/* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
#include "command.hpp"
-#include "globaldata.hpp"
#include "listvector.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "fastamap.h"
#include "groupmap.h"
#include "readmatrix.hpp"
public:
GetOTURepCommand(string);
- ~GetOTURepCommand();
- int execute();
- void help();
+ GetOTURepCommand();
+ ~GetOTURepCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.oturep"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
+ string getDescription() { return "gets a representative sequence for each OTU"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
- GlobalData* globaldata;
ListVector* list;
- ReadOTUFile* read;
InputData* input;
FastaMap* fasta;
GroupMap* groupMap;
ReadMatrix* readMatrix;
FormatMatrix* formatMatrix;
NameAssignment* nameMap;
- string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format;
+ string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
ofstream out;
ifstream in, inNames, inRow;
- bool abort, allLines, groupError, large;
+ bool abort, allLines, groupError, large, weighted;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
+ map<string, string> nameFileMap;
+ vector<string> outputNames, Groups;
+ map<string, string> outputNameFiles;
float cutoff;
int precision;
vector<SeqMap> seqVec; // contains maps with sequence index and distance
vector<int> rowPositions;
void readNamesFile();
+ void readNamesFile(bool);
int process(ListVector*);
SeqMap getMap(int);
- string findRep(int, string&, ListVector*, int&); // returns the name of the "representative" sequence of given bin,
- // fills a string containing the groups in that bin if a groupfile is given,
- // and returns the number of sequences in the given bin
-
+ string findRep(vector<string>); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+ int processNames(string, string);
+ int processFastaNames(string, string);
};
#endif