added modify names parameter to set.dir

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 1631e74ae054c834b30ed6763ad73faff10b0a13..bfa329131f341e6a0750a318cc237ead77bbd8a4 100644 (file)
--- 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 {
        
@@ -24,16 +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 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);
        
@@ -41,13 +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