341 lines
13 KiB
C++
341 lines
13 KiB
C++
/*
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* Open BEAGLE
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* Copyright (C) 2001-2007 by Christian Gagne and Marc Parizeau
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 2.1 of the License, or (at your option) any later version.
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*
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* This library is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this library; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*
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* Contact:
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* Laboratoire de Vision et Systemes Numeriques
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* Departement de genie electrique et de genie informatique
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* Universite Laval, Quebec, Canada, G1K 7P4
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* http://vision.gel.ulaval.ca
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*
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*/
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/*!
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* \file beagle/src/InitializationOp.cpp
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* \brief Source code of class InitializationOp.
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* \author Christian Gagne
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* \author Marc Parizeau
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* $Revision: 1.18.2.1 $
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* $Date: 2007/05/09 01:51:19 $
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*/
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#include "beagle/Beagle.hpp"
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#ifdef BEAGLE_HAVE_LIBZ
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#include "gzstream.h"
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#endif // BEAGLE_HAVE_LIBZ
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using namespace Beagle;
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/*!
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* \brief Construct a plain new initialization operator.
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* \param inReproProbaName Reproduction probability parameter name used in register.
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* \param inName Name of the initialization operator.
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*/
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InitializationOp::InitializationOp(Beagle::string inReproProbaName, Beagle::string inName) :
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BreederOp(inName),
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mReproProbaName(inReproProbaName)
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{ }
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/*!
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* \brief Apply the breeding operation on a breeding pool, returning a bred individual.
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* \param inBreedingPool Breeding pool to use for the breeding operation.
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* \param inChild Node handle associated to child node in the breeder tree.
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* \param ioContext Evolutionary context of the breeding operation.
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* \return Bred individual.
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*/
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Individual::Handle InitializationOp::breed(Individual::Bag& inBreedingPool,
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BreederNode::Handle inChild,
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Context& ioContext)
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{
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Beagle_StackTraceBeginM();
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Individual::Handle lNewIndiv =
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castHandleT<Individual>(ioContext.getDeme().getTypeAlloc()->allocate());
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initIndividual(*lNewIndiv, ioContext);
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if(lNewIndiv->getFitness() != NULL) lNewIndiv->getFitness()->setInvalid();
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ioContext.setIndividualHandle(lNewIndiv);
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return lNewIndiv;
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Beagle_StackTraceEndM("Individual::Handle InitializationOp::breed(Individual::Bag& inBreedingPool, BreederNode::Handle inChild, Context& ioContext)");
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}
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/*!
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* \return Return selection probability of breeder operator.
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* \param inChild Child node in the breeder tree.
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*/
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float InitializationOp::getBreedingProba(BreederNode::Handle inChild)
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{
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Beagle_StackTraceBeginM();
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return mReproductionProba->getWrappedValue();
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Beagle_StackTraceEndM("float InitializationOp::getBreedingProba(BreederNode::Handle inChild)");
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}
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/*!
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* \brief Initialize the initialization operator.
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* \param ioSystem Reference to the system to use for the initialization.
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*/
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void InitializationOp::initialize(System& ioSystem)
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{
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Beagle_StackTraceBeginM();
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BreederOp::initialize(ioSystem);
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if(ioSystem.getRegister().isRegistered(mReproProbaName)) {
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mReproductionProba =
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castHandleT<Float>(ioSystem.getRegister().getEntry(mReproProbaName));
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} else {
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mReproductionProba = new Float(0.1f);
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Register::Description lDescription(
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"Reproduction probability",
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"Float",
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"0.1",
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string("Probability that an individual is reproducted as is, without modification. ")+
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string("This parameter is useful only in selection and initialization operators that ")+
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string("are composing a breeder tree.")
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);
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ioSystem.getRegister().addEntry(mReproProbaName, mReproductionProba, lDescription);
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}
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if(ioSystem.getRegister().isRegistered("ec.pop.size")) {
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mPopSize = castHandleT<UIntArray>(ioSystem.getRegister().getEntry("ec.pop.size"));
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} else {
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mPopSize = new UIntArray(1,100);
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string lLongDescrip("Number of demes and size of each deme of the population. ");
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lLongDescrip += "The format of an UIntArray is S1,S2,...,Sn, where Si is the ith value. ";
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lLongDescrip += "The size of the UIntArray is the number of demes present in the ";
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lLongDescrip += "vivarium, while each value of the vector is the size of the corresponding ";
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lLongDescrip += "deme.";
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Register::Description lDescription(
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"Vivarium and demes sizes",
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"UIntArray",
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"100",
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lLongDescrip
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);
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ioSystem.getRegister().addEntry("ec.pop.size", mPopSize, lDescription);
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}
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if(ioSystem.getRegister().isRegistered("ec.init.seedsfile")) {
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mSeedsFile =
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castHandleT<String>(ioSystem.getRegister().getEntry("ec.init.seedsfile"));
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} else {
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mSeedsFile = new String("");
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string lMessage = "Name of file to use for seeding the evolution ";
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lMessage += "with crafted individual. An empty string means no seeding.";
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Register::Description lDescription(
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"Seeds individual filename",
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"String",
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"\"\"",
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lMessage
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);
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ioSystem.getRegister().addEntry("ec.init.seedsfile", mSeedsFile, lDescription);
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}
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Beagle_StackTraceEndM("void InitializationOp::initialize(System& ioSystem)");
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}
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/*!
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* \brief Apply the initialization operation on the deme.
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* \param ioDeme Current deme of individuals to initialize.
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* \param ioContext Context of the evolution.
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*/
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void InitializationOp::operate(Deme& ioDeme, Context& ioContext)
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{
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Beagle_StackTraceBeginM();
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#ifndef BEAGLE_NDEBUG
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if(mPopSize == NULL) {
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string lMessage;
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lMessage = string("It appears that the operator \"")+getName()+
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string("\" has not been initialized properly because the population's size has not been ")+
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string("initialized in InitializationOp (a base class of operator \"")+getName()+
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string("\"). Consider calling the initialize() method of your initialization operator. ")+
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string("If that is already being called then you might also like to consider whether a ")+
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string("call to Beagle::InitializationOp::initialize() should be added to the operator's ")+
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string("initialize() method.");
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throw Beagle_RunTimeExceptionM(lMessage);
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}
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if(ioContext.getVivariumHandle()!=NULL) {
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Beagle_AssertM(mPopSize->size() == ioContext.getVivarium().size());
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}
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#endif // BEAGLE_NDEBUG
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Beagle_LogTraceM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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string("Initializing the ")+
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uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
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);
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Beagle_LogTraceM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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string("Resizing the deme to ")+
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uint2str((*mPopSize)[ioContext.getDemeIndex()])+" individuals"
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);
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ioDeme.resize((*mPopSize)[ioContext.getDemeIndex()]);
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unsigned int lSeededIndividuals = 0;
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if(mSeedsFile->getWrappedValue().empty() == false) {
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Beagle_LogInfoM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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string("Reading seeds file \"")+mSeedsFile->getWrappedValue()+
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string("\" to initialize the ")+uint2ordinal(ioContext.getDemeIndex()+1)+
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string(" deme")
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);
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lSeededIndividuals = readSeeds(mSeedsFile->getWrappedValue(), ioDeme, ioContext);
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Beagle_LogDetailedM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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uint2str(lSeededIndividuals)+string(" individuals read to seed the deme")
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);
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}
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Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
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unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
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for(unsigned int i=lSeededIndividuals; i<ioDeme.size(); ++i) {
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Beagle_LogVerboseM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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string("Initializing the ")+uint2ordinal(i+1)+" individual"
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);
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ioContext.setIndividualHandle(ioDeme[i]);
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ioContext.setIndividualIndex(i);
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initIndividual(*ioDeme[i], ioContext);
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if(ioDeme[i]->getFitness() != NULL) ioDeme[i]->getFitness()->setInvalid();
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}
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ioContext.setIndividualIndex(lOldIndividualIndex);
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ioContext.setIndividualHandle(lOldIndividualHandle);
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Beagle_StackTraceEndM("void InitializationOp::operate(Deme& ioDeme, Context& ioContext)");
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}
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/*!
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* \brief Read individuals from a given file to seed the evolution.
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* \param inFileName File name to read seeds individual from.
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* \param ioDeme Deme to initialize with seeds.
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* \param ioContext Evolutionary context.
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* \return Number of seeds read.
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*
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* Seeds file format is quite simple: XML file with "Beagle" root tag, and then a
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* "Seeds" tag with in it the individuals representation to read. Here is a
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* seeds file example with one individual in it.
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* \verbatim
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<?xml version="1.0" encoding="ISO-8859-1"?>
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<Beagle>
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<Seeds>
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<Individual>
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<Genotype type="bitstring">11111</Genotype>
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</Individual>
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</Seeds>
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</Beagle>
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\endverbatim
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* If there is less individuals in the seed file than the population size, the
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* remaining individuals are initialized as usual. If there is more individuals
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* than needed, the last individuals of the seeds file are ignored. If more than one
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* deme is used in the evolution, each deme will be seeded with the same seeds file.
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*
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*/
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unsigned int InitializationOp::readSeeds(Beagle::string inFileName,
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Deme& ioDeme,
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Context& ioContext)
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{
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Beagle_StackTraceBeginM();
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#ifdef BEAGLE_HAVE_LIBZ
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igzstream lIFStream(inFileName.c_str());
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#else // BEAGLE_HAVE_LIBZ
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std::ifstream lIFStream(inFileName.c_str());
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#endif // BEAGLE_HAVE_LIBZ
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PACC::XML::Document lParser;
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try {
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lParser.parse(lIFStream, inFileName.c_str());
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} catch(IOException& inExcept) {
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std::ostringstream lOSS;
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lOSS << "The seeds file is invalid: " << inExcept.what();
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throw Beagle_IOExceptionMessageM(lOSS.str().c_str());
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}
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unsigned int lReadIndividuals=0;
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unsigned int lOldIndivIndex = ioContext.getIndividualIndex();
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Individual::Handle lOldIndivHandle = ioContext.getIndividualHandle();
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for(PACC::XML::ConstIterator lNode=lParser.getFirstRoot(); lNode; ++lNode) {
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if((lNode->getType()==PACC::XML::eData) && (lNode->getValue()=="Beagle")) {
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for(PACC::XML::ConstIterator lChild=lNode->getFirstChild(); lChild; ++lChild) {
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if((lChild->getType()==PACC::XML::eData) && (lChild->getValue()=="Seeds")) {
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for(PACC::XML::ConstIterator lChild2=lChild->getFirstChild(); lChild2; ++lChild2) {
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if((lChild2->getType()==PACC::XML::eData) && (lChild2->getValue()=="Individual")) {
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if(lReadIndividuals >= ioDeme.size()) break;
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Beagle_NonNullPointerAssertM(ioDeme[lReadIndividuals]);
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ioContext.setIndividualIndex(lReadIndividuals);
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ioContext.setIndividualHandle(ioDeme[lReadIndividuals]);
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Beagle_LogVerboseM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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string("Reading the ")+uint2ordinal(lReadIndividuals+1)+
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string(" individual from seeds file")
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);
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ioDeme[lReadIndividuals]->readWithContext(lChild2, ioContext);
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Beagle_LogDebugM(
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ioContext.getSystem().getLogger(),
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"initialization", "Beagle::InitializationOp",
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string("Read seeded individual: ")+ioDeme[lReadIndividuals]->serialize()
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);
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++lReadIndividuals;
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}
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}
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}
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}
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}
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}
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ioContext.setIndividualHandle(lOldIndivHandle);
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ioContext.setIndividualIndex(lOldIndivIndex);
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return lReadIndividuals;
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Beagle_StackTraceEndM("unsigned int InitializationOp::readSeeds(string inFileName, Deme& ioDeme, Context& ioContext)");
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}
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/*!
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* \brief Read a initialization operator from a XML subtree.
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* \param inIter XML iterator to use to read initialization operator.
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* \param inOpMap Operator map to use to read initialization operator.
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*/
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void InitializationOp::readWithMap(PACC::XML::ConstIterator inIter, OperatorMap& inOpMap)
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{
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Beagle_StackTraceBeginM();
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if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName().c_str())) {
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std::ostringstream lOSS;
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lOSS << "tag <" << getName() << "> expected!" << std::flush;
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throw Beagle_IOExceptionNodeM(*inIter, lOSS.str().c_str());
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}
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string mReproProbaReadName = inIter->getAttribute("repropb").c_str();
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if(mReproProbaReadName.empty() == false) mReproProbaName = mReproProbaReadName;
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Beagle_StackTraceEndM("void InitializationOp::readWithMap(PACC::XML::ConstIterator inIter, OperatorMap& inOpMap)");
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}
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/*!
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* \brief Write initialization operator into XML streamer.
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* \param ioStreamer XML streamer to write initialization operator into.
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* \param inIndent Whether XML output should be indented.
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*/
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void InitializationOp::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const
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{
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Beagle_StackTraceBeginM();
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ioStreamer.insertAttribute("repropb", mReproProbaName);
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Beagle_StackTraceEndM("void InitializationOp::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
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}
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