string getCommandName() { return "dist.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
+ string getDescription() { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- void printSims(ostream&);
+ struct linePair {
+ int start;
+ int end;
+ };
+ vector<linePair> lines;
+
+ void printSims(ostream&, vector< vector<float> >&);
int process(vector<SharedRAbundVector*>);
vector<Calculator*> matrixCalculators;
- vector< vector<float> > simMatrix;
+ //vector< vector<float> > simMatrix;
InputData* input;
vector<SharedRAbundVector*> lookup;
string exportFileName, output, sharedfile;
- int numGroups;
+ int numGroups, processors;
ofstream out;
bool abort, allLines;
set<string> labels; //holds labels to be used
string outputFile, calc, groups, label, outputDir;
vector<string> Estimators, Groups, outputNames; //holds estimators to be used
+ int process(vector<SharedRAbundVector*>, string, string);
+ int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
+
};