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#ifndef DATABASE_HPP
#define DATABASE_HPP
/*
* database.hpp
*
*
* Created by Pat Schloss on 12/16/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
/* This class is a parent to blastdb, kmerdb, suffixdb. */
#include "mothur.h"
#include "sequence.hpp"
/**************************************************************************************************/
struct seqMatch { //used to select top n matches
int seq;
int match;
seqMatch() {}
seqMatch(int s, int m) : seq(s), match(m) {}
};
/**************************************************************************************************/
inline bool compareSeqMatches (seqMatch member, seqMatch member2){ //sorts largest to smallest
if(member.match > member2.match){
return true; }
else{
return false;
}
}
/**************************************************************************************************/
inline bool compareSeqMatchesReverse (seqMatch member, seqMatch member2){ //sorts largest to smallest
if(member.match < member2.match){
return true; }
else{
return false;
}
}
/**************************************************************************************************/
class Database {
public:
Database();
virtual ~Database();
virtual void generateDB() = 0;
virtual void addSequence(Sequence) = 0; //add sequence to search engine
virtual string getName(int) { return ""; }
virtual vector<int> findClosestSequences(Sequence*, int) = 0; // returns indexes of n closest sequences to query
virtual vector<int> findClosestMegaBlast(Sequence*, int, int){return results;}
virtual float getSearchScore();
virtual vector<float> getSearchScores() { return Scores; } //assumes you already called findClosestMegaBlast
virtual int getLongestBase();
virtual void readKmerDB(ifstream&){};
virtual void setNumSeqs(int i) { numSeqs = i; }
virtual vector<int> getSequencesWithKmer(int){ vector<int> filler; return filler; };
virtual int getReversed(int) { return 0; }
virtual int getMaxKmer(){ return 1; }
protected:
MothurOut* m;
int numSeqs, longest;
float searchScore;
vector<int> results;
vector<float> Scores;
};
/**************************************************************************************************/
#endif
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