changing command name classify.shared to classifyrf.shared

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
index 186185d5ea68b08b969b6a99ef090ff75d5af72a..32be8b63d2ce751391ae5ebbc6154be221b77c9d 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
 /* 
@@ -28,26 +27,30 @@ public:
        CatchAllCommand(string);
        CatchAllCommand();
        ~CatchAllCommand() {}
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map< string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
        
-private:
-
-       GlobalData* globaldata;
-       ReadOTUFile* read;
-       InputData* input;
+       vector<string> setParameters();
+       string getCommandName()                 { return "catchall";                    }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Bunge J, Woodard L, Bohning D, Foster JA, Connolly S, Allen HK (2012). Estimating population diversity with CatchAll. Bioinformatics  28:1045.\nhttp://www.northeastern.edu/catchall/index.html\nhttp://www.mothur.org/wiki/Catchall"; }
+       string getDescription()         { return "estimate number of species"; }
        
-       string outputDir, sabundfile, rabundfile, listfile, format;
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
        bool abort, allLines;
        set<string> labels;
        vector<string> outputNames;
-       map< string, vector<string> > outputTypes;
+       vector<string> groups;
        
-       string process(SAbundVector*);
+       string process(SAbundVector*, string);
+       int createSummaryFile(string, string, ofstream&); 
+       vector<string> parseSharedFile(string);
+       string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/