/dports/math/jts/jts-jts-1.18.1/modules/core/src/test/java/org/locationtech/jts/geom/impl/ |
H A D | CoordinateArraySequenceTest.java | 94 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() [all …]
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/ |
H A D | A3MReader.cpp | 39 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 [all …]
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/dports/biology/primer3/primer3-2.3.6/test/ |
H A D | primer_position_penalty_output | 55 …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 [all …]
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H A D | primer_mispriming_output | 41 …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 [all …]
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H A D | primer_mispriming_th_output | 49 …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… [all …]
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/dports/biology/jalview/jalview/src/jalview/util/ |
H A D | MappingUtils.java | 119 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); [all …]
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/dports/x11-toolkits/gtk30/gtk+-3.24.31/gtk/compose/ |
H A D | compose-parse.py | 18 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 [all …]
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/dports/math/jts/jts-jts-1.18.1/modules/core/src/test/java/org/locationtech/jts/geom/ |
H A D | CoordinateSequencesTest.java | 192 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() [all …]
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/dports/devel/swig/swig-4.0.2/Lib/python/ |
H A D | std_array.i | 25 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()); [all …]
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/dports/lang/kawa/kawa-3.1.1/gnu/lists/ |
H A D | SeqPosition.java | 48 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() [all …]
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H A D | LListPosition.java | 33 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() [all …]
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/dports/databases/pgloader3/alexandria-20200925-git/alexandria-1/ |
H A D | sequences.lisp | 383 (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)) [all …]
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/dports/devel/cl-alexandria/alexandria-f35e232ceb2ada8d10e7fdf27ccac07f781eea0e/alexandria-1/ |
H A D | sequences.lisp | 383 (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)) [all …]
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/dports/textproc/ibus/ibus-1.5.24/src/ |
H A D | compose-parse.py | 18 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] [all …]
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/dports/editors/emacs/emacs-27.2/doc/lispref/ |
H A D | sequences.texi | 157 @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")) [all …]
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/dports/editors/emacs-devel/emacs-4d1968b/doc/lispref/ |
H A D | sequences.texi | 172 @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")) [all …]
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/dports/net-mgmt/adcli/adcli-0.9.1/library/ |
H A D | seq.c | 70 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() [all …]
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/dports/lang/kawa/kawa-3.1.1/gnu/kawa/xml/ |
H A D | KNode.java | 24 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() [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/ |
H A D | string_utils.c | 77 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() [all …]
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/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/sequence/ |
H A D | _sequence.py | 540 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))) [all …]
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/dports/games/py-pysol-cards/pysol_cards-0.14.2/pysol_cards/ |
H A D | random_base.py | 28 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
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/dports/math/gecode/gecode-0916a1a/gecode/int/ldsb/ |
H A D | sym-imp.hpp | 112 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() [all …]
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/dports/devel/swig/swig-4.0.2/Lib/ruby/ |
H A D | std_array.i | 24 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());
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/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/ |
H A D | _tabular_msa.py | 10 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: [all …]
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/dports/devel/boost-docs/boost_1_72_0/libs/mpl/doc/src/refmanual/ |
H A D | VariadicSequence.rst | 9 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; [all …]
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