added modify names parameter to set.dir

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 5e25afd2098e2fed0385178eecfcfd60a65fb461..bfa329131f341e6a0750a318cc237ead77bbd8a4 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -13,38 +13,54 @@
 
 #include "mothur.h"
 #include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
 
 class SensSpecCommand : public Command {
        
 public:
        SensSpecCommand(string);
        SensSpecCommand();
-       ~SensSpecCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SensSpecCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "sens.spec";                           }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       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);
        
-       string listFile, distFile, nameFile, sensSpecFileName;
+       string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
        string outputDir;
        string format;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
+       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