X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=database.hpp;h=3191fdfb02d5323129af949cf1eb50aea50ff3c8;hb=4d7ffb38e091e9e7425d94e112551a3f90cacb0f;hp=e497fa42fea869d84502387638279a8a9896bbab;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/database.hpp b/database.hpp
index e497fa4..3191fdf 100644
--- a/database.hpp
+++ b/database.hpp
@@ -10,14 +10,57 @@
  *
  */
 
+
+/* 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(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(string);
-	virtual Sequence* findClosestSequence(Sequence*) = 0;
+	Database();
+	virtual ~Database();
+	virtual void generateDB() = 0; 
+	virtual void addSequence(Sequence) = 0;  //add sequence to search engine
+	virtual vector<int> findClosestSequences(Sequence*, int) = 0;  // returns indexes of n closest sequences to query
+	virtual vector<int> findClosestMegaBlast(Sequence*, int){return results;}
+	virtual float getSearchScore();
+	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 getMaxKmer(){	return 1;	};
 	
 protected:
-	int numSeqs;
-	vector<Sequence*> templateSequences;	
+	MothurOut* m;
+	int numSeqs, longest;
+	float searchScore;
+	vector<int> results;
 };
-
+/**************************************************************************************************/
 #endif