#include "sharedordervector.h"
#include "inputdata.h"
#include "groupmap.h"
-#include "readotu.h"
#include "validcalculator.h"
#include "tree.h"
#include "treemap.h"
#include "sharedutilities.h"
-
-class GlobalData;
+#include "consensuscommand.h"
class BootSharedCommand : public Command {
public:
BootSharedCommand(string);
+ BootSharedCommand();
~BootSharedCommand();
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "bootstrap.shared"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- void createTree(ostream*);
+ int createTree(ostream*, Tree*);
void printSims();
- void process(SharedOrderVector*);
+ 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;
ValidCalculators* validCalculator;
SharedOrderVector* order;
vector<SharedRAbundVector*> lookup;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
+
bool abort, allLines;
- set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
- string outputFile, calc, groups, line, label;
+ string outputFile, calc, groups, label, outputDir, sharedfile;
int numGroups, iters;
- vector<string> Estimators, Groups; //holds estimators to be used
-
+ vector<string> Estimators, Groups, outputNames; //holds estimators to be used
};