X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=8099a3998c1a63de92d9c72b2c5419c08e2f96ff;hb=a8367302932de9be5434e77f6e5829d7609e2aec;hp=ceea8988a2bc0963abaa4d18d898729d88c8960a;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index ceea898..8099a39 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -53,12 +53,14 @@ private:
 	ReadMatrix* readMatrix;
 	FormatMatrix* formatMatrix;
 	NameAssignment* nameMap;
-	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir;
+	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;
 	set<string> labels; //holds labels to be used
 	map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
+	vector<string> outputNames, Groups;
+	map<string, string> outputNameFiles;
 	float cutoff;
 	int precision;
 	vector<SeqMap> seqVec;			// contains maps with sequence index and distance
@@ -68,9 +70,9 @@ private:
 	void readNamesFile();
 	int process(ListVector*);
 	SeqMap getMap(int);
-	string findRep(int, string&, ListVector*, int&); 	// returns the name of the "representative" sequence of given bin, 
-									// fills a string containing the groups in that bin if a groupfile is given,
-									// and returns the number of sequences in the given bin
+	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);
+												
 
 };