X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.h;fp=sensspeccommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=02e84c0c96e087b5acb6a664405a5427107a5d45;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/sensspeccommand.h b/sensspeccommand.h
deleted file mode 100644
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
-
-
-