 for seq in seq_iterator:
1732 self.index = [resolve_key(seq, minter) for seq in self._seqs]
1962 index = pd.Index([resolve_key(seq, minter) for seq in sequences])
2023 for sequence in sequences:
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/dports/devel/boost-docs/boost_1_72_0/libs/mpl/doc/src/refmanual/
H A DVariadicSequence.rst9 A |Variadic Sequence| is a member of a family of sequence classes with both
11 |Variadic Sequence|, its *variadic form* allows us to specify a sequence of
20 ``seq<``\ |t1...tn|\ ``>``
22 By contrast, each *numbered* sequence form accepts the exact number of elements
32 .. The variadic form of sequence ``seq`` is defined in
43 .. |seq<t1...tn>| replace:: ``seq<``\ |t1...tn|\ ``>``
44 .. |seq<t1...tn>::type| replace:: ``seq<``\ |t1...tn|\ ``>::type``
69 typedef seq<|t1...tn|> s;
73 ``s`` is a sequence of elements |t1...tn|.
89 typedef seq<|t1...tn|>::type s;
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