#include "command.hpp"
#include "sharedordervector.h"
-#include "sharedlistvector.h"
#include "inputdata.h"
-#include "groupmap.h"
#include "collect.h"
#include "display.h"
-#include "readmatrix.hpp"
#include "validcalculator.h"
#include "sharedutilities.h"
-/* The collect.shared() command:
- The collect command generates a collector's curve from the given file representing several groups.
- The collect.shared command can only be executed after a successful read.shared command.
- It outputs a file for each estimator you choose to use. The collect.shared command parameters are label, line, freq, jumble and shared.
- No parameters are required, but you may not use both the line and label parameters at the same time.
- The collect.shared command should be in the following format: collect.shared(label=yourLabel, line=yourLines,
- freq=yourFreq, jumble=yourJumble, shared=yourEstimators). Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1,
- shared=sharedChao-sharedAce-sharedJabund). The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble),
- freq is 100 and shared are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.
- The valid shared estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.
- The label and line parameters are used to analyze specific lines in your input. */
-
-
-class GlobalData;
class CollectSharedCommand : public Command {
public:
+ CollectSharedCommand(string);
CollectSharedCommand();
~CollectSharedCommand();
- int execute();
+
+ vector<string> setParameters();
+ string getCommandName() { return "collect.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ 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.shared"; }
+ string getDescription() { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- SharedUtil* util;
- GroupMap* groupmap;
- SharedListVector* SharedList;
- ReadMatrix* read;
SharedOrderVector* order;
InputData* input;
- ValidCalculators* validCalculator;
Collect* cCurve;
vector<Display*> cDisplays;
- int freq;
- string format;
+ float freq;
+ bool abort, allLines, all;
+ set<string> labels; //holds labels to be used
+ string label, calc, groups, outputDir, sharedfile;
+ vector<string> Estimators, Groups, outputNames;
};
#endif