X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getoturepcommand.h;h=ca3439d809f96f6eff93dcf3948abd1a8274a7f5;hp=f413d4f51f2a9c45e3a5d17dd0243a825eb71679;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/getoturepcommand.h b/getoturepcommand.h
index f413d4f..ca3439d 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,53 +12,79 @@
  /* 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"
 #include "groupmap.h"
+#include "readmatrix.hpp"
+#include "formatmatrix.h"
+#include "counttable.h"
 
-class GlobalData;
+typedef map<int, float> SeqMap;
 
-typedef list<PCell>::iterator MatData;
+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();
-	int execute();
-	void help();	
+	GetOTURepCommand(string);
+	GetOTURepCommand();
+	~GetOTURepCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.oturep";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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;
-	ReadOTUFile* read;
-	InputData* input;
-	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, listfile, namesfile, groupfile, line, label;
+	ReadMatrix* readMatrix;
+	FormatMatrix* formatMatrix;
+	NameAssignment* nameMap;
+    CountTable ct;
+	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups, method;
 	ofstream out;
-	ifstream in, inNames;
-	bool groupError;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it4;
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	ifstream in, inNames, inRow;
+	bool abort, allLines, groupError, large, weighted, hasGroups;
 	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();
-	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
+	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(FastaMap*&);
+	void readNamesFile(bool);
+	int process(ListVector*);
+	SeqMap getMap(int);
+	string findRep(vector<string>, string); 	// returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+    string findRepAbund(vector<string>, string);
+	int processNames(string, string);
+	int processFastaNames(string, string, FastaMap*&);
+    int readDist();
 };
 
 #endif