#include "tree.h"
#include "treemap.h"
#include "sharedutilities.h"
+#include "consensuscommand.h"
class GlobalData;
public:
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();
- void process(SharedOrderVector*);
+ int process(SharedOrderVector*);
GlobalData* globaldata;
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;
int numGroups, iters;
- vector<string> Estimators, Groups; //holds estimators to be used
+ vector<string> Estimators, Groups, outputNames; //holds estimators to be used
+ map< string, vector<string> > outputTypes;
};