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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* 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., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef STOPRULE_H
#define STOPRULE_H
#include "tools.h"
#include "checkpoint.h"
/**
Stopping rule
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class StopRule : public CheckpointFactory
{
public:
/**
constructor
*/
StopRule();
void initialize(Params ¶ms);
/**
destructor
*/
~StopRule();
void getUFBootCountCheck(int &ufboot_count, int &ufboot_count_check);
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
read improved iteration number from a file
@param fileName file name
*/
void readFile (const char *fileName);
/**
Add the iteration number that improve trees
@param iteration improved iteration number
*/
void addImprovedIteration(int iteration);
/**
Get the last iteration number that improved trees
@return the last iteration number that improved trees
*/
int getLastImprovedIteration();
/**
main function to check the stop condition
@param current_iteration current iteration number
@param cur_correlation current correlation coefficient for bootstrap convergence
@return TRUE if stop condition is met, FALSE otherwise
*/
bool meetStopCondition(int cur_iteration, double cur_correlation);
/**
return TRUE if cur_correlation is high enough
@param cur_correlation correlation coefficient
*/
bool meetCorrelation(double cur_correlation) {
return cur_correlation >= min_correlation;
}
/** get the remaining time to converge, in seconds */
double getRemainingTime(int cur_iteration);
/**
@return the number of iterations required to stop the search
*/
// int getNumIterations();
/**
@return predicted iteration, 0 if no prediction has been made
*/
// int getPredictedIteration(int cur_iteration);
int getCurIt() const {
return curIteration;
}
void setCurIt(int curIteration) {
StopRule::curIteration = curIteration;
}
void shouldStop() {
should_stop = true;
}
private:
/**
* Current iteration number
*/
int curIteration;
double predict (double &upperTime);
/**
stop condition
*/
STOP_CONDITION stop_condition;
/**
confidence value of prediction
*/
double confidence_value;
/**
minimum number of iterations
*/
int min_iteration;
/**
maximum number of iterations
*/
int max_iteration;
/**
predicted number of iterations
*/
int predicted_iteration;
/** number of unsuccessful iterations to stop the search */
int unsuccess_iteration;
/** bootstrap correlation threshold to stop */
double min_correlation;
/** step size for checking bootstrap convergence */
int step_iteration;
/** max wall-clock running time to stop */
double max_run_time;
/** starting real time of the program */
double start_real_time;
/** TRUE to override stop condition */
bool should_stop;
/* FOLLOWING CODES ARE FROM IQPNNI version 3 */
// int nTime_;
DoubleVector time_vec;
void cmpInvMat (DoubleMatrix &oriMat, DoubleMatrix &invMat, int size);
void readMat (char *fileName, DoubleMatrix &oriMat, int &size);
void multiple (DoubleMatrix &mat1, DoubleMatrix &mat2, DoubleMatrix &proMat);
void multiple (DoubleMatrix &mat1, DoubleVector &vec2, DoubleVector &proVec);
void multiple (DoubleVector &vec1, DoubleMatrix &mat2, DoubleVector &proVec);
void multiple (DoubleVector &vec1, DoubleVector &vec2, DoubleMatrix &proMat);
double multiple (DoubleVector &vec1, DoubleVector &vec2);
void readVector(DoubleVector &tmpTimeVec_);
/* THE FOLLOWING CODE COMES FROM tools.c in Yang's PAML package */
//----------------------------------------------------------------------------------------
double cmpLnGamma (double alpha);
double cmpMuy (int k);
void cmpLamdaMat (int k, DoubleMatrix &lamdaMat);
void cmpVecA (int k, DoubleVector &aVec);
double cmpExtinctTime (int k);
double cmpUpperTime (int k, double alpha);
};
#endif
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