added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / bellerophon.h

diff --git a/bellerophon.h b/bellerophon.h
index 3d05617d50ad0a9dccb05da2d21bc872e8ca842f..1333ec8f16d8d0985a2b289b65294ef1f94a95f3 100644 (file)
--- a/bellerophon.h
+++ b/bellerophon.h
@@ -12,7 +12,6 @@
 
 
 #include "chimera.h"
-#include "filterseqscommand.h"
 #include "sparsematrix.hpp"
 #include "sequence.hpp"
 #include "dist.h"
@@ -25,22 +24,41 @@ typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeun
 class Bellerophon : public Chimera {
        
        public:
-               Bellerophon(string, string);    
-               ~Bellerophon() {};
+               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&);
                
+               #ifdef USE_MPI
+               int print(MPI_File&, MPI_File&);
+               #endif
+               
        private:
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(long int i, int j) : start(i), num(j) {}
+               };
+               
+               vector<linePair> lines;
+       
                Dist* distCalculator;
-               FilterSeqsCommand* filterSeqs;
                vector<Sequence*> seqs;
-               vector<Preference> pref;
+               vector< vector<Preference> > pref; //pref[0] = preference scores for all seqs in window 0.
                string fastafile;
-               int iters;
+               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>&);
 };
 
 /***********************************************************/