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#ifndef ___INDELCODER_
#define ___INDELCODER_
#include "gaps.h"
#include "character.h"
#include "indelCoderOptions.h"
#include "amino.h"
#include "sequenceContainer.h"
#include "recognizeFormat.h"
#include "logFile.h"
#include "talRandom.h"
#include <ctime>
#include <vector>
using namespace std;
// The implementation of IndelCoding scheme MCIC (Muller)
// for "Large-scale parsimony analysis of metazoan indels in protein-coding genes"
// (Parsimony tree reconstruction using indel information - supporting the Ecdysozoa hypothesis - sponges evolutionary close to animals)
// coded as gaps only those gaps in the alignments that were shorter than 50 amino-acids and those which did not start at the N-terminus or end at the C-terminus of the alignment.
//
//
// Simple Indel Coding SIC (Simmons and Ochoterena 2000)
// each indel receives a separate 2-state character of presence/absence.
// Any overlapping indels that exceed the boundaries of this indel are scored as missing data for that indel character.
//
// Modified Complex Indel Coding MCIC (Muller 2006).
// MCIC differs from SIC only in the treatment of overlapping indels.
// uses multistate characters to code overlapping indels and assigns a distinct symmetrical step matrix to those gaps.
// Note:
// (*) implemented for Amino Acids seq. (Later, we can add parameter with Alphabet type)
class indelCoder {
public:
explicit indelCoder(){};
virtual ~indelCoder(){};
void startSequenceContainer();
void readSequenceIntoGaps();
//void delimitationOfCharacters();
void delimitationOfCharacters(indelCoderOptions::codingType type);
void delimitationOfCharactersSIC();
//void delimitationOfCharactersMCIC2();
void determinationCharacterState();
void determinationCharacterStateSIC();
void determinationStepsMatrix();
void printCharacters();
void printNexus();
void printFasta();
void printGapsInfo();
void printIndelSummary();
void run();
private:
sequenceContainer _sc;
vector< vector<int> > _matrix;
gaps _gaps;
gaps _unknowns;
vector<gaps> _gapsVperSc;
vector<character*> _characters;
};
#endif
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