#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
+#include "counttable.h"
class ClassifyOtuCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "classify.otu"; }
string getCommandCategory() { return "Phylotype Analysis"; }
+
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Classify.otu"; }
-
+ 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/Classify.otu"; }
+ string getDescription() { return "find the concensus taxonomy for each OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
-
+ GroupMap* groupMap;
+ CountTable* ct;
ListVector* list;
InputData* input;
- string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
- bool abort, allLines, probs;
+ string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
+ bool abort, allLines, probs, persample;
int cutoff;
set<string> labels; //holds labels to be used
- vector<string> outputNames;
+ vector<string> outputNames, groups;
map<string, string> nameMap;
map<string, string> taxMap;
- int readNamesFile();
- int readTaxonomyFile();
- void removeConfidences(string&);
int process(ListVector*);
- vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin
+ string addUnclassifieds(string, int);
+ vector<string> findConsensusTaxonomy(vector<string>, int&, string&); // returns the name of the "representative" taxonomy of given bin
};