X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getoturepcommand.h;h=daf5bc16cbd3640093502d315af1f35008300ef0;hp=7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 7a17c9d..daf5bc1 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,26 +12,25 @@
  /* 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"
 #include "formatmatrix.h"
+#include "counttable.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
 		string name;
-		int	bin;
+		string bin;
+        int simpleBin;
 		int size;
 		string group;
 		
 		repStruct(){}
-		repStruct(string n, int b, int s, string g) : name(n), bin(b), size(s), group(g) {}
+		repStruct(string n, string b, int sb, int s, string g) : name(n), bin(b), size(s), group(g), simpleBin(sb) { }
 		~repStruct() {}
 };
 
@@ -40,28 +39,33 @@ 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();
+	~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;
 	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, outputDir, groups;
+    CountTable ct;
+	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups, method;
 	ofstream out;
 	ifstream in, inNames, inRow;
-	bool abort, allLines, groupError, large, weighted;
+	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<string, string> nameFileMap;
@@ -72,16 +76,16 @@ private:
 	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(FastaMap*&);
 	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
+	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