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[mothur.git] / bellerophon.h

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+#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
+