#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
+#include "counttable.h"
class ClassifyOtuCommand : public Command {
public:
ClassifyOtuCommand(string);
ClassifyOtuCommand();
- ~ClassifyOtuCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ClassifyOtuCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "classify.otu"; }
+ string getCommandCategory() { return "Phylotype Analysis"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ 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;
+ string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
bool abort, allLines, probs;
int cutoff;
set<string> labels; //holds labels to be used
vector<string> outputNames;
map<string, string> nameMap;
map<string, string> taxMap;
- map<string, vector<string> > outputTypes;
- int readNamesFile();
- int readTaxonomyFile();
- void removeConfidences(string&);
int process(ListVector*);
+ string addUnclassifieds(string, int);
vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin