/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | util.cpp | 207 typedef map<CTempString, double> TCounts; 208 TCounts counts; 212 TCounts::iterator it = 222 ITERATE (TCounts, it, counts) { 237 TCounts counts; in ComputeNormalizedProteinEntropy() 241 TCounts::iterator it = in ComputeNormalizedProteinEntropy() 251 ITERATE (TCounts, it, counts) { in ComputeNormalizedProteinEntropy() 310 TCounts counts; in ComputeSlidingWindowEntropy() 314 TCounts::iterator it = in ComputeSlidingWindowEntropy() 327 TCounts::iterator it = in ComputeSlidingWindowEntropy() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
H A D | razers_window.h | 40 typename TCounts, 48 TCounts & cnts, in _mapSingleReadsToContigWindow() 71 typename TCounts, 81 TCounts & cnts, in _mapSingleReadsToContigWindow() 98 TCounts> TVerifier; in _mapSingleReadsToContigWindow()
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H A D | razers_parallel.h | 92 typename TCounts, 107 typename TCounts, 118 TCounts, 253 typename TCounts, 321 typename TCounts, 542 typename TCounts, 555 TCounts & /*cnts*/, in _mapSingleReadsParallelToContig() argument 942 typename TCounts, 952 TCounts & cnts, in _mapSingleReadsParallel() 1180 typename TCounts, [all …]
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H A D | razers_matepairs_parallel.h | 84 …tore, TFilterFinderL_, TFilterFinderR_, TFilterPattern_, TShape_, TOptions, TCounts, TRazerSMode> > 118 TCounts counts; // TODO(holtgrew): Artifact? 132 …typedef MatchVerifier<TFragmentStore, TMatches, TOptions, TRazerSMode, TFilterPattern, TCounts> TM… 431 …Store, TFilterFinderL, TFilterFinderR, TFilterPattern, TShape, TOptions, TCounts, TRazerSMode> > &… in workVerification() argument 467 TCounts> TVerifier; in workVerification() 1015 typename TCounts, 1023 TCounts & /*cnts*/, // TODO(holtgrew): What about this? in _mapMatePairReadsParallel() argument 1354 typename TCounts, 1364 TCounts & cnts, in _mapMatePairReadsParallel() 1640 typename TCounts, [all …]
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H A D | razers.h | 1556 TCounts &, 1722 TCounts & cnts, 2914 TCounts & cnts, 3003 TCounts & cnts, 3124 TCounts & cnts, 3163 TCounts & cnts, 3208 TCounts & cnts, 3239 TCounts & cnts, 3267 TCounts & cnts, 3364 TCounts & cnts, [all …]
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H A D | outputFormat.h | 332 template <typename TFSSpec, typename TFSConfig, typename TCounts, typename TOptions> 336 TCounts & cooc, in countCoocurrences() 469 typename TCounts, 475 TCounts & stats, // Match statistics (possibly empty) in dumpMatches() 1287 typename TCounts, 1295 TCounts & stats, // Match statistics (possibly empty) in dumpMatches() 1315 typename TCounts, 1320 TCounts & stats, // Match statistics (possibly empty) in dumpMatches()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/dbapi/driver/impl/ |
H A D | dbapi_impl_context.hpp | 247 typedef map<string, unsigned int> TCounts; // by server name typedef in impl::CDriverContext 248 typedef map<string, TCounts> TCountsMap; // by pool or service name 250 void GetCountsForPool(const string& pool_name, TCounts* counts) const in GetCountsForPool() 254 void GetCountsForService(const string& service, TCounts* counts) const in GetCountsForService() 335 TCounts* counts) const;
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/dbapi/driver/impl/ |
H A D | dbapi_impl_context.hpp | 247 typedef map<string, unsigned int> TCounts; // by server name typedef in impl::CDriverContext 248 typedef map<string, TCounts> TCountsMap; // by pool or service name 250 void GetCountsForPool(const string& pool_name, TCounts* counts) const in GetCountsForPool() 254 void GetCountsForService(const string& service, TCounts* counts) const in GetCountsForService() 335 TCounts* counts) const;
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/dports/biology/seqan1/seqan-1.3.1/demos/ |
H A D | index_qgram_counts.cpp | 20 typedef Infix<Fibre<TIndex, QGramCounts>::Type const>::Type TCounts; in main() typedef 26 TCounts cnts = countOccurrencesMultiple(myIndex, indexShape(myIndex)); in main()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/ |
H A D | util.hpp | 61 typedef map<CTempString, size_t> TCounts; typedef in CEntropyCalculator 64 double x_Entropy(const TCounts &counts);
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H A D | adapter_search.hpp | 49 typedef vector<TCount> TCounts; typedef in NAdapterSearch 194 TCounts m_counts; //counts of words in the seq; not position-specific.
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
H A D | casbar_calling.h | 404 TCounts &countF, TCounts &countR, in constructConstantsAndLHoods() 712 template<typename TBetas, typename TLHoods, typename TConstantSet, typename TCounts, typename TMeth… 714 …oods(TBetas &betas, TLHoods &lHoods, TConstantSet &constantSet, TCounts &countF, TCounts &countR, … in getBetasAndLHoods() 831 template<typename TConstantSet, typename TLHoods, typename TCounts> 833 setUpConstants(TConstantSet &constantSet, TLHoods &lHoods, TCounts &countF, TCounts &countR, NaiveM… in setUpConstants() 875 template<typename TConstantSet, typename TLHoods, typename TCounts> 877 setUpConstants(TConstantSet &constantSet, TLHoods &lHoods, TCounts &countF, TCounts &countR, LogFun… in setUpConstants() 924 TCounts &countF, TCounts &countR, in getCandidateProbs() 953 template<typename TCounts, typename TQualities, typename TMapqs, typename TOriginString, typename T… 955 doBsCalling(TCounts & countF, in doBsCalling() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/unassigned_or_unused/ |
H A D | index_qgram_counts.cpp | 20 typedef Infix<Fibre<TIndex, QGramCounts>::Type const>::Type TCounts; in main() typedef 27 TCounts cnts = countOccurrencesMultiple(myIndex, indexShape(myIndex)); in main()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/corelib/ |
H A D | ncbi_pool_balancer.hpp | 63 typedef map<string, unsigned int> TCounts; // by server name typedef in CPoolBalancer 65 void x_InitFromCounts(const TCounts& counts);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/corelib/ |
H A D | ncbi_pool_balancer.hpp | 63 typedef map<string, unsigned int> TCounts; // by server name typedef in CPoolBalancer 65 void x_InitFromCounts(const TCounts& counts);
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
H A D | razers.h | 379 TCounts &cnts; 1636 typename TCounts, 1826 typename TCounts, 1990 typename TCounts, 1998 TCounts & cnts, 2090 typename TCounts, 2098 TCounts & cnts, 2115 typename TCounts, 2123 TCounts & cnts, 2143 TCounts & cnts, [all …]
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H A D | razers_matepairs.h | 273 template < typename TFragmentStore, typename TCounts, typename TSpec, typename TSwiftL, typename TS… 276 TCounts &, 360 typename TCounts, 370 TCounts & cnts, 405 TCounts > TVerifier; 686 typename TCounts, 694 TCounts & cnts,
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/dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
H A D | razers.h | 1582 typename TCounts, 1590 TCounts & cnts, 1846 typename TCounts, 1856 TCounts & cnts, 2009 typename TCounts, 2017 TCounts & cnts, 2103 typename TCounts, 2113 TCounts & cnts, 2140 typename TCounts, 2148 TCounts & cnts, [all …]
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/dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
H A D | razers.h | 1603 typename TCounts, 1611 TCounts & cnts, 1867 typename TCounts, 1877 TCounts & cnts, 2030 typename TCounts, 2038 TCounts & cnts, 2124 typename TCounts, 2134 TCounts & cnts, 2152 typename TCounts, 2160 TCounts & cnts, [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
H A D | razers.h | 1594 typename TCounts, 1602 TCounts & cnts, 1853 typename TCounts, 1863 TCounts & cnts, 2010 typename TCounts, 2018 TCounts & cnts, 2104 typename TCounts, 2114 TCounts & cnts, 2132 typename TCounts, 2140 TCounts & cnts, [all …]
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H A D | razers_matepairs.h | 536 template < typename TMatches, typename TCounts, typename TSpec, typename TSwiftL, typename TSwiftR > 537 void compactPairMatches(TMatches &matches, TCounts & /*cnts*/, RazerSOptions<TSpec> &options, TSwif… 609 typename TCounts, 619 TCounts & cnts, 903 typename TCounts, 913 TCounts & cnts,
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/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/index/ |
H A D | index_assignment6.cpp | 14 typedef typename Fibre<TIndex, QGramCounts>::Type TCounts; in qgramCounting() typedef 17 typedef typename Iterator<TCounts, Standard>::Type TIterCounts; in qgramCounting()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/q_gram_index/ |
H A D | index_assignment6.cpp | 15 typedef typename Fibre<TIndex, QGramCounts>::Type TCounts; in qgramCounting() typedef 18 typedef typename Iterator<TCounts, Standard>::Type TIterCounts; in qgramCounting()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
H A D | razers.h | 1635 typename TCounts, 1643 TCounts & cnts, 1914 typename TCounts, 1924 TCounts & cnts, 2077 typename TCounts, 2085 TCounts & cnts, 2176 typename TCounts, 2186 TCounts & cnts, 2213 typename TCounts, 2221 TCounts & cnts, [all …]
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H A D | razers_matepairs.h | 244 template < typename TMatches, typename TCounts, typename TSpec, typename TSwiftL, typename TSwiftR > 245 void compactPairMatches(TMatches &matches, TCounts & /*cnts*/, RazerSOptions<TSpec> &options, TSwif… 332 typename TCounts, 342 TCounts & cnts, 654 typename TCounts, 664 TCounts & cnts,
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