X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getoturepcommand.h;fp=getoturepcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=41680008c7dc27b28eb7e9a50ea8e9e621bfeb72;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
deleted file mode 100644
index 4168000..0000000
--- a/getoturepcommand.h
+++ /dev/null
@@ -1,88 +0,0 @@
-#ifndef GETOTUREPCOMMAND_H
-#define GETOTUREPCOMMAND_H
-/*
- *  getoturepcommand.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 4/6/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
- 
- /* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
-
-#include "command.hpp"
-#include "listvector.hpp"
-#include "inputdata.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> setParameters();
-	string getCommandName()			{ return "get.oturep";				}
-	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	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:
-	ListVector* list;
-	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;
-	ofstream out;
-	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;
-
-	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
-