*
*/
-#include <iostream>
-#include <fstream>
-#include <vector>
#include "command.hpp"
#include "ordervector.hpp"
#include "inputdata.h"
#include "rarefact.h"
#include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "validcalculator.h"
-/*The rarefaction() command:
- The rarefaction command generates a rarefaction curve from a given file.
- The rarefaction command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception.
- The rarefaction command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.
- The rarefaction command outputs a file for each estimator you choose to use. It is recommended to only use rarefaction estimator.
- The rarefaction command parameters are label, line, iters, freq, rarefaction. No parameters are required,
- but you may not use both the line and label parameters at the same time. The rarefaction command should be in the following format:
- rarefaction(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, rarefaction=yourEstimators).
- Example rarefaction(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, rarefaction=rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).
- The default values for iters is 1000, freq is 100, and rarefaction is rarefaction which calculates the rarefaction curve for the observed richness.
- The valid rarefaction estimators are: rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson.
- Rarefaction is the only recommended estimator. The label and line parameters are used to analyze specific lines in your input. */
-
-
class GlobalData;
class RareFactCommand : public Command {
public:
- RareFactCommand();
+ RareFactCommand(string);
~RareFactCommand();
- int execute();
+ int execute();
+ void help();
private:
GlobalData* globaldata;
vector<Display*> rDisplays;
- ReadMatrix* read;
+ ReadOTUFile* read;
OrderVector* order;
InputData* input;
ValidCalculators* validCalculator;
Rarefact* rCurve;
- int freq, nIters;
+ int nIters, abund;
+ float freq;
+
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string label, calc;
+ vector<string> Estimators;
+ vector<string> inputFileNames;
+ vector<string> groups;
+ string outputDir;
+
+ vector<string> parseSharedFile(string);
+
+
};
#endif