X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=5af0340b4b920a4fab3decc79bd2b3b4237f85ef;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=874e43ce5a8f45178a073b9d8e8e00fa8852deb0;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 874e43c..5af0340 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,10 +12,8 @@
  /* 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"
@@ -40,18 +38,23 @@ 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 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;
 	ListVector* list;
-	ReadOTUFile* read;
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
@@ -61,9 +64,10 @@ private:
 	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
 	ofstream out;
 	ifstream in, inNames, inRow;
-	bool abort, allLines, groupError, large;
+	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;
@@ -71,15 +75,14 @@ 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(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