X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.h;h=a5072e80c4bd908ed63d0f1ab34c83a5285b2e95;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=c690d5704652b3b68635614e4cf0b6e65050278e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/sensspeccommand.h b/sensspeccommand.h
index c690d57..a5072e8 100644
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -13,6 +13,8 @@
 
 #include "mothur.h"
 #include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
 
 class SensSpecCommand : public Command {
 	
@@ -24,14 +26,17 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "sens.spec";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	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);
 	
@@ -39,13 +44,20 @@ private:
 	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