modified bin.seqs and get.oturep commands to include use of a groupfile if provided...

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 706b219917eb89c99652b8e024421869eac123c1..deafc78c5512edc5039a0425910aaa979eb8f639 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -18,7 +18,7 @@
 #include "inputdata.h"
 #include "readotu.h"
 #include "fastamap.h"
-
+#include "groupmap.h"
 
 class GlobalData;
 
@@ -39,9 +39,11 @@ private:
        ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
-       string filename, fastafile, namesfile;
+       GroupMap* groupMap;
+       string filename, fastafile, namesfile, groupfile;
        ofstream out;
        ifstream in, inNames;
+       bool groupError;
        
         
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
@@ -50,7 +52,7 @@ private:
        map<string, int>::iterator it3;
        
        void readNamesFile();
-       string FindRep(int); // returns name of "representative" sequence of given bin.
+       string FindRep(int, string&); // returns name of "representative" sequence of given bin. //and fill a string containing the groups in that bin if a groupfile is given
 
 };