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

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
deleted file mode 100644 (file)
index c409c50..0000000
--- a/chimeraslayer.h
+++ /dev/null
@@ -1,79 +0,0 @@
-#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
-
-