X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=database.hpp;h=49f39035e0aa95d6739616c0a6804858b53cdf9e;hp=01393c130adb3250ffaf5c9ed97fd8a2d4043c1e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=3abb236c602eb168ee112f080b563ebe2c705029

diff --git a/database.hpp b/database.hpp
index 01393c1..49f3903 100644
--- a/database.hpp
+++ b/database.hpp
@@ -11,24 +11,61 @@
  */
 
 
-/* This class is a parent to blastdb, distancedb, kmerdb, suffixdb.  Which are used to convert a squencedb object into that form. */
+/* 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() {}
+		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);
+	Database();
 	virtual ~Database();
-	virtual Sequence findClosestSequence(Sequence*) = 0;
+	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<Sequence> templateSequences;
+	vector<int> results;
+	vector<float> Scores;
 };
-
+/**************************************************************************************************/
 #endif