#include "command.hpp"
#include "sharedordervector.h"
-#include "sharedlistvector.h"
#include "inputdata.h"
#include "groupmap.h"
#include "readotu.h"
#include "tree.h"
#include "treemap.h"
#include "sharedutilities.h"
+#include "consensuscommand.h"
class GlobalData;
class BootSharedCommand : public Command {
public:
- BootSharedCommand();
+ BootSharedCommand(string);
+ BootSharedCommand();
~BootSharedCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
private:
- void createTree(ostream*);
+ int createTree(ostream*, Tree*);
void printSims();
+ int process(SharedOrderVector*);
+
GlobalData* globaldata;
SharedUtil* util;
ReadOTUFile* read;
TreeMap* tmap;
Tree* t;
+ Tree* tempTree;
+ ConcensusCommand* consensus;
+ vector< vector<Tree*> > trees; //a vector of trees for each calculator chosen
vector<Calculator*> treeCalculators;
vector<ofstream*> out;
vector< vector<float> > simMatrix;
map<int, int> index; //maps row in simMatrix to vector index in the tree
InputData* input;
ValidCalculators* validCalculator;
- SharedListVector* SharedList;
SharedOrderVector* order;
vector<SharedRAbundVector*> lookup;
- string format, outputFile;
+
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string outputFile, calc, groups, label, outputDir;
int numGroups, iters;
+ vector<string> Estimators, Groups, outputNames; //holds estimators to be used
+ map< string, vector<string> > outputTypes;
};