X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=database.hpp;fp=database.hpp;h=49f39035e0aa95d6739616c0a6804858b53cdf9e;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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