added groups option to get.oturep command

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 86c5434034aae9c7900428bb8ff323385f89b837..8099a3998c1a63de92d9c72b2c5419c08e2f96ff 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -53,13 +53,13 @@ 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;
+       vector<string> outputNames, Groups;
        map<string, string> outputNameFiles;
        float cutoff;
        int precision;
@@ -70,7 +70,7 @@ private:
        void readNamesFile();
        int process(ListVector*);
        SeqMap getMap(int);
-       string findRep(int, ListVector*);       // returns the name of the "representative" sequence of 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);