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

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
deleted file mode 100644 (file)
index 918b4e5..0000000
--- a/chimeracheckcommand.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef CHIMERACHECKCOMMAND_H
-#define CHIMERACHECKCOMMAND_H
-
-/*
- *  chimeracheckcommand.h
- *  Mothur
- *
- *  Created by westcott on 3/31/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "chimera.h"
-#include "chimeracheckrdp.h"
-
-
-/***********************************************************/
-
-class ChimeraCheckCommand : public Command {
-public:
-       ChimeraCheckCommand(string);
-       ChimeraCheckCommand();
-       ~ChimeraCheckCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "chimera.check";               }
-       string getCommandCategory()             { return "Sequence Processing"; }
-       string getHelpString(); 
-       string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
-       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);
-       int createProcesses(string, string);
-               
-       #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
-       #endif
-
-       bool abort, svg, save;
-       string fastafile, templatefile, namefile, outputDir;
-       int processors, increment, ksize, numSeqs, templateSeqsLength;
-       Chimera* chimera;
-       vector<string> fastaFileNames;
-       vector<string> nameFileNames;
-       vector<string> outputNames;
-};
-
-/***********************************************************/
-
-#endif
-
-