X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=58fec8d4f3e3aaaf148a9ff8455c4fba93c6b35f;hb=f27b66ce6415eb14c434f9850019c7cf140e023e;hp=4f755d0fccfe68dd1e03b5b36d57ce4b76287df9;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 4f755d0..58fec8d 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -13,7 +13,6 @@
 
 #include "command.hpp"
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
 #include "readotu.h"
@@ -23,6 +22,17 @@
 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:
@@ -33,26 +43,18 @@ public:
 
 private:
 	GlobalData* globaldata;
-	SparseMatrix* matrix;
 	ListVector* list;
 	ReadOTUFile* read;
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, listfile, namesfile, groupfile, line, label;
+	string filename, fastafile, listfile, namesfile, groupfile, label, sorted, phylipfile, columnfile, namefile;
 	ofstream out;
 	ifstream in, inNames;
-	bool groupError;
-
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	bool abort, allLines, groupError;
 	set<string> labels; //holds labels to be used
 	map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
 
-	vector<SeqMap> seqVec;			// contains maps with sequence index and distance
-									// for all distances related to a certain sequence
-
-
 	void readNamesFile();
 	int process(ListVector*);
 	string findRep(int, string&, ListVector*, int&); 	// returns the name of the "representative" sequence of given bin,