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[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
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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