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#ifndef _BLASR_SEQUENCE_INDEX_DATABASE_HPP_
#define _BLASR_SEQUENCE_INDEX_DATABASE_HPP_
#include <fstream>
#include <iostream>
#include <vector>
#include <assert.h>
#include <stdlib.h>
#include <sstream>
#include <cstring>
#include <algorithm>
#include "../Types.h"
#include "../DNASequence.hpp"
#include "../StringUtils.hpp"
#define SEQUENCE_INDEX_DATABASE_MAGIC 1233211233
template<typename TSeq>
class SequenceIndexDatabase {
public:
std::vector<DNALength> growableSeqStartPos;
std::vector<std::string> growableName;
DNALength *seqStartPos;
bool deleteSeqStartPos;
char **names;
bool deleteNames;
int *nameLengths;
bool deleteNameLengths;
int nSeqPos;
bool deleteStructures;
//
// This is stored after reading in the sequence.
//
std::vector<std::string> md5;
SequenceIndexDatabase(int final=0);
~SequenceIndexDatabase();
DNALength GetLengthOfSeq(int seqIndex);
// Return index of a reference sequence with name "seqName".
int GetIndexOfSeqName(std::string seqName);
void GetName(int seqIndex, std::string &name);
void MakeSAMSQString(std::string &sqString);
DNALength ChromosomePositionToGenome(int chrom, DNALength chromPos);
int SearchForIndex(DNALength pos);
std::string GetSpaceDelimitedName(unsigned int index);
int SearchForStartBoundary(DNALength pos);
int SearchForEndBoundary(DNALength pos);
DNALength SearchForStartAndEnd(DNALength pos, DNALength &start,
DNALength &end);
void WriteDatabase(ofstream &out);
void ReadDatabase(ifstream &in);
void SequenceTitleLinesToNames();
VectorIndex AddSequence(TSeq &sequence);
void Finalize();
void FreeDatabase();
};
template< typename TSeq >
class SeqBoundaryFtr {
public:
SequenceIndexDatabase<TSeq> *seqDB;
SeqBoundaryFtr(SequenceIndexDatabase<TSeq> *_seqDB);
int GetIndex(DNALength pos);
int GetStartPos(int index);
DNALength operator()(DNALength pos);
// This is misuse of a functor, but easier interface coding for now.
DNALength Length(DNALength pos);
};
#include "SequenceIndexDatabaseImpl.hpp"
#endif
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