#include "command.hpp"
+#include "inputdata.h"
+#include "listvector.hpp"
+#include "sharedrabundvector.h"
/**************************************************************************************************/
vector<string> setParameters();
string getCommandName() { return "get.otulabels"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
string getDescription() { return "Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
private:
bool abort;
- string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile;
+ string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile, listfile, sharedfile, label;
vector<string> outputNames;
set<string> labels;
+ ListVector* list;
+ vector<SharedRAbundVector*> lookup;
int readClassifyOtu();
int readOtuAssociation();
int readCorrAxes();
- int readAccnos();
-
+ int readList();
+ int readShared();
+ int getListVector();
+ int getShared();
};
/**************************************************************************************************/