/***************************************************************************************************

* The PolyMoSim project is distributed under the following license:

*

* Copyright (c) 2006-2025, Christoph Mayer, Leibniz Institute for the Analysis of Biodiversity Change,

* Bonn, Germany

* All rights reserved.

*

* Redistribution and use in source and binary forms, with or without

* modification, are permitted provided that the following conditions are met:

* 1. Redistributions of source code (complete or in parts) must retain

* the above copyright notice, this list of conditions and the following disclaimer.

* 2. Redistributions in binary form must reproduce the above copyright

* notice, this list of conditions and the following disclaimer in the

* documentation and/or other materials provided with the distribution.

* 3. All advertising materials mentioning features or any use of this software

* e.g. in publications must display the following acknowledgement:

* This product includes software developed by Christoph Mayer, Forschungsmuseum

* Alexander Koenig, Bonn, Germany.

* 4. Neither the name of the organization nor the

* names of its contributors may be used to endorse or promote products

* derived from this software without specific prior written permission.

*

* THIS SOFTWARE IS PROVIDED BY CHRISTOPH MAYER ''AS IS'' AND ANY

* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHTHOLDER OR ITS ORGANISATION BE LIABLE FOR ANY

* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES

* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND

* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*

* IMPORTANT (needs to be included, if code is redistributed):

* Please not that this license is not compatible with the GNU Public License (GPL)

* due to paragraph 3 in the copyright. It is not allowed under any

* circumstances to use the code of this software in projects distributed under the GPL.

* Furthermore, it is not allowed to redistribute the code in projects which are

* distributed under a license which is incompatible with one of the 4 paragraphs above.

*

* This project makes use of code coming from other projects. What follows is a complete

* list of files which make use of external code. Please refer to the copyright within

* these files.

*

* Files in tclap foler: Copyright (c) 2003 Michael E. Smoot

* See copyright in tclap/COPYRIGHT file for details.

* discrete_gamma.c: Copyright 1993-2004 by Ziheng Yang.

* See copyright in this file for details.

* CRandom.h: Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura

* See copyright in this file for details.

***************************************************************************************************/

#include "tclap/CmdLine.h"

// #define GLOBAL_VARS

#include "global-types-and-parameters.hpp"

#include "PolyMoSim.h"

#include <string>

#include <ctime>

using namespace TCLAP;

using namespace std;

string global_tree_file;

string global_model_file;

string global_preanalysis_file;

string global_postanalysis_file;

string global_log_file;

bool global_logging;

string global_output_filename;

string global_ancestral_sequence_file;

string global_siterateshist_file;

string global_siteratesdata_file;

unsigned global_num_repetitions;

bool global_use_GUI;

unsigned global_seed_random_generator;

enum_rg global_rg;

enum_outputformat global_outputformat;

unsigned global_verbosity;

void ReportErrorMessage(const char *e)

{

if (global_use_GUI)

{

}

else

{

fputs(e, stderr); // fprintf(stderr, e);

}

}

void myPrint(FILE *of, const char *s1)

{

if (of == stderr && global_use_GUI)

{

}

else

{

fputs(s1, of); // fprintf(of, s1);

}

}

void myPrint(FILE *of, const char *s1, const char *s2)

{

if (of == stderr && global_use_GUI)

{

}

else

{

fputs(s1, of); // fprintf(of, s1);

fputs(s2, of); // fprintf(of, s2);

}

}

void myPrint(FILE *of, const char *s1, const char *s2, const char *s3)

{

if (of == stderr && global_use_GUI)

{

}

else

{

fputs(s1, of); // fprintf(of, s1);

fputs(s2, of); // fprintf(of, s2);

fputs(s3, of); // fprintf(of, s3);

}

}

void myPrint(FILE *of, const char *s1, const char *s2, const char *s3, const char *s4)

{

if (of == stderr && global_use_GUI)

{}

else

{

fputs(s1, of); // fprintf(of, s1);

fputs(s2, of); // fprintf(of, s2);

fputs(s3, of); // fprintf(of, s3);

fputs(s4, of); // fprintf(of, s4);

}

}

void myPrint(ostream &os, const char *s1)

{

if (os.rdbuf() == cerr.rdbuf() && global_use_GUI)

{

}

else

{

os << s1;

}

}

void myPrint(ostream &os, const char *s1, const char *s2)

{

if (os.rdbuf() == cerr.rdbuf() && global_use_GUI)

{

}

else

{

os << s1 << s2;

}

}

void myPrint(ostream &os, const char *s1, const char *s2, const char *s3)

{

if (os.rdbuf() == cerr.rdbuf() && global_use_GUI)

{

}

else

{

os << s1 << s2 << s3;

}

}

void myPrint(ostream &os, const char *s1, const char *s2, const char *s3, const char *s4)

{

if (os.rdbuf() == cerr.rdbuf() && global_use_GUI)

{}

else

{

os << s1 << s2 << s3 << s4;

}

}

// void PrintMessage(FILE *of, const char *s1)

// {

// fprintf(of, s1);

// }

// void PrintMessage(FILE *of, const char *s1, const char *s2)

// {

// fprintf(of, s1);

// fprintf(of, s2);

// }

// void PrintMessage(FILE *of, const char *s1, const char *s2, const char *s3)

// {

// fprintf(of, s1);

// fprintf(of, s2);

// fprintf(of, s3);

// }

// void PrintMessage(FILE *of, const char *s1, const char *s2, const char *s3, const char *s4)

// {

// fprintf(of, s1);

// fprintf(of, s2);

// fprintf(of, s3);

// fprintf(of, s4);

// }

void init_param()

{

global_num_repetitions = 1;

global_use_GUI = false;

global_seed_random_generator = (unsigned)time(NULL);

global_rg = rg_MT19937;

global_outputformat = outputformat_fasta;

global_log_file = ""; // string("PolyMoSim_") + number2str((unsigned)time(NULL)) + ".log";

global_logging = false;

global_verbosity = 1; // 0: essential output

// 1: and basic information,

// 2: and model and tree information,

// 3: more progress

// 4: more progress and inheritance information

// 100: Debug code

// 200: More debug code

}

int read_and_init_parameters(int argc, char** argv)

{

string errormsg;

init_param();

try

{

CmdLine cmd("This program simulates the evolution of molecular (nucleotide and amino acid) sequences.",

' ', VERSION);

vector<string> allowed;

allowed.push_back("nexus");

allowed.push_back("phylip");

allowed.push_back("phylip_no_spaces");

allowed.push_back("fasta");

allowed.push_back("site_pattern_freq_absolute");

allowed.push_back("site_pattern_freq_relative");

allowed.push_back("site_pattern_freq_absolute_fill");

allowed.push_back("site_pattern_freq_relative_fill");

ValueArg<string> global_outputformat_Arg("f", "outputFormat",

"Output format of sequence data. Default: fasta. The site_pattern* format list the site pattern frequencies instead of the alignment. The site_pattern*_fill formats list all patterns the non fill formats only the site patterns that occured in the simulated data set.",

false, "fasta", allowed);

cmd.add( global_outputformat_Arg );

ValueArg<unsigned> global_seed_random_generator_Arg("s", "seed",

"The seed value for the random number generator. Default: time.",

false, global_seed_random_generator, "unsigned int");

cmd.add( global_seed_random_generator_Arg );

// SwitchArg global_use_GUI_Arg("", "gui",

// "Use graphical user interface.",

// global_use_GUI);

// cmd.add( global_use_GUI_Arg );

// SwitchArg global_use_NOGUI_Arg("", "nogui",

// "Do not use graphical user interface.",

// !global_use_GUI);

// cmd.add( global_use_NOGUI_Arg );

ValueArg<string> global_preanalysis_file_Arg("", "pre",

"File included in output before each generated data set.",

false, "", "string");

cmd.add( global_preanalysis_file_Arg );

ValueArg<string> global_postanalysis_file_Arg("", "post",

"File included in output after each generated data set.",

false, "", "string");

cmd.add( global_postanalysis_file_Arg );

ValueArg<string> global_ancestral_sequence_file_Arg("", "print_ancestral_seq",

"With this option and by providing a file name, the ancestral sequence is printed to this file. Default: ancestral sequence is not printed",

false, "", "string");

cmd.add( global_ancestral_sequence_file_Arg );

ValueArg<string> global_siterateshist_file_Arg("", "print_siterate_histogram",

"Print site rates histogram for each model to given file. Default: No siterate information is printed.",

false, "", "string");

cmd.add( global_siterateshist_file_Arg );

ValueArg<string> global_siteratesdata_file_Arg("", "print_siterate_data",

"Print full site rates of all models to given file. Default: No siterate information is printed.",

false, "", "string");

cmd.add( global_siteratesdata_file_Arg );

ValueArg<unsigned> global_num_repetitions_Arg("n", "nreps",

"Number of independent data generated in simulation. "

"Default: 1",

false, global_num_repetitions, "unsigned");

cmd.add( global_num_repetitions_Arg );

ValueArg<string> global_log_file_Arg("l", "log",

"File to write log information to.",

false, global_log_file, "string");

cmd.add( global_log_file_Arg );

ValueArg<string> output_filename_Arg("o", "outfile",

"Name of output file. If not specified, results are printed to standard output.",

false, global_output_filename, "string");

cmd.add( output_filename_Arg );

ValueArg<string> global_tree_file_Arg("t", "treefile",

"Tree file for simulation.",

true, global_tree_file, "string");

cmd.add( global_tree_file_Arg );

ValueArg<string> global_model_file_Arg("m", "modelfile",

"Model file for simulation.",

true, global_model_file, "string");

cmd.add( global_model_file_Arg );

ValueArg<unsigned> global_verbosity_file_Arg("", "verbosity",

"Adjust the level of additional information given to the user. Values from 0-200 are valid. "

"Default 1. Verbosity levels 0: essential output only, 1: add basic information, 2: add model and tree information, "

"3: add more progress, 4: add progress details and inheritance information, 100: add debug outout, 200: add more debug outut.",

false, global_verbosity, "integer");

cmd.add( global_verbosity_file_Arg );

cmd.parse( argc, argv );

// Assigning parameters to variables:

// global_input_filename = infilename_Arg.getValue();

global_output_filename = output_filename_Arg.getValue();

global_model_file = global_model_file_Arg.getValue();

global_tree_file = global_tree_file_Arg.getValue();

global_log_file = global_log_file_Arg.getValue();

if (global_log_file != "")

global_logging = true;

global_ancestral_sequence_file = global_ancestral_sequence_file_Arg.getValue();

global_siterateshist_file = global_siterateshist_file_Arg.getValue();

global_siteratesdata_file = global_siteratesdata_file_Arg.getValue();

global_preanalysis_file = global_preanalysis_file_Arg.getValue();

global_postanalysis_file = global_postanalysis_file_Arg.getValue();

global_num_repetitions = global_num_repetitions_Arg.getValue();

// global_use_GUI = global_use_GUI_Arg.getValue();

// global_use_GUI = global_use_NOGUI_Arg.getValue();

global_seed_random_generator = global_seed_random_generator_Arg.getValue();

// global_rg = global_rg_Arg.getValue();

global_verbosity = global_verbosity_file_Arg.getValue();

if (global_outputformat_Arg.getValue() == "nexus")

{

global_outputformat = outputformat_nexus;

}

else if ( global_outputformat_Arg.getValue() == "phylip" )

{

global_outputformat = outputformat_phylip;

}

else if ( global_outputformat_Arg.getValue() == "phylip_no_spaces" )

{

global_outputformat = outputformat_phylip_no_spaces;

}

else if ( global_outputformat_Arg.getValue() == "site_pattern_freq_absolute" )

{

global_outputformat = outputformat_pattern_absolute;

}

else if ( global_outputformat_Arg.getValue() == "site_pattern_freq_relative" )

{

global_outputformat = outputformat_pattern_relative;

}

else if ( global_outputformat_Arg.getValue() == "site_pattern_freq_absolute_fill" )

{

global_outputformat = outputformat_pattern_absolute_fill;

}

else if ( global_outputformat_Arg.getValue() == "site_pattern_freq_relative_fill" )

{

global_outputformat = outputformat_pattern_relative_fill;

}

else

{

global_outputformat = outputformat_fasta;

}

}

catch (TCLAP::ArgException &e)

{

errormsg = string("Error: ") + e.error().c_str() + " for arg " + e.argId().c_str() + "\n";

ReportErrorMessage(errormsg.c_str() );

return (-1);

}

//Checking rest of parameters:

// Do some immediate error checking

if ( !FileExists(global_model_file.c_str() ) )

{

errormsg = string("Error: the model file \"") + global_model_file.c_str() + "\" does not exist.\n";

ReportErrorMessage(errormsg.c_str());

return -2;

}

if ( !FileExists(global_tree_file.c_str() ) )

{

errormsg = string("Error: the tree file \"") + global_tree_file.c_str() + "\" does not exist.\n";

ReportErrorMessage(errormsg.c_str());

return -2;

}

if ( !global_preanalysis_file.empty() && !FileExists(global_preanalysis_file.c_str() ) )

{

errormsg = string("Error: the pre-analysis file \"") + global_preanalysis_file.c_str() + "\" does not exist.\n";

ReportErrorMessage(errormsg.c_str());

return -2;

}

if ( !global_postanalysis_file.empty() && !FileExists(global_postanalysis_file.c_str() ) )

{

errormsg = string("Error: the post-analysis file \"") + global_postanalysis_file.c_str() + "\" does not exist.\n";

ReportErrorMessage(errormsg.c_str());

return -2;

}

return 0;

} // End: read_and_init_parameters(int argc, char** argv)

void print_analysis_parameters(FILE *of, const char *s)

{

// TODO: not fully implwmwnted in this version.

myPrint(of, s, "Parameters used in this simulation:\n");

myPrint(of, s, "Name of model file: ", global_model_file.c_str(), "\n");

myPrint(of, s, "Name of tree file: ", global_tree_file.c_str(), "\n");

myPrint(of, s, "Name of pre-analysis file: ", global_preanalysis_file.c_str(), "\n");

myPrint(of, s, "Name of post-analysis file: ", global_postanalysis_file.c_str(), "\n");

myPrint(of, s, "Name of log file: ", global_log_file.c_str(), "\n");

if (!global_output_filename.empty())

myPrint(of, s, "Output filename: ", global_output_filename.c_str(), "\n");

else

myPrint(of, s, "Output filename: ", "Not specified. Output is printed to standard output.", "\n");

myPrint(of, s, "Print ancestral sequence to file: ");

if (!global_ancestral_sequence_file.empty() )

myPrint(of, global_ancestral_sequence_file.c_str(), "\n");

else

myPrint(of, "-\n");

myPrint(of, s, "Print siterates histogram data to file: ");

if (!global_siterateshist_file.empty() )

{

myPrint(of, global_siterateshist_file.c_str(), "\n");

}

else

myPrint(of, "-\n");

myPrint(of, s, "Print siterates data to file: ");

if (!global_siteratesdata_file.empty() )

{

myPrint(of, global_siteratesdata_file.c_str(), "\n");

}

else

myPrint(of, "-\n");

myPrint(of, s, "Logging in effect: ", (global_logging) ? "yes\n" : "no\n");

myPrint(of, s, "Number of repetition: ", faststring(global_num_repetitions).c_str(), "\n");

myPrint(of, s, "Random number seed: (default if not specified: ", faststring(global_seed_random_generator).c_str(), "\n");

switch(global_rg)

{

case rg_MT19937: myPrint(of, s, randomNumberGeneratorNames[global_rg], "\n"); break;

}

switch(global_outputformat)

{

case outputformat_nexus: myPrint(of, s, "Output format: nexus\n"); break;

case outputformat_fasta: myPrint(of, s, "Output format: fasta\n"); break;

case outputformat_phylip: myPrint(of, s, "Output format: phylip\n"); break;

case outputformat_phylip_no_spaces: myPrint(of, s, "Output format: phylip_no_spaces\n"); break;

case outputformat_pattern_absolute: myPrint(of, s, "Output format: site patterns absolute\n"); break;

case outputformat_pattern_relative: myPrint(of, s, "Output format: site patterns relative\n"); break;

case outputformat_pattern_absolute_fill: myPrint(of, s, "Output format: site patterns absolute and fill in missing patterns.\n"); break;

case outputformat_pattern_relative_fill: myPrint(of, s, "Output format: site patterns relative and fill in missing patterns.\n"); break;

case outputformat_logfile: myPrint(of, s, "Output format: special logfile format\n"); break;

}

myPrint(of, s, "Level of verbosity: ", faststring(global_verbosity).c_str(), "\n");

}

void print_analysis_parameters(ofstream &of, const char *s)

{

// TODO: not fully implwmwnted in this version.

myPrint(of, s, "Parameters used in this simulation:\n");

myPrint(of, s, "Name of model file: ", global_model_file.c_str(), "\n");

myPrint(of, s, "Name of tree file: ", global_tree_file.c_str(), "\n");

myPrint(of, s, "Name of pre-analysis file: ", global_preanalysis_file.c_str(), "\n");

myPrint(of, s, "Name of post-analysis file: ", global_postanalysis_file.c_str(), "\n");

myPrint(of, s, "Name of log file: ", global_log_file.c_str(), "\n");

myPrint(of, s, "Print ancestral sequence to file: ");

if (!global_ancestral_sequence_file.empty())

myPrint(of, global_ancestral_sequence_file.c_str(), "\n");

else

myPrint(of, "-\n");

myPrint(of, s, "Print siterates histogram information to file: ");

if (!global_siterateshist_file.empty())

{

myPrint(of, global_siterateshist_file.c_str(), "_data.txt, ");

myPrint(of, global_siterateshist_file.c_str(), "_hist.txt\n");

}

else

myPrint(of, "-\n");

myPrint(of, s, "Print siterates data to file: ");

if (!global_siteratesdata_file.empty() )

{

myPrint(of, global_siteratesdata_file.c_str(), "\n" );

}

else

myPrint(of, "-\n");

myPrint(of, s, "Logging in effect: ", (global_logging) ? "yes\n" : "no\n");

myPrint(of, s, "Number of repetition: ", faststring(global_num_repetitions).c_str(), "\n");

myPrint(of, s, "Random number seed: (default if not specified: ", faststring(global_seed_random_generator).c_str(), "\n");

switch(global_rg)

{

case rg_MT19937: myPrint(of, s, randomNumberGeneratorNames[global_rg], "\n"); break;

}

switch(global_outputformat)

{

case outputformat_nexus: myPrint(of, s, "Output format: nexus\n"); break;

case outputformat_fasta: myPrint(of, s, "Output format: fasta\n"); break;

case outputformat_phylip: myPrint(of, s, "Output format: phylip\n"); break;

case outputformat_phylip_no_spaces: myPrint(of, s, "Output format: phylip_no_spaces\n"); break;

case outputformat_pattern_absolute: myPrint(of, s, "Output format: site patterns absolute\n"); break;

case outputformat_pattern_relative: myPrint(of, s, "Output format: site patterns relative\n"); break;

case outputformat_pattern_absolute_fill: myPrint(of, s, "Output format: site patterns absolute and fill in missing patterns\n"); break;

case outputformat_pattern_relative_fill: myPrint(of, s, "Output format: site patterns relative and fill in missing patterns\n"); break;

case outputformat_logfile: myPrint(of, s, "Output format: special logfile format\n"); break;

}

myPrint(of, s, "Level of verbosity: ", faststring(global_verbosity).c_str(), "\n");

}