moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
deleted file mode 100644 (file)
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