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

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
deleted file mode 100644 (file)
index ddbb648..0000000
--- a/chimerapintailcommand.h
+++ /dev/null
@@ -1,68 +0,0 @@
-#ifndef CHIMERAPINTAILCOMMAND_H
-#define CHIMERAPINTAILCOMMAND_H
-
-/*
- *  chimerapintailcommand.h
- *  Mothur
- *
- *  Created by westcott on 4/1/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "chimera.h"
-#include "referencedb.h"
-
-/***********************************************************/
-
-class ChimeraPintailCommand : public Command {
-
-public:
-
-       ChimeraPintailCommand(string);
-       ChimeraPintailCommand();
-       ~ChimeraPintailCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "chimera.pintail";             }
-       string getCommandCategory()             { return "Sequence Processing"; }
-       string getHelpString(); 
-       string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
-       string getDescription()         { return "detect chimeric sequences"; }
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }          
-private:
-       ReferenceDB* rdb;
-       
-       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, consfile, quanfile, maskfile, outputDir, inputDir;
-       int processors, window, increment, numSeqs, templateSeqsLength;
-       Chimera* chimera;
-       vector<string> outputNames;
-       vector<string> fastaFileNames;
-};
-
-/***********************************************************/
-
-#endif
-
-