#ifndef __FILE_SNPUSR_H_SEEN__ #define __FILE_SNPUSR_H_SEEN__ /*----------------------------------------------------------------------------- Copyright (C) 2004, 2006, 2009. A. Ronald Gallant Post Office Box 659 Chapel Hill NC 27514-0659 USA This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. -----------------------------------------------------------------------------*/ #include "libscl.h" #include "snp_base.h" #include "libsnp.h" #include "snp.h" namespace snp { class datread; // These are the classes defined here. class resmusig; class plot; class simulate; class leverage; class quadrature; class rhostats; typedef datread datread_type; // The type names are used in snp.cpp. typedef resmusig residual_type; // Change the class reference to typedef resmusig mean_type; // substitute user written classes. typedef resmusig variance_type; // Leave the distribution code intact. typedef plot plot_type; // Hopefully the constructor call in typedef simulate simulate_type; // snp.cpp is general enough that // snp.cpp changes will be unnecessary. /* typedef leverage user_type; typedef quadrature user_type; */ typedef rhostats user_type; class datread : public datread_base { private: datparms dpm; public: datread(); void initialize(datparms dp); bool read_data(scl::realmat& data); }; class resmusig : public ancillary_base { private: optparms opm; datparms dpm; tranparms tpm; libsnp::snpden f; libsnp::afunc af; libsnp::ufunc uf; libsnp::rfunc rf; std::ostream& detail; const trnfrm* tr; const scl::realmat* X; const scl::realmat* Y; std::ostream* os; public: resmusig(optparms op, datparms dp, tranparms tp, libsnp::snpden fn, libsnp::afunc afn, libsnp::ufunc ufn, libsnp::rfunc rfn, libsnp::afunc afm, libsnp::ufunc ufm, libsnp::rfunc rfm, std::ostream& dos, const trnfrm* trn); void set_XY(const scl::realmat* x, const scl::realmat* y); bool initialize(std::ostream* out_stream); bool initialize(std::string out_filename) { return true; } bool calculate(); bool finalize(); }; class simulate : public ancillary_base { private: optparms opm; datparms dpm; tranparms tpm; libsnp::snpden f; libsnp::afunc af; libsnp::ufunc uf; libsnp::rfunc rf; std::ostream& detail; const trnfrm* tr; const scl::realmat* X; const scl::realmat* Y; std::ostream* os; public: simulate(optparms op, datparms dp, tranparms tp, libsnp::snpden fn, libsnp::afunc afn, libsnp::ufunc ufn, libsnp::rfunc rfn, libsnp::afunc afm, libsnp::ufunc ufm, libsnp::rfunc rfm, std::ostream& dos, const trnfrm* trn); void set_XY(const scl::realmat* x, const scl::realmat* y); bool initialize(std::ostream* out_stream); bool initialize(std::string out_filename) { return true; } bool calculate(); bool finalize(); }; class plot : public ancillary_base { private: optparms opm; datparms dpm; tranparms tpm; libsnp::snpden f; libsnp::afunc af; libsnp::ufunc uf; libsnp::rfunc rf; std::ostream& detail; const trnfrm* tr; const scl::realmat* X; const scl::realmat* Y; std::ostream* os; public: plot(optparms op, datparms dp, tranparms tp, libsnp::snpden fn, libsnp::afunc afn, libsnp::ufunc ufn, libsnp::rfunc rfn, libsnp::afunc afm, libsnp::ufunc ufm, libsnp::rfunc rfm, std::ostream& dos, const trnfrm* trn); void set_XY(const scl::realmat* x, const scl::realmat* y); bool initialize(std::ostream* out_stream); bool initialize(std::string out_filename) { return true; } bool calculate(); bool finalize(); }; class leverage : public ancillary_base { private: optparms opm; datparms dpm; tranparms tpm; libsnp::snpden f; libsnp::afunc af; libsnp::ufunc uf; libsnp::rfunc rf; std::ostream& detail; const trnfrm* tr; const scl::realmat* X; const scl::realmat* Y; std::ostream* os; public: leverage(optparms op, datparms dp, tranparms tp, libsnp::snpden fn, libsnp::afunc afn, libsnp::ufunc ufn, libsnp::rfunc rfn, libsnp::afunc afm, libsnp::ufunc ufm, libsnp::rfunc rfm, std::ostream& dos, const trnfrm* trn); void set_XY(const scl::realmat* x, const scl::realmat* y); bool initialize(std::ostream* out_stream); bool initialize(std::string out_filename) { return true; } bool calculate(); bool finalize(); }; class quadrature : public ancillary_base { private: optparms opm; datparms dpm; tranparms tpm; libsnp::snpden f; libsnp::afunc af; libsnp::ufunc uf; libsnp::rfunc rf; std::ostream& detail; const trnfrm* tr; const scl::realmat* X; const scl::realmat* Y; std::ostream* os; public: quadrature(optparms op, datparms dp, tranparms tp, libsnp::snpden fn, libsnp::afunc afn, libsnp::ufunc ufn, libsnp::rfunc rfn, libsnp::afunc afm, libsnp::ufunc ufm, libsnp::rfunc rfm, std::ostream& dos, const trnfrm* trn); void set_XY(const scl::realmat* x, const scl::realmat* y); bool initialize(std::ostream* out_stream); bool initialize(std::string out_filename) { return true; } bool calculate(); bool finalize(); }; class rhostats : public ancillary_base { private: optparms opm; datparms dpm; tranparms tpm; libsnp::snpden f; libsnp::afunc af; libsnp::ufunc uf; libsnp::rfunc rf; libsnp::afunc af_mask; libsnp::ufunc uf_mask; libsnp::rfunc rf_mask; std::ostream& detail; const trnfrm* tr; const scl::realmat* X; const scl::realmat* Y; std::ostream* os; std::string filename; public: rhostats(optparms op, datparms dp, tranparms tp, libsnp::snpden fn, libsnp::afunc afn, libsnp::ufunc ufn, libsnp::rfunc rfn, libsnp::afunc afm, libsnp::ufunc ufm, libsnp::rfunc rfm, std::ostream& dos, const trnfrm* trn); void set_XY(const scl::realmat* x, const scl::realmat* y); bool initialize(std::ostream* out_stream); bool initialize(std::string out_filename); bool calculate(); bool finalize(); }; } #endif