/* 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 "sparsematrix.hpp"
#include "listvector.hpp"
#include "inputdata.h"
-#include "readotu.h"
#include "fastamap.h"
-
-
-class GlobalData;
+#include "groupmap.h"
+#include "readmatrix.hpp"
+#include "formatmatrix.h"
typedef list<PCell>::iterator MatData;
+typedef map<int, float> SeqMap;
+
+struct repStruct {
+ string name;
+ int bin;
+ int size;
+ string group;
+
+ repStruct(){}
+ repStruct(string n, int b, int s, string g) : name(n), bin(b), size(s), group(g) {}
+ ~repStruct() {}
+};
class GetOTURepCommand : public Command {
-
+
public:
- GetOTURepCommand();
- ~GetOTURepCommand();
- int execute();
+ GetOTURepCommand(string);
+ 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;
- SparseMatrix* matrix;
ListVector* list;
- ListVector* listOfNames;
- ReadOTUFile* read;
InputData* input;
FastaMap* fasta;
- string filename, fastafile, namesfile;
+ GroupMap* groupMap;
+ ReadMatrix* readMatrix;
+ FormatMatrix* formatMatrix;
+ NameAssignment* nameMap;
+ string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
ofstream out;
- ifstream in, inNames;
-
-
+ ifstream in, inNames, inRow;
+ 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<int, string>::iterator it;
- map<int, string>::iterator it2;
- map<string, int>::iterator it3;
-
- void readNamesFile();
- string FindRep(int); // returns name of "representative" sequence of given bin.
+ 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
+ // for all distances related to a certain sequence
+ vector<int> rowPositions;
+ void readNamesFile();
+ void readNamesFile(bool);
+ int process(ListVector*);
+ SeqMap getMap(int);
+ 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