#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(string);
+ RareFactCommand(string);
+ RareFactCommand();
~RareFactCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
ValidCalculators* validCalculator;
Rarefact* rCurve;
- int freq, nIters, abund;
-
+ int nIters, abund, processors;
+ float freq;
+
bool abort, allLines;
- set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
- string line, label, calc;
+ string label, calc;
vector<string> Estimators;
+ vector<string> inputFileNames, outputNames;
+ vector<string> groups;
+ map<string, vector<string> > outputTypes;
+ string outputDir;
+
+ vector<string> parseSharedFile(string);
+
};