#include "command.hpp"
#include "ordervector.hpp"
#include "inputdata.h"
-#include "groupmap.h"
#include "collect.h"
#include "display.h"
-#include "readotu.h"
#include "validcalculator.h"
/*The collect() command:
The collect command generates a collector's curve from the given file.
- The collect command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception.
- The collect command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.
The collect command outputs a file for each estimator you choose to use. The collect command parameters are label, freq, single, abund.
No parameters are required.
The collect command should be in the following format: collect(label=yourLabel, freq=yourFreq, single=yourEstimators, abund=yourAbund).
The label parameter is used to analyze specific labels in your input. */
-
-class GlobalData;
-
class CollectCommand : public Command {
public:
CollectCommand(string);
- ~CollectCommand();
- int execute();
- void help();
+ CollectCommand();
+ ~CollectCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "collect.single"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.single"; }
+ string getHelpString();
+ string getDescription() { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
OrderVector* order;
InputData* input;
Collect* cCurve;
- ValidCalculators* validCalculator;
vector<Display*> cDisplays;
- int freq, abund, size;
+ int abund, size;
+ float freq;
+ vector<string> outputNames;
bool abort, allLines;
set<string> labels; //holds labels to be used
- string label, calc;
+ string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
vector<string> inputFileNames;
vector<string> groups;