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#ifndef DATABASE_HPP
#define DATABASE_HPP
/*
* searchdatabase.hpp
*
*
* Created by Pat Schloss on 12/16/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
/* This class is a parent to kmerdb, suffixdb. */
#include "mothur.h"
#include "sequence.hpp"
#include "currentfile.h"
#include "utils.hpp"
/**************************************************************************************************/
struct seqMatch { //used to select top n matches
int seq;
int match;
seqMatch()=default;
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 SearchDatabase {
public:
SearchDatabase(){ longest = 0; numSeqs = 0; m = MothurOut::getInstance(); }
virtual ~SearchDatabase(){};
virtual void generateDB() = 0;
virtual void readDB(ifstream&){};
virtual void addSequence(Sequence) = 0; //add sequence to search engine
virtual void addSequences(vector<Sequence> seqs) { for (int i = 0; i < seqs.size(); i++) { addSequence(seqs[i]); } }
virtual void setNumSeqs(int i) { numSeqs = i; }
virtual vector<int> findClosestSequences(Sequence*, int, vector<float>&) const = 0; // returns indexes of n closest sequences to query
virtual vector< vector<int> > get(int i, char& s) { s='x'; vector< vector<int> > blank; return blank; }
virtual vector<int> getIndicatorColumns() { return nullIntVector; }
virtual map<int, int> getFilteredIndicatorColumns(string, vector<int>&) { return nullIntMap; }
virtual int getLongestBase() { return longest+1; }
virtual vector<int> getSequencesWithKmer(int){ vector<int> filler; return filler; };
virtual int getReversed(int) { return 0; }
virtual int getMaxKmer(){ return 1; }
virtual string getName(int) { return ""; }
protected:
MothurOut* m;
int numSeqs, longest;
Utils util;
};
/**************************************************************************************************/
#endif
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