X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sensspeccommand.h;h=bfa329131f341e6a0750a318cc237ead77bbd8a4;hp=a5072e80c4bd908ed63d0f1ab34c83a5285b2e95;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/sensspeccommand.h b/sensspeccommand.h
index a5072e8..bfa3291 100644
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -26,9 +26,10 @@ 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 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(); 
@@ -47,7 +48,7 @@ private:
 	set<string> labels; //holds labels to be used
 
 	long int truePositives, falsePositives, trueNegatives, falseNegatives;
-	bool abort, allLines;
+	bool abort, allLines, square;
 	bool hard;
 	//string lineLabel;
 	double cutoff;
@@ -57,6 +58,8 @@ private:
 	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();
 
 };