X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.h;h=bfa329131f341e6a0750a318cc237ead77bbd8a4;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=47d6e4e5fedfd92ec15700b931ce06681e5daf2c;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 47d6e4e..bfa3291 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 {
 	
@@ -24,15 +26,18 @@ public:
 	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 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);
 	
@@ -40,13 +45,22 @@ 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, 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