*
*/
-#include <iostream>
-#include <fstream>
-#include <vector>
#include "command.hpp"
-#include "sharedordervector.h"
-#include "sharedlistvector.h"
#include "inputdata.h"
#include "rarefact.h"
#include "display.h"
-#include "readmatrix.hpp"
-
-/* The rarefaction.shared() command:
- The rarefaction command generates a rarefaction curve from a given file representing several groups.
- The rarefaction.shared command can only be executed after a successful read.shared command. It outputs a file for each estimator you choose to use.
- The rarefaction.shared command parameters are label, line, iters, jumble and sharedrarefaction.
- 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.shared(label=yourLabel, line=yourLines, iters=yourIters,
- jumble= yourJumble, sharedrarefaction=yourEstimators). Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000,
- jumble=1, sharedrarefaction =sharedobserved). The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble),
- iters is 1000 and sharedrarefaction is sharedobserved which calculates the shared rarefaction curve for the observed richness.
- The valid sharedrarefaction estimator is sharedobserved. The label and line parameters are used to analyze specific lines in your input. */
-
-
-class GlobalData;
+#include "validcalculator.h"
class RareFactSharedCommand : public Command {
public:
- RareFactSharedCommand();
- ~RareFactSharedCommand();
- int execute();
+ RareFactSharedCommand(string);
+ RareFactSharedCommand();
+ ~RareFactSharedCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "rarefaction.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
+ string getDescription() { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- SharedListVector* SharedList;
- ReadMatrix* read;
- SharedOrderVector* order;
- InputData* input;
- Rarefact* rCurve;
- vector<Display*> rDisplays;
- int freq, nIters;
+
+ vector<SharedRAbundVector*> lookup;
+ int nIters;
+ string format;
+ float freq;
+
+ map<int, string> file2Group; //index in outputNames[i] -> group
+ bool abort, allLines, jumble, groupMode;
+ set<string> labels; //holds labels to be used
+ string label, calc, groups, outputDir, sharedfile, designfile;
+ vector<string> Estimators, Groups, outputNames, Sets;
+
+ int process(GroupMap&, string);
+ vector<string> createGroupFile(vector<string>&);
};