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

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
deleted file mode 100644 (file)
index 5b8092b..0000000
--- a/chimeraccodecommand.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef CHIMERACCODECOMMAND_H
-#define CHIMERACCODECOMMAND_H
-
-/*
- *  chimeraccodecommand.h
- *  Mothur
- *
- *  Created by westcott on 3/30/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "chimera.h"
-
-
-/***********************************************************/
-
-class ChimeraCcodeCommand : public Command {
-public:
-       ChimeraCcodeCommand(string);
-       ChimeraCcodeCommand();
-       ~ChimeraCcodeCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "chimera.ccode";               }
-       string getCommandCategory()             { return "Sequence Processing"; }
-       string getHelpString(); 
-       string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
-       string getDescription()         { return "detect chimeric sequences"; }
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-               
-private:
-       struct linePair {
-               unsigned long long start;
-               unsigned long long end;
-               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
-       };
-       vector<int> processIDS;   //processid
-       vector<linePair*> lines;
-       
-       int driver(linePair*, string, string, string);
-       int createProcesses(string, string, string);
-       
-       #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
-       #endif
-
-       bool abort, filter, save;
-       string fastafile, templatefile, outputDir, maskfile;
-       int processors, window, numwanted, numSeqs, templateSeqsLength;
-       Chimera* chimera;
-       vector<string> fastaFileNames;
-       vector<string> outputNames;
-};
-
-/***********************************************************/
-
-#endif
-