#include "sharedrabundvector.h"
#include "inputdata.h"
#include "calculator.h"
-#include "readotu.h"
#include "validcalculator.h"
-class GlobalData;
-
class SummarySharedCommand : public Command {
public:
SummarySharedCommand(string);
- ~SummarySharedCommand();
- int execute();
- void help();
+ SummarySharedCommand();
+ ~SummarySharedCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "summary.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
+ struct linePair {
+ int start;
+ int end;
+ };
+ vector<linePair> lines;
vector<Calculator*> sumCalculators;
InputData* input;
- ValidCalculators* validCalculator;
- bool abort, allLines, mult;
+ bool abort, allLines, mult, all, createPhylip;
set<string> labels; //holds labels to be used
- string label, calc, groups;
- vector<string> Estimators, Groups;
+ string label, calc, groups, sharedfile;
+ vector<string> Estimators, Groups, outputNames;
vector<SharedRAbundVector*> lookup;
- string outputFileName, format, outAllFileName;
- ofstream outputFileHandle, outAll;
- void process(vector<SharedRAbundVector*>);
+ string format, outputDir;
+ int numGroups, processors;
+ int process(vector<SharedRAbundVector*>, string, string);
+ int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
};