X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=4f755d0fccfe68dd1e03b5b36d57ce4b76287df9;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 4f755d0..7a17c9d 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -13,51 +13,74 @@
 
 #include "command.hpp"
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
 #include "readotu.h"
 #include "fastamap.h"
 #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(string);
+	GetOTURepCommand();
 	~GetOTURepCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 
 private:
 	GlobalData* globaldata;
-	SparseMatrix* matrix;
 	ListVector* list;
 	ReadOTUFile* read;
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, listfile, namesfile, groupfile, line, label;
+	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;
-	bool groupError;
-
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	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<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;
+	map<string, vector<string> > outputTypes;
 
 	void readNamesFile();
+	void readNamesFile(bool);
 	int process(ListVector*);
-	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
+	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);
+												
 
 };