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

[mothur.git] / bellerophon.h

diff --git a/bellerophon.h b/bellerophon.h
deleted file mode 100644 (file)
index 36555bf..0000000
--- a/bellerophon.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef BELLEROPHON_H
-#define BELLEROPHON_H
-
-/*
- *  bellerophon.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 7/9/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-
-#include "chimera.h"
-#include "sparsematrix.hpp"
-#include "sequence.hpp"
-#include "dist.h"
-
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
-
-/***********************************************************/
-
-class Bellerophon : public Chimera {
-       
-       public:
-               Bellerophon(string, bool, bool, int, int, int, string); //fastafile, filter, correction, window, increment, processors, outputDir);     
-               ~Bellerophon() { delete distCalculator; for (int i = 0; i < seqs.size(); i++) { delete seqs[i];  }  seqs.clear(); }
-               
-               int getChimeras();
-               int print(ostream&, ostream&, string);
-               
-               #ifdef USE_MPI
-               int print(MPI_File&, MPI_File&, string);
-               #endif
-               
-       private:
-               struct linePair {
-                       unsigned long long start;
-                       int num;
-                       linePair(unsigned long long i, int j) : start(i), num(j) {}
-               };
-               
-               vector<linePair> lines;
-       
-               Dist* distCalculator;
-               vector<Sequence*> seqs;
-               vector< vector<Preference> > pref; //pref[0] = preference scores for all seqs in window 0.
-               string fastafile;
-               int iters, count, window, increment, numSeqs, processors; //iters = number of windows
-               bool correction;
-               
-               int generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
-               int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
-               vector<Preference> getBestPref();
-               int driverChimeras(vector<int>, linePair);
-               int createProcesses(vector<int>);
-               int writePrefs(string, linePair);
-               int readPrefs(string);
-               vector<string> getBestWindow(linePair line);
-               int fillPref(int, vector<string>&);
-};
-
-/***********************************************************/
-
-#endif
-