made get.oturep more memory efficient by breaking the work into 2 pieces.

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 7890d93db045be399a2854d5d17b314fb748358d..86c5434034aae9c7900428bb8ff323385f89b837 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -60,6 +60,7 @@ private:
        set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
        vector<string> outputNames;
+       map<string, string> outputNameFiles;
        float cutoff;
        int precision;
        vector<SeqMap> seqVec;                  // contains maps with sequence index and distance
@@ -69,9 +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(int, ListVector*);       // returns the name of the "representative" sequence of given bin
+       int processNames(string, string);
+                                                                                               
 
 };