X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;fp=getoturepcommand.h;h=7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a;hb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;hp=874e43ce5a8f45178a073b9d8e8e00fa8852deb0;hpb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 874e43c..7a17c9d 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -61,9 +61,10 @@ 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;
@@ -74,6 +75,7 @@ private:
 	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