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// File: Bpp0SubstitutionModelFormat.h
// Created by: Laurent Guéguen
// Created on: mercredi 4 juillet 2012, à 13h 26
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _BPPOSUBSTITUTIONMODELFORMAT_H_
#define _BPPOSUBSTITUTIONMODELFORMAT_H_
#include "IoSubstitutionModelFactory.h"
#include "../Model/MixedSubstitutionModel.h"
namespace bpp
{
/**
* @brief Substitution model I/O in BppO format.
*
* Creates a new substitution model object according to model description syntax
* (see the Bio++ Progam Suite manual for a detailed description of this syntax).
*
*/
class BppOSubstitutionModelFormat :
public ISubstitutionModel,
public OSubstitutionModel
{
public:
static unsigned char DNA;
static unsigned char RNA;
static unsigned char NUCLEOTIDE;
static unsigned char PROTEIN;
static unsigned char CODON;
static unsigned char WORD;
static unsigned char BINARY;
static unsigned char ALL;
private:
unsigned char alphabetCode_;
bool allowCovarions_;
bool allowMixed_;
bool allowGaps_;
bool verbose_;
std::map<std::string, std::string> unparsedArguments_;
public:
/**
* @brief Create a new BppOSubstitutionModelFormat object.
*
* @param alphabetCode Bit saying which alphabets are allowed in the model specification.
* @param allowCovarions Tell is a covarion model can be returned.
* @param allowMixed Tell is a mixture model can be returned.
* @param allowGaps Tell is a gap model can be returned.
* @param verbose Tell if the construction is verbose.
*/
BppOSubstitutionModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose):
alphabetCode_(alphabetCode),
allowCovarions_(allowCovarions),
allowMixed_(allowMixed),
allowGaps_(allowGaps),
verbose_(verbose),
unparsedArguments_()
{}
virtual ~BppOSubstitutionModelFormat() {}
public:
const std::string getFormatName() const { return "BppO"; }
const std::string getFormatDescription() const { return "Bpp Options format."; }
SubstitutionModel* read(const Alphabet* alphabet, const std::string& modelDescription, const SiteContainer* data = 0, bool parseArguments = true);
const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
/**
* @brief Write a substitution model to a stream.
*
* @param model A substitution model object;
* @param out The output stream;
* @param globalAliases parameters linked to global alias. The
* output will be "name=alias_name";
* @param writtenNames is the vector of the written
* parameters so far [in, out];
* @throw Exception If an error occured.
*/
void write(const SubstitutionModel& model,
OutputStream& out,
std::map<std::string, std::string>& globalAliases,
std::vector<std::string>& writtenNames) const;
private:
MixedSubstitutionModel* readMixed_(const Alphabet* alphabet, const std::string& modelDescription, const SiteContainer* data);
SubstitutionModel* readWord_(const Alphabet* alphabet, const std::string& modelDescription, const SiteContainer* data);
/**
* @brief Set parameter initial values of a given model according to options.
*
* Parameters actually depends on the model passed as argument.
* See getSubstitutionModel for more information.
*
* This function is mainly for internal usage, you're probably looking for the getSubstitutionModel or getSubstitutionModelSet function.
*
* @param model The model to set.
* @param data A pointer toward the SiteContainer for which the substitution model is designed.
* The alphabet associated to the data must be of the same type as the one specified for the model.
* May be equal to NULL, but in this case use_observed_freq option will be unavailable.
* @throw Exception if an error occured.
*/
void initialize_(SubstitutionModel& model, const SiteContainer* data) throw (Exception);
void writeMixed_(const MixedSubstitutionModel& model,
OutputStream& out,
std::map<std::string, std::string>& globalAliases,
std::vector<std::string>& writtenNames) const;
};
} // end of namespace bpp.
#endif // _BPPOSUBSTITUTIONMODELFORMAT_H_
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