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/********************************************************************************************
indelCoderOptions - a class that contains all the parameters for the indelCoderProjest as static
use the 'Parameters' class to read info from txt file.
initDefault. (+Parameters::addParameter)
getParamsFromFile. ->with alterations of defults for consistancy
verifyConsistParams.
*********************************************************************************************/
#include "indelCoderOptions.h"
#include "errorMsg.h"
#include "someUtil.h"
#include "Parameters.h"
#include <iostream>
#include <cmath>
using namespace std;
// recognize all the static members defined at .h
string indelCoderOptions::_seqFile;
string indelCoderOptions::_logFile;
int indelCoderOptions::_logValue;
//string indelCoderOptions::_outDir;
string indelCoderOptions::_indelOutputInfoFile;
string indelCoderOptions::_indelOutputFastaFile;
string indelCoderOptions::_nexusFileName;
indelCoderOptions::codingType indelCoderOptions::_codingType;
//bool indelCoderOptions::_isMCIC2;
bool indelCoderOptions::_isCheckForTriangleInequality;
bool indelCoderOptions::_isOmitLeadingAndEndingGaps;
/********************************************************************************************
*********************************************************************************************/
void indelCoderOptions::initOptions(const string& paramFileName)
{
//getOutDirFromFile(paramFileName); // first set _outDir to be used next
//createDir("", indelCoderOptions::_outDir);
ifstream params(paramFileName.c_str());
if(params.good())
Parameters::readParameters(params);
params.close();
initDefault();
getParamsFromFile(paramFileName);
//verifyConsistParams();
}
/********************************************************************************************
*********************************************************************************************/
//void indelCoderOptions::getOutDirFromFile(const string& paramFileName)
//{
// _outDir = "INDEL_CODER_RES";
// Parameters::addParameter("_outDir", _outDir);
//
// _outDir = Parameters::getString("_outDir");
//}
/********************************************************************************************
initDefault
*********************************************************************************************/
void indelCoderOptions::initDefault()
{
// all the default values are stored in the gainLossOptions:: static members
//################### Basic parameters:
// input (general)
_seqFile = ""; // essential - fasta file with presence(1)/absence(0) for each species over all gene families (positions)
_indelOutputInfoFile= "";
_indelOutputFastaFile="";
_nexusFileName="";
// output
//_outDir = "RESULTS"; // concatenated after current dir location 'pwd'
_logFile = "log.txt"; // print-outs of the running progress including the estimated parameters optimization
_logValue = 4; // verbosity level - ~4 - normal, >7 - load of info
//_isMCIC2 = true;
_codingType =SIC;
_isCheckForTriangleInequality = false;
_isOmitLeadingAndEndingGaps = true; // The typical approach is to omit (SeqState)
Parameters::addParameter("_seqFile", _seqFile);
Parameters::addParameter("_logFile", _logFile);
Parameters::addParameter("_indelOutputInfoFile", _indelOutputInfoFile);
Parameters::addParameter("_indelOutputFastaFile", _indelOutputFastaFile);
Parameters::addParameter("_nexusFileName", _nexusFileName);
Parameters::addParameter("_logValue", _logValue);
Parameters::addParameter("_codingType", getCodingType(_codingType));
//Parameters::addParameter("_isMCIC2", (_isMCIC2 == true) ? 1 : 0);
Parameters::addParameter("_isCheckForTriangleInequality", (_isCheckForTriangleInequality == true) ? 1 : 0);
Parameters::addParameter("_isOmitLeadingAndEndingGaps", (_isOmitLeadingAndEndingGaps == true) ? 1 : 0);
}
/********************************************************************************************
getParamsFromFile
*********************************************************************************************/
void indelCoderOptions::readParameters(const string& paramFileName)
{
ifstream params(paramFileName.c_str());
if(params.good())
Parameters::readParameters(params); // only place where params are read, updateParameter(paramName, param.c_str()) used
params.close();
}
/********************************************************************************************
getParamsFromFile
*********************************************************************************************/
void indelCoderOptions::getParamsFromFile(const string& paramFileName)
{
readParameters(paramFileName);
_logFile = Parameters::getString("_logFile");
_seqFile = Parameters::getString("_seqFile");
_indelOutputFastaFile = Parameters::getString("_indelOutputFastaFile");
_nexusFileName = Parameters::getString("_nexusFileName");
_indelOutputInfoFile = Parameters::getString("_indelOutputInfoFile");
if(_seqFile=="") errorMsg::reportError("_seqFile is needed");
if(_indelOutputFastaFile=="") errorMsg::reportError("_indelOutputFastaFile is needed");
if(_nexusFileName=="") errorMsg::reportError("_nexusFileName is needed");
if(_indelOutputInfoFile=="") errorMsg::reportError("_indelOutputInfoFile is needed");
//_isMCIC2 = (Parameters::getInt("_isMCIC2") == 1) ? true : false;
_codingType = getCodingType(Parameters::getString("_codingType"));
_isCheckForTriangleInequality = (Parameters::getInt("_isCheckForTriangleInequality") == 1) ? true : false;
_isOmitLeadingAndEndingGaps = (Parameters::getInt("_isOmitLeadingAndEndingGaps") == 1) ? true : false;
_logValue = Parameters::getInt("_logValue");
}
/********************************************************************************************
enum distributionType {SIC, MCIC, MCIC2};
*********************************************************************************************/
string indelCoderOptions::getCodingType(codingType type)
{
string res = "";
switch (type)
{
case SIC:
res = "SIC";
break;
case MCIC:
res = "MCIC";
break;
case MCIC2:
res = "MCIC2";
break;
default:
errorMsg::reportError("unknown type in codingType - {SIC, MCIC, MCIC2}");
}
return res;
}
//////////////////////////////////////////////////////////////////////////
indelCoderOptions::codingType indelCoderOptions::getCodingType(const string& str)
{
if (str == "SIC")
return SIC;
if (str == "MCIC")
return MCIC;
if (str == "MCIC2")
return MCIC2;
else
errorMsg::reportError("unknown type in codingType - {SIC, MCIC, MCIC2}");
return SIC;
}
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