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Searched refs:TCounts (Results 1 – 25 of 59) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dutil.cpp207 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/
H A Drazers_window.h40 typename TCounts,
48 TCounts & cnts, in _mapSingleReadsToContigWindow()
71 typename TCounts,
81 TCounts & cnts, in _mapSingleReadsToContigWindow()
98 TCounts> TVerifier; in _mapSingleReadsToContigWindow()
H A Drazers_parallel.h92 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,
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H A Drazers_matepairs_parallel.h84 …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,
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H A Drazers.h1556 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 …]
H A DoutputFormat.h332 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/dbapi/driver/impl/
H A Ddbapi_impl_context.hpp247 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;
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/dbapi/driver/impl/
H A Ddbapi_impl_context.hpp247 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;
/dports/biology/seqan1/seqan-1.3.1/demos/
H A Dindex_qgram_counts.cpp20 typedef Infix<Fibre<TIndex, QGramCounts>::Type const>::Type TCounts; in main() typedef
26 TCounts cnts = countOccurrencesMultiple(myIndex, indexShape(myIndex)); in main()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dutil.hpp61 typedef map<CTempString, size_t> TCounts; typedef in CEntropyCalculator
64 double x_Entropy(const TCounts &counts);
H A Dadapter_search.hpp49 typedef vector<TCount> TCounts; typedef in NAdapterSearch
194 TCounts m_counts; //counts of words in the seq; not position-specific.
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar_calling.h404 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/unassigned_or_unused/
H A Dindex_qgram_counts.cpp20 typedef Infix<Fibre<TIndex, QGramCounts>::Type const>::Type TCounts; in main() typedef
27 TCounts cnts = countOccurrencesMultiple(myIndex, indexShape(myIndex)); in main()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/corelib/
H A Dncbi_pool_balancer.hpp63 typedef map<string, unsigned int> TCounts; // by server name typedef in CPoolBalancer
65 void x_InitFromCounts(const TCounts& counts);
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/corelib/
H A Dncbi_pool_balancer.hpp63 typedef map<string, unsigned int> TCounts; // by server name typedef in CPoolBalancer
65 void x_InitFromCounts(const TCounts& counts);
/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A Drazers.h379 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,
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H A Drazers_matepairs.h273 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,
/dports/biology/seqan1/seqan-1.3.1/apps/razers/
H A Drazers.h1582 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 …]
/dports/biology/seqan1/seqan-1.3.1/apps/splazers/
H A Drazers.h1603 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/
H A Drazers.h1594 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 …]
H A Drazers_matepairs.h536 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,
/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/index/
H A Dindex_assignment6.cpp14 typedef typename Fibre<TIndex, QGramCounts>::Type TCounts; in qgramCounting() typedef
17 typedef typename Iterator<TCounts, Standard>::Type TIterCounts; in qgramCounting()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/q_gram_index/
H A Dindex_assignment6.cpp15 typedef typename Fibre<TIndex, QGramCounts>::Type TCounts; in qgramCounting() typedef
18 typedef typename Iterator<TCounts, Standard>::Type TIterCounts; in qgramCounting()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/
H A Drazers.h1635 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 …]
H A Drazers_matepairs.h244 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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