config.h
config_8h.html
- #define HAVE_AVX config_8h.html aa7e976f67cb76f04c38c346b91719182
- #define HAVE_BLAS config_8h.html a55bac73840c244b1326a808edb8b2aac
- #define HAVE_BOOST config_8h.html a1644f282a4f84575a270f96b98d4f3c6
- #define HAVE_BOOST_PROGRAM_OPTIONS config_8h.html aecd1bc7fdfc4affb8ebbf9d332e5197d
- #define HAVE_DLFCN_H config_8h.html a0ee1617ff2f6885ef384a3dd46f9b9d7
- #define HAVE_INTTYPES_H config_8h.html ab90a030ff2790ebdc176660a6dd2a478
- #define HAVE_LAPACK config_8h.html a0c84d3b456f7e3dae8c3ae5ae22a2bee
- #define HAVE_MMX config_8h.html ab788c25a32f94c57383cb1f68d5d038d
- #define HAVE_OPENMP config_8h.html a853088bdfdc193404c261bf3e25f8f04
- #define HAVE_PTHREAD config_8h.html aac699f6be8f38e3c8a5f375df9a12aaf
- #define HAVE_PTHREAD_PRIO_INHERIT config_8h.html a428591e6b13dacf3451dc891e385f51b
- #define HAVE_SSE config_8h.html ae1009c604232a499433fddbc60782888
- #define HAVE_SSE2 config_8h.html a2cde8953a3c0685181e8fdf51d3bdaab
- #define HAVE_SSE3 config_8h.html a853bbc5127966feb7750ccf5d8c89ac1
- #define HAVE_SSE4_1 config_8h.html aa501febe6a45730d89cc279465324a76
- #define HAVE_SSE4_2 config_8h.html a511df4e0192ce26eed35b69deddfb57f
- #define HAVE_SSSE3 config_8h.html ac2929e721cddf17243908ac8dd584618
- #define HAVE_STDINT_H config_8h.html ab6cd6d1c63c1e26ea2d4537b77148354
- #define HAVE_STDIO_H config_8h.html ae021ce4fe74984428cc97427b7358fda
- #define HAVE_STDLIB_H config_8h.html a9e0e434ec1a6ddbd97db12b5a32905e0
- #define HAVE_STRINGS_H config_8h.html a405d10d46190bcb0320524c54eafc850
- #define HAVE_STRING_H config_8h.html ad4c234dd1625255dc626a15886306e7d
- #define HAVE_SYS_STAT_H config_8h.html ace156430ba007d19b4348a950d0c692b
- #define HAVE_SYS_TYPES_H config_8h.html a69dc70bea5d1f8bd2be9740e974fa666
- #define HAVE_UNISTD_H config_8h.html a219b06937831d0da94d801ab13987639
- #define HAVE_XSDCXX config_8h.html a85f7c68f186d1c804119a60688507988
- #define LT_OBJDIR config_8h.html ac2d5925d76379847dd9fc4747b061659
- #define PACKAGE config_8h.html aca8570fb706c81df371b7f9bc454ae03
- #define PACKAGE_BUGREPORT config_8h.html a1d1d2d7f8d2f95b376954d649ab03233
- #define PACKAGE_NAME config_8h.html a1c0439e4355794c09b64274849eb0279
- #define PACKAGE_STRING config_8h.html ac73e6f903c16eca7710f92e36e1c6fbf
- #define PACKAGE_TARNAME config_8h.html af415af6bfede0e8d5453708afe68651c
- #define PACKAGE_URL config_8h.html a5c93853116d5a50307b6744f147840aa
- #define PACKAGE_VERSION config_8h.html aa326a05d5e30f9e9a4bb0b4469d5d0c0
- #define STDC_HEADERS config_8h.html a550e5c272cc3cf3814651721167dcd23
- #define VERSION config_8h.html a1c6d5de492ac61ad29aec7aa9a436bbf
freecontact.cpp
freecontact_8cpp.html
config.h
freecontact.h
freecontact::ct_vector
freecontact::af_vector
freecontact::pf_vector
freecontact::cov_vector
freecontact::_rawscore_calc_t
freecontact::d2matrix
freecontact::_glasso_timer
freecontact
- #define CAN_VECW freecontact_8cpp.html a2de2789904ae67b5ee548eab4411ce6c
- #define _fill_pfi freecontact_8cpp.html aaaf4e3fcae5b30304306e976c5d97007 (__i)
- float g_fp_t freecontact_8cpp.html ad7a2b4ac8fe1e98449202b128fd3025a
- void glassofast_ freecontact_8cpp.html a94039a2beb873605b7a20e5a7b95d9c5 (int *, g_fp_t *, g_fp_t *, g_fp_t *, int *, int *, int *, g_fp_t *, g_fp_t *, g_fp_t *, g_fp_t *, int *, int *)
- void spotrf_ freecontact_8cpp.html a47155893c27b3a0d2bea295ba06b2035 (const char *UPLO, const int *N, float *A, const int *LDA, int *INFO)
- void sgetrf_ freecontact_8cpp.html aeaee28c6fe6eed9f57e918dc31a17afb (int *M, int *N, float *A, int *LDA, int *IPIV, int *INFO)
- void sgetri_ freecontact_8cpp.html a9808abd70f1d1b9b4040709d25636252 (int *N, float *A, int *lda, int *IPIV, float *WORK, int *LWORK, int *INFO)
freecontact.h
freecontact_8h.html
freecontact::alilen_error
freecontact::icme_timeout_error
freecontact::ali_t
freecontact::contact_t
freecontact::parset_t
freecontact::predictor
freecontact
- #define LIBFREEC_API freecontact_8h.html afece13c25b7bc83b3748b39207b60099
- #define LIBFREEC_LOCAL freecontact_8h.html afe36a0a88885a99b189d3c8766cbdc44
glassofast-real.f90
glassofast-real_8f90.html
- subroutine glassofast glassofast-real_8f90.html a0c9f3066182c33be3be1e9cad7f10e4f (n, s, l, thr, maxit, msg, warm, x, w, wd, wxj, info, brk
freecontact::_glasso_timer
classfreecontact_1_1__glasso__timer.html
- _glasso_timer
  classfreecontact_1_1__glasso__timer.html
  a0d8108776465bafba7f9bb88cc576ba4
  (int *__sival_ptr, time_t __tv_sec, bool __dbg=false)
- virtual ~_glasso_timer classfreecontact_1_1__glasso__timer.html abeb1c8385bbe5b6b92787c2de3bd1a7b ()
- bool dbg classfreecontact_1_1__glasso__timer.html a5f31c0f817ed47307224a1a666f684d0
freecontact::_rawscore_calc_t
classfreecontact_1_1__rawscore__calc__t.html
- virtual double operator() classfreecontact_1_1__rawscore__calc__t.html add939e90702bfef4ffafbf0146cc2c6e (const uint16_t i, const uint16_t j) const =0
freecontact::af_vector
classfreecontact_1_1af__vector.html
typename _Tp
- af_vector
  classfreecontact_1_1af__vector.html
  a11e1c88ffea6ae5d7e0a2de7cb3e8e71
  (uint16_t __alilen, uint8_t __q, _Tp __v)
- _Tp & operator() classfreecontact_1_1af__vector.html a2ecf84c7a7ea13525b37dbf6a706f302 (uint16_t __i, uint8_t __ai)
- const _Tp & operator() classfreecontact_1_1af__vector.html aa06b5f290fa71b855a9a4064b72d0bc9 (uint16_t __i, uint8_t __ai) const
- uint16_t alilen classfreecontact_1_1af__vector.html a66b3dd779a2f5ef53ec28fbd6ef81d4f
- uint8_t q classfreecontact_1_1af__vector.html a8c127b8ad601de72b85dd5ecdbbb6e8a
freecontact::ali_t
classfreecontact_1_1ali__t.html
- ali_t
  classfreecontact_1_1ali__t.html
  adc1faa96cac0d20260a49261ed2ded16
  (const uint16_t __alilen=0)
- virtual ~ali_t classfreecontact_1_1ali__t.html a48db3e4c88df4d8ab9404b10a6962942 ()
- uint8_t & operator() classfreecontact_1_1ali__t.html aeef9c083d20f31e5b6b4eb9671794df9 (uint32_t __k, uint16_t __ai)
- const uint8_t & operator() classfreecontact_1_1ali__t.html a514cbd2ca0e59c3cda9d250333defc18 (uint32_t __k, uint16_t __ai) const
- ali_t & push classfreecontact_1_1ali__t.html a27bbedfd1bbfca4e0c5653a0a2c2a8ca (const std::vector< uint8_t > &__al)
- ali_t & push classfreecontact_1_1ali__t.html a194f54a4efc5805685e49441de9deef7 (const std::string &__l)
- static std::vector< uint8_t > read_a_seq classfreecontact_1_1ali__t.html a65900fa171a89a95df9a0e2cd975ad91 (const std::string &__l)
- uint32_t seqcnt classfreecontact_1_1ali__t.html a0d0fb8987dd3753403178d74c8ac5e04
- uint16_t alilen classfreecontact_1_1ali__t.html a2341c9fb8d57e95a2ce89b9704d76386
- uint16_t alilen16 classfreecontact_1_1ali__t.html a9645bb267ec8c7fdec0a49d5001d02c2
- uint16_t alilenpad classfreecontact_1_1ali__t.html a99f3fdaa31e1b6675641d3444d2af1ca
freecontact::alilen_error
classfreecontact_1_1alilen__error.html
- alilen_error
  classfreecontact_1_1alilen__error.html
  a6b4e74d7a727b4abb9ff6cd34d24d24e
  (const std::string &__arg)
freecontact::contact_t
structfreecontact_1_1contact__t.html
- contact_t
  structfreecontact_1_1contact__t.html
  a35542bdb254de23639b289ae4c5ac53a
  (uint16_t __i=0, uint16_t __j=0, float __score=0)
- bool operator< structfreecontact_1_1contact__t.html a4fed9ae3171e56db626848425e3ff9e7 (const contact_t &__b) const
- bool operator> structfreecontact_1_1contact__t.html ac829d4edc18c6f71bdadbd7b91136764 (const contact_t &__b) const
- uint16_t i structfreecontact_1_1contact__t.html ac07d70260ddab5a213ea58f96c77b350
- uint16_t j structfreecontact_1_1contact__t.html a64b84f0de8fa19b82b12f7e7e2e45259
- float score structfreecontact_1_1contact__t.html a9b852e178f7b28ac0aa156b658bdd023
freecontact::cov_vector
classfreecontact_1_1cov__vector.html
typename _Tp
- cov_vector
  classfreecontact_1_1cov__vector.html
  ada2626f30786a94d65d1af78b77c0482
  ()
- cov_vector
  classfreecontact_1_1cov__vector.html
  ae0bb6fe1e54c0b62fbca796d8b2fcc72
  (uint16_t __alilen, uint8_t __q)
- cov_vector
  classfreecontact_1_1cov__vector.html
  a81a7f761b2afe638892652cdb3cda854
  (uint16_t __alilen, uint8_t __q, _Tp __v)
- _Tp & operator() classfreecontact_1_1cov__vector.html a3fd01c22aee374e6b80e0e9a157d256e (size_t __row, size_t __col)
- const _Tp & operator() classfreecontact_1_1cov__vector.html a79b7e397c59325ec430151f1ea199c6a (size_t __row, size_t __col) const
- _Tp & operator() classfreecontact_1_1cov__vector.html aaecd5168b1e3a08dcf006b1925cde508 (uint16_t __i, uint16_t __j, uint8_t __ai, uint8_t __aj)
- const _Tp & operator() classfreecontact_1_1cov__vector.html acc31ead71ce1c909d4f7017bfbbf3848 (uint16_t __i, uint16_t __j, uint8_t __ai, uint8_t __aj) const
- uint16_t alilen classfreecontact_1_1cov__vector.html a8c931ced2da5532682eada559d15f102
- uint8_t q classfreecontact_1_1cov__vector.html af62bdb972b6e27d6a0e59841007b2b90
- size_t d1 classfreecontact_1_1cov__vector.html a1ae0ac11c6a6045a2ab8041d7ccf3c51
freecontact::ct_vector
classfreecontact_1_1ct__vector.html
typename _Tp
- ct_vector
  classfreecontact_1_1ct__vector.html
  ac93acc36c13b6d021ddcde389e4ec61a
  (uint16_t __alilen=0)
- _Tp & operator() classfreecontact_1_1ct__vector.html a58a0494e8b7dc4a9b5765c77067335d6 (uint16_t __i, uint16_t __j)
- const _Tp & operator() classfreecontact_1_1ct__vector.html a049e8f427c895209194f7c0f46b206bf (uint16_t __i, uint16_t __j) const
- uint16_t alilen classfreecontact_1_1ct__vector.html a3a085bd6ca05321e6ce99f6a6bdd0776
freecontact::d2matrix
classfreecontact_1_1d2matrix.html
typename _Tp
typename _Tri
typename _Tci
- d2matrix
  classfreecontact_1_1d2matrix.html
  aa8567419597744784da379a9820c12f4
  (_Tri __rows, _Tci __cols)
- _Tp & operator() classfreecontact_1_1d2matrix.html a1c5752fbdd4e5569fadae54142b22a40 (_Tri __r, _Tci __c)
- const _Tp & operator() classfreecontact_1_1d2matrix.html a61a8dc628429bf2728a1ca4ae458a639 (_Tri __r, _Tci __c) const
- _Tri rows classfreecontact_1_1d2matrix.html ab744e837264b13380ddb57f5106da6bd
- _Tci cols classfreecontact_1_1d2matrix.html a17836224c5079e294c977a24f063b5a6
freecontact::icme_timeout_error
classfreecontact_1_1icme__timeout__error.html
- icme_timeout_error
  classfreecontact_1_1icme__timeout__error.html
  a172287e4e0390a05642e954f000f18ec
  (const std::string &__arg)
freecontact::parset_t
structfreecontact_1_1parset__t.html
- parset_t
  structfreecontact_1_1parset__t.html
  acb40904ea9efb8180523bf7ba7ccf137
  (double __clustpc=0, double __density=0, double __gapth=0, uint16_t __mincontsep=0, double __pseudocnt=0, double __pscnt_weight=0, bool __estimate_ivcov=0, double __shrink_lambda=0, bool __cov20=0, bool __apply_gapth=0, double __rho=0)
- double clustpc structfreecontact_1_1parset__t.html a7500d01d2e2ca7d9f8bf9c3c0e66fd90
- double density structfreecontact_1_1parset__t.html a67e002f68302fc4d28a1e0e7162b2bc7
- double gapth structfreecontact_1_1parset__t.html aa02be18253e40111daef91e6abfcb808
- uint16_t mincontsep structfreecontact_1_1parset__t.html a2b91e5a85776ca5d7db677420d6e0d56
- double pseudocnt structfreecontact_1_1parset__t.html accc7e5c8aab465a1be4e0748099d10b4
- double pscnt_weight structfreecontact_1_1parset__t.html af405692fa0f49858b49c974663d024ed
- bool estimate_ivcov structfreecontact_1_1parset__t.html a7af5f0424d951104c4c12f9c72e4218a
- double shrink_lambda structfreecontact_1_1parset__t.html a537441daba9deb02f67f0beed007e0b2
- bool cov20 structfreecontact_1_1parset__t.html a45d6bcd68f2aab12d24c0ea847919745
- bool apply_gapth structfreecontact_1_1parset__t.html aa5dc46e03834a38dc6ec5e4eceb99ee9
- double rho structfreecontact_1_1parset__t.html a72d8ec88d692d8863f8143ecab17a87a
freecontact::pf_vector
classfreecontact_1_1pf__vector.html
- pf_vector
  classfreecontact_1_1pf__vector.html
  a9c81f0993ff41ad49471a766e449289a
  ()
- pf_vector
  classfreecontact_1_1pf__vector.html
  aaf6a3bc0e85b225e8f5823815e1cd848
  (uint16_t __alilen, uint8_t __q, _Tp __v)
- _Tp & operator() classfreecontact_1_1pf__vector.html af77540610f3a28b7435606b22e25cc29 (uint16_t __i, uint16_t __j, uint8_t __ai, uint8_t __aj)
- const _Tp & operator() classfreecontact_1_1pf__vector.html a332589902749ba03d9ae3db7b509491d (uint16_t __i, uint16_t __j, uint8_t __ai, uint8_t __aj) const
- uint16_t alilen classfreecontact_1_1pf__vector.html ac9e54bc4758580d3e9d19713a7122e19
- uint8_t q classfreecontact_1_1pf__vector.html acdde71e2d4aa1a66ff789e4a6f3d4649
- size_t d3 classfreecontact_1_1pf__vector.html a93bddad71a1a3eaccc67ae3f21dbb4a7
- size_t d2 classfreecontact_1_1pf__vector.html ac2191e06d1d45bb952d769628d4ea0e3
- size_t d1 classfreecontact_1_1pf__vector.html a3df7f7e334cc36d0244f63a763a46773
freecontact::predictor
classfreecontact_1_1predictor.html
- std::map< std::string, std::vector< contact_t > > cont_res_t classfreecontact_1_1predictor.html a0a75e0272008e4e405e49dc82831e3e2
- double freq_t classfreecontact_1_1predictor.html ae272f45e95c1d1ccd58d17ca137f3da3
- float pairfreq_t classfreecontact_1_1predictor.html a5054b4f980d5bd2b7d83404bb7c18e0a
- std::vector< freq_t > freq_vec_t classfreecontact_1_1predictor.html ad9419230887212ba0b77e97592df1f10
- std::map< std::string, double > time_res_t classfreecontact_1_1predictor.html a1d8a9bb6c5e1f99f2017a67d27fb7ff6
- predictor
  classfreecontact_1_1predictor.html
  a5b3acba7459ea63588430c640d29711b
  (bool __dbg=false)
- virtual ~predictor classfreecontact_1_1predictor.html a2bad7f3d97cb9f9acd44758240086646 ()
- void get_seq_weights classfreecontact_1_1predictor.html aaa85bdee06a6d92bd64f24add6786f01 (freq_vec_t &__aliw, double &__wtot, const ali_t &__ali, double __clustpc, bool __veczw=true, int __num_threads=0)
- cont_res_t run classfreecontact_1_1predictor.html af15b96aaec6461bfc3e1bdcc9e917a4c (const ali_t &__ali, const freq_vec_t &__aliw, const double __wtot, double __density, double __gapth, uint16_t __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __apply_gapth, double __rho, int __num_threads=0, time_t __icme_timeout=1800, time_res_t *__timing=NULL)
- cont_res_t run classfreecontact_1_1predictor.html a7c41fd33d30f661746becc5c2acf6156 (const ali_t &__ali, double __clustpc, double __density, double __gapth, uint16_t __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __apply_gapth, double __rho, bool __veczw=true, int __num_threads=0, time_t __icme_timeout=1800, time_res_t *__timing=NULL)
- cont_res_t run classfreecontact_1_1predictor.html a536df577952ccdb8636532e926152ea8 (const ali_t &__ali, const parset_t &__parset, bool __veczw=true, int __num_threads=0, time_t __icme_timeout=1800, time_res_t *__timing=NULL)
- bool dbg classfreecontact_1_1predictor.html a11c0748eaab37bd6c7102f706ad8bf77
freecontact
namespacefreecontact.html
freecontact::ct_vector
freecontact::af_vector
freecontact::pf_vector
freecontact::cov_vector
freecontact::_rawscore_calc_t
freecontact::d2matrix
freecontact::_glasso_timer
freecontact::alilen_error
freecontact::icme_timeout_error
freecontact::ali_t
freecontact::contact_t
freecontact::parset_t
freecontact::predictor
- float cov_fp_t namespacefreecontact.html ab3fcbb8eace26400143602de7a52b250
- float fp_t namespacefreecontact.html a1509da532ff5eb86ac994aadb82819d7
- d2matrix< uint32_t, uint32_t, int > simcnt_t namespacefreecontact.html a50e3585fadb19ab5b87e97560021df80
- long long __m128i __attribute__ namespacefreecontact.html a5d52092b9ce46fe5b3052637fed9fa02 ((__vector_size__(16), __may_alias__))
- static void _raw_score_matrix namespacefreecontact.html a00faa540aab7e4a18d6b667b8cfb3cea (map< string, ct_vector< fp_t > > &__raw_ctscore, map< string, vector< double > > &__apc_bg, map< string, double > &__apc_mean, const uint16_t __alilen, const string &__key, const _rawscore_calc_t &__fo)
- static vector< contact_t > _apc namespacefreecontact.html a97ce3cb0c52dd2caac0ef11bfda15861 (const ct_vector< fp_t > &__raw_ctscore, const vector< double > &__apc_bg, const double __apc_mean, const uint16_t __mincontsep, bool __filt)
- static vector< contact_t > _raw_as_is namespacefreecontact.html a88636cd377a3298d8c03749610d3450f (const ct_vector< fp_t > &__raw_ctscore, const uint16_t __mincontsep)
- static uint32_t _cache_holds_nseq namespacefreecontact.html a871c5bc33c4f82512123cf0d9d4423cc (uint16_t __seqsize)
- static __m128i _mm_setzero_si128 namespacefreecontact.html a125fee0592d6510ee355c35c27871f29 ()
- const parset_t ps_evfold namespacefreecontact.html a7829e364e73633e52a50432336bb073e (0.70, 0.0, 0.9, 1, 0.0, 0.5, false, 0.0, true, true, -1)
- const parset_t ps_psicov namespacefreecontact.html aa04798faaad9cccc574dff97c2936ce2 (0.62, 0.03, 0.9, 5, 1.0, 0.0, true, 0.1, false, false, -1)
- const parset_t ps_psicov_sd namespacefreecontact.html a1ec93d0398ea325d48721441da5e0daa (0.62, 0.0, 0.9, 5, 1.0, 0.0, true, 0.1, false, false, 0.001)
- static const uint8_t aamap_gapidx namespacefreecontact.html a3eda07fc84a407b262052bc2990c1e17
- static const uint8_t aamap namespacefreecontact.html ac2f5df04647861769de567ed36636abc []
- static const uint8_t mapaa namespacefreecontact.html ad43b86635de3822859fb2497f75922b4 []