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