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/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
//! @file ErrorMotifs.h
//! @ingroup VariantCaller
//! @brief Handles motifs with high systematic error
#ifndef ERRORMOTIFS_H
#define ERRORMOTIFS_H
#include <iostream>
#include <fstream>
#include <string>
#include <stdlib.h>
#include <sstream>
#include <cstdlib>
#include <map>
#include <vector>
using namespace std;
//-----------------------------------------------------
struct TMetaData
{
unsigned short covered_sse_;
unsigned short covered_nonsse_;
TMetaData(unsigned short cov_sse,unsigned short cov_nonsse) {
covered_sse_ = cov_sse;
covered_nonsse_ = cov_nonsse;
}
inline bool operator=(const TMetaData & md) {
covered_sse_ = md.covered_sse_;
covered_nonsse_ = md.covered_nonsse_;
return false;
}
inline double calculate_probability() const {
// Divide by zero protection
double denominator = (double)(covered_sse_ + covered_nonsse_);
if (denominator > 0)
return (double)covered_sse_ / denominator;
else
return -1.0;
}
};
//-----------------------------------------------------
class TIonMotif
{
map <unsigned, TMetaData> motif_list;
public:
short left_size;
short right_size;
TIonMotif(){ left_size = 0; right_size = 0; };
inline void add(unsigned hashKey, const TMetaData &mdata) {
map <unsigned, TMetaData>::iterator itr;
itr = motif_list.find(hashKey);
if (itr == motif_list.end())
motif_list.insert(make_pair(hashKey, mdata));
else if (itr->second.calculate_probability() > mdata.calculate_probability())
motif_list.at(hashKey) = mdata;
};
inline bool has_hashkey(unsigned hashKey, TMetaData &md) const {
map <unsigned, TMetaData>::const_iterator itr;
itr = motif_list.find(hashKey);
if (itr == motif_list.end())
return false;
else {
md = itr->second;
return true;
}
};
inline bool isEmpty() const {
return (motif_list.size()==0);
};
};
//-----------------------------------------------------
class TIonMotifSet
{
unsigned MAX_HP_SIZE;
vector<TIonMotif> motif_table;
bool isempty;
void add_my_motif(short key, string motif, const TMetaData &mdata, unsigned pos);
public:
TIonMotifSet() {
MAX_HP_SIZE = 20;
motif_table.resize(4*(MAX_HP_SIZE+1));
isempty=true;
};
void load_from_file(const char * fname);
void add_motif(string motif, const TMetaData &mdata);
short get_key(char hpChar, int hpSize) const;
unsigned make_hashkey(string motif) const;
float get_sse_probability(string context, unsigned err_base_pos) const;
inline bool isEmpty() { return isempty; };
};
//-----------------------------------------------------
#endif //ERRORMOTIFS_H
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