vector<string> setParameters();
string getCommandName() { return "otu.association"; }
string getCommandCategory() { return "Hypothesis Testing"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
string getDescription() { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
void help() { m->mothurOut(getHelpString()); }
private:
- string sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+ string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
bool abort, pickedGroups, allLines;
set<string> labels;
+ vector<SharedRAbundFloatVector*> metadataLookup;
+ vector< vector< double> > metadata;
- vector<string> outputNames, Groups;
+ vector<string> outputNames, Groups, metadataLabels;
int processShared();
int process(vector<SharedRAbundVector*>&);
int processRelabund();
int process(vector<SharedRAbundFloatVector*>&);
+ int readMetadata();
+ int getMetadata();
};