changes while testing

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index a5072e80c4bd908ed63d0f1ab34c83a5285b2e95..bfa329131f341e6a0750a318cc237ead77bbd8a4 100644 (file)
--- 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();
 
 };