#include "readotu.h"
#include "validcalculator.h"
-/* 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. */
-
-
class GlobalData;
class SummaryCommand : public Command {
public:
SummaryCommand(string);
+ SummaryCommand();
~SummaryCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
ValidCalculators* validCalculator;
SAbundVector* sabund;
- string outputFileName;
- ofstream outputFileHandle;
int abund, size;
- bool abort, allLines;
- set<int> lines; //hold lines to be used
+ bool abort, allLines, groupMode;
set<string> labels; //holds labels to be used
- string line, label, calc;
+ string label, calc, outputDir;
vector<string> Estimators;
+ vector<string> inputFileNames, outputNames;
+ map<string, vector<string> > outputTypes;
+ vector<string> groups;
+
+ vector<string> parseSharedFile(string);
+ string createGroupSummaryFile(int, int, vector<string>&);
+
};
#endif