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#ifndef __indelCoderOptionsParams_OPTION
#define __indelCoderOptionsParams_OPTION
#include "definitions.h"
#include <string>
#include <fstream>
using namespace std;
class indelCoderOptions{
public:
enum codingType {SIC, MCIC, MCIC2};
public:
virtual ~indelCoderOptions();
static void initOptions(const string& paramFileName);
static void initDefault();
static void readParameters(const string& paramFileName);
static void getParamsFromFile(const string& paramFileName);
static void getOutDirFromFile(const string& paramFileName);
static void verifyConsistParams();
static string getCodingType(codingType type);
static codingType getCodingType(const string& str);
public:
//################### Basic parameters:
// input (general)
static string _seqFile; // essential - fasta file with presence(1)/absence(0) for each species over all gene families (positions)
static string _indelOutputInfoFile; // a file in which all the indel information is given (not just the 0/1 codes)
static string _indelOutputFastaFile; // a file in which ajust the 0/1 coding is given
static string _nexusFileName; // a file in which the 0/1 coding is given in nexus format
//static string _outDir; // _outDir = "RESULTS", concatenated after current dir location 'pwd'
static string _logFile; // print-outs of the running progress including the estimated parameters optimization
static int _logValue; // verbosity level - ~4 - normal, >7 - load of info
//static bool _isMCIC2;
static codingType _codingType; // SIC, MCIC, MCIC2
static bool _isCheckForTriangleInequality;
static bool _isOmitLeadingAndEndingGaps; // ignore gaps that either start at 5' or end at 3'
private:
};
#endif
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