X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=database.hpp;h=3191fdfb02d5323129af949cf1eb50aea50ff3c8;hb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;hp=09fea858247b23cf33b351b0d56278522cf930af;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/database.hpp b/database.hpp
index 09fea85..3191fdf 100644
--- a/database.hpp
+++ b/database.hpp
@@ -10,19 +10,57 @@
  *
  */
 
+
+/* This class is a parent to blastdb, kmerdb, suffixdb.  */
+
 #include "mothur.h"
+#include "sequence.hpp"
 
-class Sequence;
+/**************************************************************************************************/
+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;
+	MothurOut* m;
+	int numSeqs, longest;
 	float searchScore;
-	vector<Sequence*> templateSequences;
+	vector<int> results;
 };
-
+/**************************************************************************************************/
 #endif