continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / alignedsimilarity.h

diff --git a/alignedsimilarity.h b/alignedsimilarity.h
deleted file mode 100644 (file)
index 716b8b7..0000000
--- a/alignedsimilarity.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef ALIGNSIM_H
-#define ALIGNSIM_H
-
-/*
- *  alignedsimilarity.h
- *  Mothur
- *
- *  Created by westcott on 8/18/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "chimera.h"
-#include "dist.h"
-
-//This class was created using the algorythms described in the 
-//"Evaluation of Nearest Neighbor Methods for Detection of Chimeric Small-Subunit rRna Sequences" paper 
-//by J.F. Robison-Cox 1, M.M. Bateson 2 and D.M. Ward 2
-
-
-/***********************************************************/
-
-class AlignSim : public Chimera {
-       
-       public:
-               AlignSim(string, string);       
-               ~AlignSim();
-               
-               void getChimeras();
-               void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) { quanfile = q; };
-               
-               
-       private:
-               
-               Dist* distCalc;
-               vector<linePair*> lines;
-               vector<linePair*> templateLines;
-               
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
-               
-               vector< vector<sim> > IS;  //IS[0] is the vector os sim values for each window for querySeqs[0]
-               vector< vector<sim> > templateIS;  //templateIS[0] is the vector os sim values for each window for templateSeqs[0]
-               vector<int> windowBreak;
-               
-               string fastafile, templateFile;
-               int iters;
-               
-               vector< vector<sim> > findIS(int, int, vector<Sequence*>);
-               vector<Sequence*> findClosestSides(Sequence*, int, vector<int>&, int);
-               int findNumMatchedBases(Sequence, Sequence);
-               vector<int> findWindows();
-               
-               vector< vector<float> > quantile;
-               
-               vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
-               
-};
-
-/***********************************************************/
-
-#endif
-