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/**
* This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.
* It is possible to improve your patternset and read patterns from a file.
*
* patternset object header
*
* For theory please have a look at:
*
* B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)
* Estimating evolutionary distances between genomic sequences from spaced-word matches
* Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)
*
*
* @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen
* @version: 1.0.2 11/2015
*/
#ifndef PATTERNSET_H_
#define PATTERNSET_H_
#include <iostream>
#include <fstream>
#include <random>
#include <vector>
#include <string>
#include <algorithm>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <inttypes.h>
#include "extkey.h"
class patternset {
public:
patternset();
patternset(char* pattern_file);
patternset(int size, int *length, int weight);
patternset(char* pattern_file, int size, int *length, int weight);
~patternset();
void ReInitPattern();
void ChangeBits(int number);
uint64_t ChangeBitPos(int pos, int pos_one, int pos_zero);
bool UniqPattern(int number);
std::vector<std::string> GetStringPattern();
std::string GetString(int number);
uint64_t GetPattern(int number);
int GetWeight();
int GetSize();
int* GetLength();
int GetLengthMean();
bool GetImprove();
bool GetUpdate();
double GetValue(int number);
void SetPattern(int number, uint64_t patt);
void Print();
void Silent();
void RandPatLength();
protected:
void Clear();
void TestPattern();
void VerifyConditions();
std::vector<std::string> SplitString(std::string pattern, char* tokens);
bool ValidatePatternsFormat(std::string pattern_form);
bool ValidatePatternConditions();
int PatternWeight(std::string pattern_wght);
int* PatternLength(std::vector<std::string> pattern_length);
void CreateLengths();
void CreateRandomPattern();
bool IsSetScore(int pattern);
int SymbolRandPos(int number, char symb);
int SymbolCalcPos(int number, char symb);
std::vector<int> GetSymbol(int number, char symb);
void ToString();
uint64_t ToBit(std::string p);
std::string BitString(uint64_t p);
double MaxNumberPattern(int p_weight, int p_length);
double Faculty(int value);
void SecureMessage(std::string errmsg, int pos);
private:
std::vector<uint64_t> pattern_set;
std::vector<std::string> string_pat;
std::vector<int> lengths;
int size;
int *length;
int length_mean;
int weight;
char* pattern_file = NULL;
bool improve;
bool update;
bool silent;
bool randpatleng;
};
#endif
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