| /dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/editor/ |
| H A D | Consensus.java | 56 public Consensus(File matrixFile, Vector seqs, float fplural, in Consensus()
79 Vector seqs, float fplural, in Consensus()
100 Vector seqs, float fplural, in Consensus()
123 private void calculateCons(Matrix mat, Vector seqs, float fplural, in calculateCons()
298 public boolean isEqualSequenceLength(Vector seqs) in isEqualSequenceLength()
324 public int getMaxSequenceLength(Vector seqs) in getMaxSequenceLength()
357 public float getSequenceWeight(Vector seqs, int i) in getSequenceWeight()
371 public String getResidue(Vector seqs, int i, int k) in getResidue()
386 Vector seqs = new Vector(); in main() local
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| H A D | PlotConsensus.java | 69 public PlotConsensus(File matrixFile, Vector seqs, int winsize, in PlotConsensus()
87 public PlotConsensus(File matrixFile, Vector seqs, int winsize, in PlotConsensus()
105 Vector seqs, int winsize, in PlotConsensus()
121 public PlotConsensus(Matrix mat, Vector seqs, int winsize, in PlotConsensus()
139 Vector seqs, int winsize, in PlotConsensus()
154 private void createPlot(Matrix mat, Vector seqs, int winsize) in createPlot()
243 public String getResidue(Vector seqs, int i, int k) in getResidue()
262 public float getSequenceWeight(Vector seqs, int i) in getSequenceWeight()
275 public int getMaxSequenceLength(Vector seqs) in getMaxSequenceLength()
346 Vector seqs = new Vector(); in main() local
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| H A D | SequenceSaver.java | 42 public SequenceSaver(Vector seqs, File fsave) in SequenceSaver()
82 public SequenceSaver(Vector seqs) in SequenceSaver()
94 private void saveFile(File fsave,Vector seqs) in saveFile()
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| /dports/biology/jalview/jalview/test/jalview/gui/ |
| H A D | PopupMenuTest.java | 137 List<SequenceI> seqs = new ArrayList<>(); in testConfigureReferenceAnnotationsMenu_noSequenceSelected() local
161 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testConfigureReferenceAnnotationsMenu_noReferenceAnnotations() local
176 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testConfigureReferenceAnnotationsMenu_alreadyAdded() local
196 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testConfigureReferenceAnnotationsMenu() local
219 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testConfigureReferenceAnnotationsMenu_notOnAlignment() local
240 private void attachReferenceAnnotations(List<SequenceI> seqs, in attachReferenceAnnotations()
310 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testBuildAnnotationTypesMenus() local
388 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testBuildAnnotationTypesMenus_showDisabled() local
446 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testBuildAnnotationTypesMenus_hideDisabled() local
502 List<SequenceI> seqs = parentPanel.getAlignment().getSequences(); in testBuildLinkMenu() local
[all …]
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| /dports/biology/jalview/jalview/test/jalview/analysis/ |
| H A D | ConservationTest.java | 75 List<SequenceI> seqs = new ArrayList<SequenceI>(); in testCountConservationAndGaps() local
99 List<SequenceI> seqs = new ArrayList<SequenceI>(); in testCalculate_noThreshold() local
208 List<SequenceI> seqs = new ArrayList<SequenceI>(); in testCalculate_threshold() local
300 List<SequenceI> seqs = new ArrayList<SequenceI>(); in testVerdict() local
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| H A D | AAFrequencyTest.java | 54 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCalculate_noProfile() local
103 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCalculate_withProfile() local
138 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCalculate_withProfileTiming() local
169 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCompleteConsensus_includeGaps_showLogo() local
210 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; in testCompleteConsensus_ignoreGaps_noLogo() local
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| /dports/biology/checkm/CheckM-1.0.18/checkm/ |
| H A D | binTools.py | 41 def __removeSeqs(self, seqs, seqsToRemove): argument
51 def __addSeqs(self, seqs, refSeqs, seqsToAdd): argument
148 def gcDist(self, seqs): argument
168 def codingDensityDist(self, seqs, prodigalParser): argument
186 def binTetraSig(self, seqs, tetraSigs): argument
203 def tetraDiffDist(self, seqs, genomicSig, tetraSigs, binSig): argument
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seq_io/ |
| H A D | test_sequence_file.h | 152 seqan::StringSet<seqan::Dna5String> seqs; in SEQAN_DEFINE_TEST() local
184 seqan::StringSet<seqan::Dna5String> seqs; in SEQAN_DEFINE_TEST() local
211 seqan::StringSet<seqan::Dna5String> seqs; in SEQAN_DEFINE_TEST() local
237 seqan::StringSet<seqan::Dna5QString> seqs; in SEQAN_DEFINE_TEST() local
262 seqan::StringSet<seqan::Dna5String> seqs; in SEQAN_DEFINE_TEST() local
293 seqan::StringSet<seqan::Dna5QString> seqs; in SEQAN_DEFINE_TEST() local
320 seqan::StringSet<seqan::Dna5String> seqs; in SEQAN_DEFINE_TEST() local
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| /dports/biology/jalview/jalview/src/vamsas/objects/simple/ |
| H A D | SequenceSet.java | 25 private vamsas.objects.simple.Sequence[] seqs; field in SequenceSet
31 public SequenceSet(vamsas.objects.simple.Sequence[] seqs) in SequenceSet()
51 public void setSeqs(vamsas.objects.simple.Sequence[] seqs) in setSeqs()
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| H A D | Alignment.java | 30 private vamsas.objects.simple.SequenceSet seqs; field in Alignment
37 vamsas.objects.simple.SequenceSet seqs) in Alignment()
99 public void setSeqs(vamsas.objects.simple.SequenceSet seqs) in setSeqs()
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| /dports/biology/treepuzzle/tree-puzzle-5.2/src/ |
| H A D | subsetmatr.c | 121 int seqs) in fprintsubsets()
139 int seqs) in printsubsets()
148 int seqs) in printssmatr()
194 int *seqs) in readssmatr()
245 int seqs) in writessmatr()
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| /dports/devel/py-toolz/toolz-0.11.2/toolz/ |
| H A D | itertoolz.py | 108 def merge_sorted(*seqs, **kwargs):
136 def _merge_sorted_binary(seqs): argument
179 def _merge_sorted_binary_key(seqs, key): argument
225 def interleave(seqs): argument
478 def concat(seqs): argument
496 def concatv(*seqs):
508 def mapcat(func, seqs): argument
769 def pluck(ind, seqs, default=no_default): argument
925 def diff(*seqs, **kwargs):
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| /dports/biology/jalview/jalview/src/jalview/commands/ |
| H A D | RemoveGapsCommand.java | 28 public RemoveGapsCommand(String description, SequenceI[] seqs, in RemoveGapsCommand()
44 public RemoveGapsCommand(String description, SequenceI[] seqs, int start, in RemoveGapsCommand()
51 void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al) in findGaps()
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| /dports/biology/seqan1/seqan-1.3.1/demos/tutorial/seeds/ |
| H A D | seeds_assignment1.cpp | 9 writeSeed(TSeed & seed, TStringSet const & seqs) { in writeSeed()
21 StringSet<DnaString> seqs; in main() local
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| /dports/biology/jalview/jalview/src/jalview/analysis/ |
| H A D | AlignmentSorter.java | 104 SequenceI[] seqs = new SequenceI[nSeq]; in sortByPID() local
130 private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) in setReverseOrder()
179 public static void setOrder(AlignmentI align, SequenceI[] seqs) in setOrder()
215 SequenceI[] seqs = new SequenceI[nSeq]; in sortByID() local
248 SequenceI[] seqs = new SequenceI[nSeq]; in sortByLength() local
318 List<SequenceI> seqs = new ArrayList<SequenceI>(); in sortByGroup() local
360 ArrayList<SequenceI> seqs = new ArrayList<SequenceI>(); in vectorSubsetToArray() local
609 SequenceI[] seqs = alignment.getSequencesArray(); in sortByAnnotationScore() local
720 SequenceI[] seqs = alignment.getSequencesArray(); in sortByFeature() local
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| /dports/biology/canu/canu-2.2/src/seqrequester/src/seqrequester/ |
| H A D | simulate.C | 59 vector<dnaSeq *> &seqs, in doSimulate_loadSequences()
86 vector<dnaSeq *> &seqs, in doSimulate_extract()
212 vector<dnaSeq *> seqs; in doSimulate() local
245 delete seqs[ii]; in doSimulate() local
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| /dports/biology/diamond/diamond-2.0.13/src/data/ |
| H A D | enum_seeds.h | 12 Search::SeedStats enum_seeds(SequenceSet* seqs, F* f, unsigned begin, unsigned end, const Filter* f… in enum_seeds()
48 void enum_seeds_hashed(SequenceSet* seqs, F* f, unsigned begin, unsigned end, const Filter* filter,… in enum_seeds_hashed()
76 void enum_seeds_contiguous(SequenceSet* seqs, F* f, unsigned begin, unsigned end, const Filter* fil… in enum_seeds_contiguous()
99 static void enum_seeds_worker(F* f, SequenceSet* seqs, const unsigned begin, const unsigned end, co… in enum_seeds_worker()
151 Search::SeedStats enum_seeds(Block& seqs, PtrVector<F>& f, const Filter* filter, const EnumCfg& cfg) in enum_seeds()
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| /dports/biology/jalview/jalview/test/jalview/io/ |
| H A D | ClustalFileTest.java | 34 SequenceI[] seqs = cf.getSeqsAsArray(); in testParse_withNumbering() local
60 SequenceI[] seqs = cf.getSeqsAsArray(); in testParse_noNumbering() local
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| /dports/devel/boost-docs/boost_1_72_0/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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| /dports/devel/hyperscan/boost_1_75_0/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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| /dports/science/py-scipy/scipy-1.7.1/scipy/_lib/boost/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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| /dports/devel/R-cran-BH/BH/inst/include/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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| /dports/databases/percona57-pam-for-mysql/boost_1_59_0/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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| /dports/math/stanmath/math-4.2.0/lib/boost_1.75.0/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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| /dports/databases/mysqlwsrep57-server/boost_1_59_0/boost/fusion/algorithm/transformation/detail/preprocessed/ |
| H A D | zip10.hpp | 35 fusion::vector<const T0& , const T1&> seqs( in zip() local
57 fusion::vector<const T0& , const T1& , const T2&> seqs( in zip() local
79 fusion::vector<const T0& , const T1& , const T2& , const T3&> seqs( in zip() local
101 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4&> seqs( in zip() local
123 fusion::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5&> seqs( in zip() local
145 …on::vector<const T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6&> seqs( in zip() local
167 …onst T0& , const T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7&> seqs( in zip() local
189 …onst T1& , const T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8&> seqs( in zip() local
211 …onst T2& , const T3& , const T4& , const T5& , const T6& , const T7& , const T8& , const T9&> seqs( in zip() local
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