X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=37c4194a8c16e0664d7cb834b4777c054b61268d;hb=cd37904452dc95b183ff313ff05720c562902487;hp=d0343daa3cb647957e694cfa101ec5406edf3304;hpb=d0939d3ab83988cc068f9ebe60596cf5decb65e5;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d0343da..37c4194 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -8,15 +8,17 @@
  *  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 "globaldata.hpp"
 #include "sparsematrix.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "fastamap.h"
-
+#include "groupmap.h"
 
 class GlobalData;
 
@@ -25,30 +27,32 @@ typedef list<PCell>::iterator MatData;
 class GetOTURepCommand : public Command {
 	
 public:
-	GetOTURepCommand();	
+	GetOTURepCommand(string);	
 	~GetOTURepCommand();
-	int execute();	
+	int execute();
+	void help();	
 	
 private:
 	GlobalData* globaldata;
 	SparseMatrix* matrix;
 	ListVector* list;
-	ListVector* listOfNames;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	InputData* input;
 	FastaMap* fasta;
-	string filename, fastafile, namesfile;
+	GroupMap* groupMap;
+	string filename, fastafile, listfile, namesfile, groupfile, line, label;
 	ofstream out;
 	ifstream in, inNames;
+	bool groupError;
 	
-	 
+	bool abort, allLines;
+	set<int> lines; //hold lines to be used
+	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();
-	string FindRep(int); // returns name of "representative" sequence of given bin.
+	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
 
 };