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

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
deleted file mode 100644 (file)
index 02e84c0..0000000
--- a/sensspeccommand.h
+++ /dev/null
@@ -1,65 +0,0 @@
-#ifndef SENSSPECCOMMAND_H
-#define SENSSPECCOMMAND_H
-
-
-/*
- *  sensspeccommand.h
- *  Mothur
- *
- *  Created by Pat Schloss on 7/6/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "listvector.hpp"
-#include "inputdata.h"
-
-class SensSpecCommand : public Command {
-       
-public:
-       SensSpecCommand(string);
-       SensSpecCommand();
-       ~SensSpecCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "sens.spec";                           }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
-       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Sens.spec"; }
-       string getDescription()         { return "sens.spec"; }
-
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       int processPhylip();
-       int processColumn();
-       void setUpOutput();
-       void outputStatistics(string, string);
-       
-       string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
-       string outputDir;
-       string format;
-       vector<string> outputNames;
-       set<string> labels; //holds labels to be used
-
-       long int truePositives, falsePositives, trueNegatives, falseNegatives;
-       bool abort, allLines;
-       bool hard;
-       //string lineLabel;
-       double cutoff;
-       int precision;
-       
-       int fillSeqMap(map<string, int>&, ListVector*&);
-       int fillSeqPairSet(set<string>&, ListVector*&);
-       int process(map<string, int>&, string, bool&, string&);
-       int process(set<string>&, string, bool&, string&, int);
-
-};
-
-#endif
-
-
-