fixed indicator command bug

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 874e43ce5a8f45178a073b9d8e8e00fa8852deb0..7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a 100644 (file)
--- 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