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// $Id: fromInstructionFile.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ____FROM_INSTRUCTION__FILE
#define ____FROM_INSTRUCTION__FILE
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "alphabet.h"
#include "sequenceContainer.h"
#include "someUtil.h"
#include <string>
#include <iostream>
#include <vector>
#include <map>
using namespace std;
class fromInstructionFile {
public:
explicit fromInstructionFile(const string& instructionFileName);
void readInstructionFile(const string& str);
const string&searchStringInLines(const string& key) const;
bool doesWordExistInLines(const string& key) const;
const string& searchStringInLines(const string& key, const int index) const;
bool getIntValueConnectedWithWord(const string& wordToSearch, int & res);
void setLogFile();
void getStartingStochasticProcess(vector<stochasticProcess>& spPtrVec,VVdouble* freqs=NULL);
void getOneStartingStochasticProcess(stochasticProcess& sp, Vdouble * freqs = NULL);
void getOneStartingGammaParameter(stochasticProcess& sp);
bool getStartingEvolTrees(vector<tree>& vtree);// true if thelist tree1 file1, tree2 file2 is found.
bool getStartingEvolTrees(vector<tree>& vtree, vector<char>& constraintsOfT0);// true if thelist tree1 file1, tree2 file2 is found.
tree* getOneStartingEvolTree(vector<char>* constraintsOfT0);// ALOCATE NEW TREE AND NEW CONSTRAINT VECTOR.
void getStartingSequenceData(vector<sequenceContainer>& sdPtrVec,
const vector<alphabet* >& _alphabets);
void getOneStartingSequenceData(sequenceContainer& sdPtrVec,
const alphabet* _alphabets);
void getAlphabets(vector<alphabet* >& _alphabets);// alocate with new
// have to be deleted by the users!
alphabet* getOneAlphabet();
bool useGamma() {
return doesWordExistInLines("gamma");
}
void getStartingGammaParameters(vector<stochasticProcess>& spPtrVec);
void getStartingGlobalRates(vector<stochasticProcess>& spPtrVec);
string getOutFile();
protected:
map<string, string> _lines;
const int _maxNumOfFiles;// = 1000;
void getStartingGammaParameter(vector<stochasticProcess>& spPtrVec);
// tree getStartingEvolTree();
};
#endif
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