*
*/
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
+
#include "command.hpp"
#include "sharedordervector.h"
#include "sharedlistvector.h"
#include "groupmap.h"
#include "collect.h"
#include "display.h"
-#include "readmatrix.hpp"
-
-/* 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. */
-
+#include "readotu.h"
+#include "validcalculator.h"
+#include "sharedutilities.h"
class GlobalData;
class CollectSharedCommand : public Command {
public:
- CollectSharedCommand();
+ CollectSharedCommand(string);
~CollectSharedCommand();
int execute();
+ void help();
private:
GlobalData* globaldata;
+ SharedUtil* util;
GroupMap* groupmap;
SharedListVector* SharedList;
- ReadMatrix* read;
+ ReadOTUFile* read;
SharedOrderVector* order;
InputData* input;
+ ValidCalculators* validCalculator;
Collect* cCurve;
vector<Display*> cDisplays;
- int freq;
+ float freq;
+ string format;
+
+ bool abort, allLines, all;
+ set<string> labels; //holds labels to be used
+ string label, calc, groups, outputDir;
+ vector<string> Estimators, Groups, outputNames;
+
};
-#endif
\ No newline at end of file
+#endif