X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sensspeccommand.h;h=bfa329131f341e6a0750a318cc237ead77bbd8a4;hp=5e25afd2098e2fed0385178eecfcfd60a65fb461;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=afeb767205e3e7efd11bb7a36a36ad79ad05a779

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 5e25afd..bfa3291 100644
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -13,38 +13,54 @@
 
 #include "mothur.h"
 #include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
 
 class SensSpecCommand : public Command {
 	
 public:
 	SensSpecCommand(string);
 	SensSpecCommand();
-	~SensSpecCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~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();
+	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;
-	map<string, vector<string> > outputTypes;
+	set<string> labels; //holds labels to be used
 
 	long int truePositives, falsePositives, trueNegatives, falseNegatives;
-	bool abort;
+	bool abort, allLines, square;
 	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();
+    bool testFile();
+
 };
 
 #endif