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

[mothur.git] / suffixdb.cpp

diff --git a/suffixdb.cpp b/suffixdb.cpp
deleted file mode 100644 (file)
index 4fc342d..0000000
--- a/suffixdb.cpp
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- *  suffixdb.cpp
- *  
- *
- *  Created by Pat Schloss on 12/16/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *     This is a child class of the Database abstract datatype.  The class is basically a database of suffix trees and an
- *     encapsulation of the method for finding the most similar tree to an inputted sequence.  the suffixForest objecct
- *     is a vector of SuffixTrees, with each template sequence being represented by a different SuffixTree.  The class also
- *     provides a method to take an unaligned sequence and find the closest sequence in the suffixForest.  The search
- *     method is inspired by the article and Perl source code provided at http://www.ddj.com/web-development/184416093.  I 
- *     would estimate that the time complexity is O(LN) for each search, which is slower than the kmer searching, but 
- *     faster than blast
- *
- */
-
-#include "database.hpp"
-#include "sequence.hpp"
-#include "suffixtree.hpp"
-#include "suffixdb.hpp"
-
-/**************************************************************************************************/
-
-SuffixDB::SuffixDB(int numSeqs) : Database() {
-       suffixForest.resize(numSeqs);
-       count = 0;
-}
-/**************************************************************************************************/
-
-SuffixDB::SuffixDB() : Database() {
-       count = 0;
-}
-
-/**************************************************************************************************/
-//assumes sequences have been added using addSequence
-vector<int> SuffixDB::findClosestSequences(Sequence* candidateSeq, int num){
-       try {
-               vector<int> topMatches;
-               string processedSeq = candidateSeq->convert2ints();             //      the candidate sequence needs to be a string of ints
-               
-               vector<seqMatch> seqMatches;
-               for(int i=0;i<suffixForest.size();i++){                                 //      scan through the forest and see what the minimum
-                       int count = suffixForest[i].countSuffixes(processedSeq);        //      return score is and keep track of the
-                       seqMatch temp(i, count);
-                       seqMatches.push_back(temp);
-               }
-               
-               //sorts putting smallest matches first
-               sort(seqMatches.begin(), seqMatches.end(), compareSeqMatchesReverse);
-               
-               searchScore = seqMatches[0].match;
-               searchScore = 100 * (1. - searchScore / (float)processedSeq.length());
-               
-               //save top matches
-               for (int i = 0; i < num; i++) {
-                       topMatches.push_back(seqMatches[i].seq);
-               }
-
-               //      return the Sequence object that has the minimum score
-               return topMatches;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SuffixDB", "findClosestSequences");
-               exit(1);
-       }       
-}
-/**************************************************************************************************/
-//adding the sequences generates the db
-void SuffixDB::addSequence(Sequence seq) {
-       try {
-               suffixForest[count].loadSequence(seq);          
-               count++;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SuffixDB", "addSequence");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-
-SuffixDB::~SuffixDB(){                                                                                                         
-       for (int i = (suffixForest.size()-1); i >= 0; i--) {  suffixForest.pop_back();  }
-}
-/**************************************************************************************************/