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#ifndef SEQUENCE_H
#define SEQUENCE_H
/*
* sequence.h
*
*
* Created by Pat Schloss on 12/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
* A sequence object has three components: i) an accession number / name, ii) the unaligned primary sequence, iii) a
* pairwise aligned sequence, and iv) a sequence that is aligned to a reference alignment. This class has methods
* to set and get these values for the other classes where they are needed. *
*
*/
//Data Structure for a fasta file.
#include "mothurout.h"
#include "utils.hpp"
#include "writer.h"
class Protein;
/**************************************************************************************************/
class Sequence {
#ifdef UNIT_TEST
friend class TestSequence;
#endif
public:
Sequence();
Sequence(string, string);
Sequence(ifstream&);
Sequence(ifstream&, string&, bool);
Sequence(istringstream&);
#ifdef USE_BOOST
Sequence(boost::iostreams::filtering_istream&);
#endif
~Sequence() = default;
void setName(string);
string getName();
void setUnaligned(string);
string getUnaligned();
void setAligned(string);
string getAligned();
void setComment(string);
string getComment();
void setPairwise(string);
string getPairwise();
Protein getProtein(int, bool); //starting frame, trim
Protein getProtein(); //assumes starting frame 1, trim=false
bool isAligned();
string getInlineSeq();
int getNumNs();
int getNumBases();
int getStartPos();
int getEndPos();
void reverseComplement();
void trim(int);
void padToPos(int);
void padFromPos(int);
int filterToPos(int); //any character before the pos is changed to . and aligned and unaligned strings changed
int filterFromPos(int); //any character after the pos is changed to . and aligned and unaligned strings changed
int getAlignLength();
int getAmbigBases();
void removeAmbigBases();
int getLongHomoPolymer();
string convert2ints();
void printSequence(ostream&);
void printSequence(OutputWriter*);
void printUnAlignedSequence(ostream&);
protected:
MothurOut* m;
void initialize();
string getSequenceString(ifstream&, int&);
string getCommentString(ifstream&);
string getSequenceString(istringstream&, int&);
string getCommentString(istringstream&);
string getSequenceName(ifstream&);
#ifdef USE_BOOST
string getCommentString(boost::iostreams::filtering_istream&);
string getSequenceString(boost::iostreams::filtering_istream&, int&);
string getSequenceName(boost::iostreams::filtering_istream&);
#endif
string getSequenceName(istringstream&);
string name;
string unaligned;
string aligned;
string pairwise;
string comment;
int numBases;
int alignmentLength;
int longHomoPolymer;
int ambigBases;
int startPos, endPos;
Utils util;
};
/**************************************************************************************************/
#endif
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