X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.h;h=02e84c0c96e087b5acb6a664405a5427107a5d45;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=818667a1c52729a2610564334d13225472eaac39;hpb=37309a2552995e5f7f2e04be99b808c803472311;p=mothur.git

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 818667a..02e84c0 100644
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -13,31 +13,53 @@
 
 #include "mothur.h"
 #include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
 
 class SensSpecCommand : public Command {
 	
 public:
 	SensSpecCommand(string);
-	~SensSpecCommand();
-	int execute();
-	void help();
+	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:
-	void processPhylip();
-	void processColumn();
+	int processPhylip();
+	int processColumn();
 	void setUpOutput();
 	void outputStatistics(string, string);
 	
-	string listFile, distFile, nameFile, sensSpecFileName;
+	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;
+	bool abort, allLines;
 	bool hard;
-	string lineLabel;
+	//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
\ No newline at end of file
+#endif
+
+
+