#include "rabundvector.hpp"
#include "inputdata.h"
#include "sequence.hpp"
+#include "counttable.h"
class SubSampleCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "sub.sample"; }
- string getCommandCategory() { return "General"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
string getDescription() { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
private:
bool abort, pickedGroups, allLines, persample;
- string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
+ string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile, taxonomyfile;
set<string> labels; //holds labels to be used
string groups, label, outputDir;
vector<string> Groups, outputNames;
int size;
vector<string> names;
map<string, vector<string> > nameMap;
+ CountTable ct;
int getSubSampleShared();
int getSubSampleList();
int processList(ListVector*&, ofstream&, set<string>&);
int getNames();
int readNames();
+ int getTax(set<string>&);
};