X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sensspeccommand.h;h=7d85a39bea25ced837551589cf21e2c431c8d7ca;hp=52ab31ea6c96c88edb1b9b360cac7f9e38979a4e;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=bc4c4d63e983a3e91e74b5038bfec6705e1a3a2e

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 52ab31e..7d85a39 100644
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -13,27 +13,56 @@
 
 #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 getOutputPattern(string);	
+	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 77:3219.\nhttp://www.mothur.org/wiki/Sens.spec"; }
+	string getDescription()		{ return "sens.spec"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void processPhylip();
-///	void processColumn(map<string, int>);
+	int processPhylip();
+	int processColumn();
+	void setUpOutput();
+	void outputStatistics(string, string);
 	
-	string listFile, distFile, nameFile, outputDir;
+	string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
+	string outputDir;
 	string format;
-//	int numSeqs, numDists;
-	int truePositives, falsePositives, trueNegatives, falseNegatives;
-	bool abort;
+	vector<string> outputNames;
+	set<string> labels; //holds labels to be used
+
+	long int truePositives, falsePositives, trueNegatives, falseNegatives;
+	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);
+    string preProcessList();
+
 };
 
-#endif
\ No newline at end of file
+#endif
+
+
+