X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=8153c3645fc5de028a6a9812426889297991ab85;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 8153c36..7a17c9d 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -13,47 +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"
-
-class GlobalData;
+#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(string);
+	GetOTURepCommand();
 	~GetOTURepCommand();
-	int execute();	
-	
+	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;
-	ListVector* listOfNames;
 	ReadOTUFile* read;
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, namesfile, groupfile;
+	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;
-	
-	 
+	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;
-	
+	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*); // returns name of "representative" sequence of given bin. //and fill a string containing the groups in that bin if a groupfile is given
+	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);
+												
 
 };