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

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
deleted file mode 100644 (file)
index d6cca18..0000000
--- a/decalc.h
+++ /dev/null
@@ -1,80 +0,0 @@
-#ifndef DECALC_H
-#define DECALC_H
-/*
- *  decalc.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 7/22/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "sequence.hpp"
-
-/***********************************************************************/
-
-//This class was created using the algorythms described in the 
-// "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper 
-//by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
-
-/***********************************************************************/
-
-//this structure is necessary to determine the sequence that contributed to the outliers when we remove them
-//this way we can remove all scores that are contributed by outlier sequences.
-struct quanMember {
-       float score;
-       int member1;
-       int member2;
-       quanMember (float s, int m, int n) : score(s), member1(m),  member2(n) {}
-       quanMember() {}
-       
-};
-               
-//********************************************************************************************************************
-class DeCalculator {
-
-       public:
-               
-               DeCalculator() { m = MothurOut::getInstance(); }
-               ~DeCalculator() {};
-               
-               vector<Sequence> findClosest(Sequence, vector<Sequence*>&, vector<Sequence*>&, int, int);  //takes querySeq, a reference db, filteredRefDB, numWanted, minSim 
-               Sequence* findClosest(Sequence*, vector<Sequence*>);
-               set<int> getPos() {  return h;  }
-               void setMask(string); 
-               void setAlignmentLength(int l) {  alignLength = l;  }
-               void runMask(Sequence*);
-               void trimSeqs(Sequence*, Sequence*, map<int, int>&);
-               map<int, int> trimSeqs(Sequence&, vector<Sequence>&);
-               void removeObviousOutliers(vector< vector<float> >&, int);
-               vector<float> calcFreq(vector<Sequence*>, string);
-               vector<int> findWindows(Sequence*, int, int, int&, int);
-               vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
-               vector<float>  calcExpected(vector<float>, float);
-               vector<float>  findQav(vector<int>, int, vector<float>);  
-               float calcDE(vector<float>, vector<float>);
-               float calcDist(Sequence*, Sequence*, int, int);
-               float getCoef(vector<float>, vector<float>);
-               vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
-               
-               vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
-               
-               map<int, int> getMaskMap() { return maskMap; }
-               
-       private:
-               //vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
-               float findAverage(vector<float>);
-               //int findLargestContrib(vector<int>);
-               //void removeContrib(int, vector<quanMember>&);
-               string seqMask;
-               set<int> h;
-               int alignLength;
-               map<int, int> maskMap;
-               MothurOut* m;
-
-};
-
-/***********************************************************************/
-
-#endif