X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=database.hpp;fp=database.hpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=49f39035e0aa95d6739616c0a6804858b53cdf9e;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/database.hpp b/database.hpp
deleted file mode 100644
index 49f3903..0000000
--- a/database.hpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#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