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Settings.h
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Settings.h
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/*
* Settings.h
*
* Created on: Jan 15, 2010
* Author: mikee
*/
#ifndef SETTINGS_H_
#define SETTINGS_H_
#include "FileMgr.h"
#include <iostream>
#include <sstream>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <vector>
class FileMgr;
class Settings {
public:
Settings(int, char**);
std::string getAlignmentFileName(void) { return alignmentFileName; }
std::string getTreeFileName(void) { return treeFileName; }
std::string getOutputFileName(void) { return outputFileName; }
std::string getSettingsFileName(void) { return settingsFileName; }
std::string getCodonMatrixFileName(void) { return codonMatrixFileName; }
std::string getCodonFreqFileName(void) { return codonFreqFileName; }
std::string getCoordinatesFileName(void) { return coordinatesFileName; }
std::string getFreeEnergyFileName(void) { return freeEnergyFileName; }
double getBrlenLambda(void) { return brlenLambda; }
double getContactDistance(void) { return contactDistance; }
int getSiteChangesPerCycle(void) { return siteChangesPerCycle; }
int getChainLength(void) { return numCycles; }
int getPrintFrequency(void) { return printFrequency; }
int getSampleFrequency(void) { return sampleFrequency; }
int getSummarizeFrequency(void) { return summarizeFrequency; }
int getSVESamplesPerCycle(void) { return SVESamplesPerCycle; }
int getNumOmegaCats(void) { return numOmegaCats; }
bool getUseECM(void) { return useECM; }
void setAlignmentFileName(std::string s) { alignmentFileName = s; }
void setTreeFileName(std::string s) { treeFileName = s; }
void setOutputFileName(std::string s) { outputFileName = s; }
void setSettingsFileName(std::string s) { settingsFileName = s; }
void setCodonMatrixFileName(std::string s) { codonMatrixFileName = s; }
void setCodonFreqFileName(std::string s) { codonFreqFileName = s; }
void setCoordinatesFileName(std::string s) { coordinatesFileName = s; }
void setFreeEnergyFileName(std::string s) { freeEnergyFileName = s; }
void setBrlenLambda(double x) { brlenLambda = x; }
void setContactDistance(double x) { contactDistance = x; }
void setSiteChangesPerCycle(int x) { siteChangesPerCycle = x; }
void setSVESamplesPerCycle(int x) { SVESamplesPerCycle = x; }
private:
std::string alignmentFileName;
std::string treeFileName;
std::string outputFileName;
std::string settingsFileName;
std::string codonMatrixFileName;
std::string codonFreqFileName;
std::string coordinatesFileName;
std::string freeEnergyFileName;
double brlenLambda;
double contactDistance;
int numOmegaCats;
int numCycles;
int printFrequency;
int sampleFrequency;
int summarizeFrequency;
int SVESamplesPerCycle;
int siteChangesPerCycle;
bool useECM;
};
#endif /* SETTINGS_H_ */