#include "command.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "sabundvector.hpp"
/*
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 getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
+ string getDescription() { return "estimate number of species"; }
- string outputDir, sabundfile, rabundfile, listfile, format, path;
+ 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 createSummaryFile(string, string);
+ string process(SAbundVector*, string);
+ int createSummaryFile(string, string, ofstream&);
+ vector<string> parseSharedFile(string);
+ string combineSummmary(vector<string>&);
};
/****************************************************************************/