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cleanup, prepare vecSigmaInit change

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kuepper 2005-10-10 21:42:31 +00:00
commit 4510b6d712
4 changed files with 126 additions and 118 deletions
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2
eo/NEWS
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@ -4,7 +4,7 @@
clean up the code considerably. Assume availability of sstream and limits. clean up the code considerably. Assume availability of sstream and limits.
* releases 0.9.3... (latest release is 0.9.3zz, 1. Oct. 2005) * release 0.9.3z.1 (1. Oct. 2005)
- Support gcc-3.4 and gcc.4.x. - Support gcc-3.4 and gcc.4.x.
- Provide full automake/autoconf/configure support. - Provide full automake/autoconf/configure support.

76
eo/src/utils/eoParser.h
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@ -1,33 +1,27 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*- /* (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2000
//----------------------------------------------------------------------------- This library is free software; you can redistribute it and/or modify it under
// eoParser.h the terms of the GNU Lesser General Public License as published by the Free
// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2000 Software Foundation; either version 2 of the License, or (at your option) any
/* later version.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful, This library is distributed in the hope that it will be useful, but WITHOUT ANY
but WITHOUT ANY WARRANTY; without even the implied warranty of WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public You should have received a copy of the GNU Lesser General Public License along
License along with this library; if not, write to the Free Software with this library; if not, write to the Free Software Foundation, Inc., 59
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es Contact: http://eodev.sourceforge.net
todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr Marc.Schoenauer@polytechnique.fr
mkeijzer@dhi.dk mkeijzer@dhi.dk
*/
//-----------------------------------------------------------------------------
/**
CVS Info: $Date: 2005-09-28 21:49:26 $ $Version$ $Author: kuepper $
*/ */
#ifndef eoParser_h
#define eoParser_h
#ifndef EO_PARSER_H
#define EO_PARSER_H
#include <map> #include <map>
#include <sstream> #include <sstream>
@ -37,10 +31,11 @@ CVS Info: $Date: 2005-09-28 21:49:26 $ $Version$ $Author: kuepper $
#include "eoObject.h" #include "eoObject.h"
#include "eoPersistent.h" #include "eoPersistent.h"
/** /** Parameter saving and loading
eoParameterLoader is an abstract class that can be used as a base for your own
parameter loading and saving. The command line parser eoParser is derived from eoParameterLoader is an abstract class that can be used as a base for your own
this class. parameter loading and saving. The command line parser eoParser is derived from
this class.
*/ */
class eoParameterLoader class eoParameterLoader
{ {
@ -49,11 +44,10 @@ public :
/** Need a virtual destructor */ /** Need a virtual destructor */
virtual ~eoParameterLoader(); virtual ~eoParameterLoader();
/** /** Register a parameter and set its value if it is known
* processParam is used to register a parameter and set its value if it is known
* @param param the parameter to process
* @param param the parameter to process @param section the section where this parameter belongs
* @param section the section where this parameter belongs
*/ */
virtual void processParam(eoParam& param, std::string section = "") = 0; virtual void processParam(eoParam& param, std::string section = "") = 0;
@ -147,8 +141,9 @@ public:
std::string ProgramName() { return programName; } std::string ProgramName() { return programName; }
/** /** Has param been entered by user?
* checks if _param has been actually entered by the user
Checks if _param has been actually entered by the user
*/ */
virtual bool isItThere(eoParam& _param) const virtual bool isItThere(eoParam& _param) const
{ return getValue(_param).first; } { return getValue(_param).first; }
@ -278,4 +273,15 @@ private:
}; };
#endif
#endif // EO_PARSER_H
// Local Variables:
// coding: iso-8859-1
// mode:C++
// c-file-style: "Stroustrup"
// comment-column: 35
// fill-column: 80
// End:

6
eo/test/Makefile.am
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@ -54,6 +54,9 @@ EXTRA_DIST = run_tests
# extra flags for specific targets # extra flags for specific targets
t_eoVirus_CXXFLAGS = $(AM_CXXFLAGS) -I$(top_srcdir)/contrib t_eoVirus_CXXFLAGS = $(AM_CXXFLAGS) -I$(top_srcdir)/contrib
t_MGE_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
t_MGE1bit_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
t_MGE_control_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
# Specify source-files, # Specify source-files,
# otherwise automake/make looks for C sources # otherwise automake/make looks for C sources
@ -63,11 +66,8 @@ t_eofitness_SOURCES = t-eofitness.cpp
t_eoFitnessAssembledEA_SOURCES = t-eoFitnessAssembledEA.cpp t_eoFitnessAssembledEA_SOURCES = t-eoFitnessAssembledEA.cpp
t_eobin_SOURCES = t-eobin.cpp t_eobin_SOURCES = t-eobin.cpp
t_eoVirus_SOURCES = t-eoVirus.cpp t_eoVirus_SOURCES = t-eoVirus.cpp
t_MGE1bit_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
t_MGE1bit_SOURCES = t-MGE1bit.cpp t_MGE1bit_SOURCES = t-MGE1bit.cpp
t_MGE_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
t_MGE_SOURCES = t-MGE.cpp t_MGE_SOURCES = t-MGE.cpp
t_MGE_control_CXXFLAGS = -I$(top_srcdir)/contrib/MGE
t_MGE_control_SOURCES = t-MGE-control.cpp t_MGE_control_SOURCES = t-MGE-control.cpp
t_eoStateAndParser_SOURCES = t-eoStateAndParser.cpp t_eoStateAndParser_SOURCES = t-eoStateAndParser.cpp
t_eoCheckpointing_SOURCES = t-eoCheckpointing.cpp t_eoCheckpointing_SOURCES = t-eoCheckpointing.cpp

36
eo/test/t-eoESAll.cpp
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@ -35,14 +35,16 @@ int main_function(int argc, char *argv[])
{ {
// Create the command-line parser // Create the command-line parser
eoParser parser(argc, argv); // for user-parameter reading eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated eoState state; // keeps all things allocated
eoValueParam<bool>& simpleParam = parser.getORcreateParam(true, "Isotropic",
"Isotropic self-adaptive mutation",
eoValueParam<bool>& simpleParam = parser.createParam(true, "Isotropic", "Isotropic self-adaptive mutation", 'i', "ES mutation"); 'i', "ES mutation");
eoValueParam<bool>& stdevsParam = parser.createParam(false, "Stdev", "One self-adaptive stDev per variable", 's', "ES mutation"); eoValueParam<bool>& stdevsParam = parser.getORcreateParam(false, "Stdev",
eoValueParam<bool>& corrParam = parser.createParam(false, "Correl", "Use correlated mutations", 'c', "ES mutation"); "One self-adaptive stDev per variable",
's', "ES mutation");
eoValueParam<bool>& corrParam = parser.getORcreateParam(false, "Correl",
"Use correlated mutations",
'c', "ES mutation");
// Run the appropriate algorithm // Run the appropriate algorithm
if (simpleParam.value() == false) if (simpleParam.value() == false)
{ {
@ -64,12 +66,12 @@ int main_function(int argc, char *argv[])
std::cout << "Using eoEsFull" << std::endl; std::cout << "Using eoEsFull" << std::endl;
runAlgorithm(eoEsFull<FitT>(), parser, state); runAlgorithm(eoEsFull<FitT>(), parser, state);
} }
return 0; return 0;
} }
// A main that catches the exceptions
// A main that catches the exceptions
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
#ifdef _MSC_VER #ifdef _MSC_VER
@ -77,9 +79,8 @@ int main(int argc, char **argv)
int flag = _CrtSetDbgFlag(_CRTDBG_LEAK_CHECK_DF); int flag = _CrtSetDbgFlag(_CRTDBG_LEAK_CHECK_DF);
flag |= _CRTDBG_LEAK_CHECK_DF; flag |= _CRTDBG_LEAK_CHECK_DF;
_CrtSetDbgFlag(flag); _CrtSetDbgFlag(flag);
// _CrtSetBreakAlloc(100); // _CrtSetBreakAlloc(100);
#endif #endif
try try
{ {
main_function(argc, argv); main_function(argc, argv);
@ -88,13 +89,15 @@ int main(int argc, char **argv)
{ {
std::cout << "Exception: " << e.what() << '\n'; std::cout << "Exception: " << e.what() << '\n';
} }
} }
/** The templatized main (sort of) /** The templatized main (sort of)
* quite similar to the main of other genotypes
* (e.g. t-eoReal and t-eoGA in test dir) quite similar to the main of other genotypes (e.g. t-eoReal and t-eoGA
*/ in test dir)
*/
template <class EOT> template <class EOT>
void runAlgorithm(EOT, eoParser& _parser, eoState& _state) void runAlgorithm(EOT, eoParser& _parser, eoState& _state)
{ {
@ -104,8 +107,7 @@ void runAlgorithm(EOT, eoParser& _parser, eoState& _state)
////////////////////////////////////////////////////// //////////////////////////////////////////////////////
// The evaluation fn - encapsulated into an eval counter for output // The evaluation fn - encapsulated into an eval counter for output
eoEvalFuncPtr<EOT, double, const std::vector<double>&> eoEvalFuncPtr<EOT, double, const std::vector<double>&> mainEval( real_value );
mainEval( real_value );
eoEvalFuncCounter<EOT> eval(mainEval); eoEvalFuncCounter<EOT> eval(mainEval);
// the genotype - through a genotype initializer // the genotype - through a genotype initializer