user_options.h

/*
 *
 * user_options.h
 * Hetero2
 *
 * CSIRO Open Source Software License Agreement (variation of the BSD / MIT License)
 * Copyright (c) 2014, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230.
 * All rights reserved. CSIRO is willing to grant you a license to this Hetero Version 2 on the following terms,
 * except where otherwise indicated for third party material.
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 * provided that the following conditions are met:
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 * ___________________________________________________________________
 * 
 * JACOBI_EIGENVALUE.C (http://people.sc.fsu.edu/~jburkardt/c_src/jacobi_eigenvalue/jacobi_eigenvalue.c)
 * Copyright (C) 2003-2013 John Burkardt
 * This software is licensed under GNU LGPL (http://www.gnu.org/licenses/lgpl.html)
 * ___________________________________________________________________
 */

#ifndef __RAL_RAS__user_options__
#define __RAL_RAS__user_options__

#include <vector>
#include <cstring>
#include <string>
#include <iostream>
#include <cstdlib>
#include <unistd.h>
#include "tool_box.h"
#include "definitions.h"

using namespace std;

class GetOptions {
public:
    vector<char> flags;
    vector<string> values;
    
    int size();
    
    void read(int argc, char** argv);
};

class UserOptions {
public:
    
    // ======================================================
    // Variables
    // ======================================================
    
    // treeFile            : the tree file
    //                       (compulsory)
    char* treeFile;
    
    // siteIntoFile        : the site info file
    //                       (compulsory)
    char* siteIntoFile;
    
    // param file list     : the list of parameter files
    //                       (compulsory)
    char* paramFileList;
    
    // outputFormat        : the format of the output multiple sequence alignment file
    //                       1 - FASTA format
    //                       2 - sequential PHYLIP format
    //                       (default: 2)
    int outputFormat;
    
    // outputPrefix        : prefix for output files
    //                       (default: <tree file w/o .ext)
    string outputPrefix;

    // seqLen              : the length of sequences to be simulated
    //                       (default: 10000)
    int seqLen;
    
    // edgeRepresent       : edge length representation
    //                       1 - Average number of substitutions per site
    //                       2 - Time
    //                       (default: 1)
    int edgeRepresent;
    
    // to simulate a perfect sequence
    int perfectSeq;
    
    // input seed number
    unsigned long seed_number;

    // =================================
    // Functions
    // =================================
    
	// constructor
	UserOptions();
	
    // To show the usage
    void outputUsage(char* progName);

    // read the arguments and collect the user options
    int readArguments(int argc, char** argv, string* errMsg);
    
    // To show the summary of the parameters
    void showSummary();
    
    // by default, prefixOut = <alignment file> w/o .ext
    void setDefaultOutputPrefix();
};


#endif /* defined(__RAL_RAS__user_options__) */