*
*/
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
#include "command.hpp"
#include "sabundvector.hpp"
#include "inputdata.h"
#include "calculator.h"
-#include "readmatrix.hpp"
-
-/* The summary() command:
- The summary command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception.
- The summary command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.
- The summary command outputs a file for each estimator you choose to use. The summary command parameters are label, line, summary.
- No parameters are required, but you may not use both the line and label parameters at the same time.
- The summary command should be in the following format: summary(label=yourLabel, line=yourLines, summary=yourEstimators).
- Example summary(label=unique-.01-.03, line=0,5,10, summary=collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson).
- The default value for summary is collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.
- The valid summary estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.
- The label and line parameters are used to analyze specific lines in your input. */
-
+#include "readotu.h"
+#include "validcalculator.h"
class GlobalData;
class SummaryCommand : public Command {
public:
- SummaryCommand();
+ SummaryCommand(string);
~SummaryCommand();
int execute();
+ void help();
private:
GlobalData* globaldata;
- ReadMatrix* read;
+ ReadOTUFile* read;
vector<Calculator*> sumCalculators;
InputData* input;
+ ValidCalculators* validCalculator;
SAbundVector* sabund;
- string outputFileName;
- ofstream outputFileHandle;
+ int abund, size;
+
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string label, calc, outputDir;
+ vector<string> Estimators;
+ vector<string> inputFileNames;
+ vector<string> groups;
+
+ vector<string> parseSharedFile(string);
+
+
};
-#endif
\ No newline at end of file
+#endif