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The project aims at realizing the prototype of a software environment dedicated to modeling with Markov chains.
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felsenstein81.h
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/* Marmote is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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Marmote 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
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with Marmote. If not, see <http://www.gnu.org/licenses/>.
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Copyright 2015 Alain Jean-Marie, Jean-Michel Fourneau, Jean-Marc Vincent, Issam Rabhi */
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#ifndef FELSENSTEIN81_H
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#define FELSENSTEIN81_H
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#include "markovChain.h"
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#include "Distribution/discreteDistribution.h"
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class
felsenstein81
:
public
markovChain
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{
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public
:
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felsenstein81
(
double
p[4] ,
double
mu);
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felsenstein81
(
discreteDistribution
* d,
double
mu);
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~felsenstein81
();
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void
makeMarkovChain
();
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discreteDistribution
*
transientDistribution
(
double
);
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discreteDistribution
*
stationaryDistribution
();
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simulationResult
*
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simulateChain
(
double
tMax,
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bool
stats,
bool
traj,
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bool
withIncrements,
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bool
trace );
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Distribution
*
hittingTimeDistribution
(
int
iState,
bool
* hittingSet);
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double
*
averageHittingTime
(
bool
* hittingSet );
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protected
:
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int
_size
;
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double
*
_stateSpace
;
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discreteDistribution
*
_transDistrib
;
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double
_transSpeed
;
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};
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#endif // FELSENSTEIN81_H
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