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[mothur.git] / chimeraslayer.h

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+#ifndef CHIMERASLAYER_H
+#define CHIMERASLAYER_H
+
+/*
+ *  chimeraslayer.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/25/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "chimera.h"
+#include "maligner.h"
+#include "slayer.h"
+
+
+
+//***********************************************************************/
+//This class was modeled after the chimeraSlayer written by the Broad Institute
+/***********************************************************************/
+
+class ChimeraSlayer : public Chimera {
+       
+       public:
+               ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+               ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+               ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int, bool);
+
+               ~ChimeraSlayer();
+               
+               int getChimeras(Sequence*);
+               Sequence print(ostream&, ostream&);
+               Sequence print(ostream&, ostream&, data_results, data_results);
+               void printHeader(ostream&);
+               int doPrep();
+               int getNumNoParents() { return numNoParents; }
+               data_results getResults() { return printResults; }
+               
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               Sequence print(MPI_File&, MPI_File&, data_results, data_results);
+               #endif
+               
+       private:
+               Sequence querySeq;
+               Sequence trimQuery;
+               DeCalculator decalc;
+               Database* databaseRight;
+               Database* databaseLeft;
+               map<string, int> priority; //for template=self, seqname, seqAligned, abundance
+               set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
+               int numNoParents, threadID;
+       
+               vector<data_struct>  chimeraResults;
+               data_results printResults;
+               string chimeraFlags, searchMethod, fastafile, blastlocation;
+               bool realign, trimChimera;
+               int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+               float divR;
+       
+               void printBlock(data_struct, string, ostream&);
+               void printBlock(data_results, data_results, bool, bool, string, ostream&);
+               string getBlock(data_struct, string);
+               string getBlock(data_results, data_results, bool, bool, string);
+               //int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence, vector<Sequence*>&);
+               vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
+               vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
+               vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
+               
+};
+
+/************************************************************************/
+
+#endif
+
+