vector<string> setParameters();
string getCommandName() { return "make.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
-
+ string getDescription() { return "make a shared file from a list and group file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- void printSharedData(vector<SharedRAbundVector*>);
- int createMisMatchFile();
+ void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+ int createMisMatchFile(SharedListVector*, GroupMap*);
int readOrderFile();
bool isValidGroup(string, vector<string>);
int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+ int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+ int createSharedFromListGroup(string);
+ int createSharedFromBiom(string);
+ string getTag(string&);
+ vector<string> readRows(string, ifstream&, int&);
+ int getDims(string, int&, int&);
+ vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
- SharedListVector* SharedList;
- InputData* input;
- GroupMap* groupMap;
vector<string> Groups, outputNames, order;
set<string> labels;
- ofstream out;
- string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+ string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
bool firsttime, pickedGroups, abort, allLines;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;