X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.h;h=e0fbad80064157e99c3ff21fb97ddfd95bc97317;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=642107dafc9d567aa93270195740030d33698e52;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 642107d..e0fbad8 100644
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -36,7 +36,10 @@ public:
 	
 private:
 	set<string> names;
-	string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+	map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+										   //then the other files need to change the unique name in their file to match.
+										   //only add the names that need to be changed to keep the map search quick
+	string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
 	bool abort;
 	vector<string> outputNames, Groups;
 	GroupMap* groupMap;
@@ -48,6 +51,7 @@ private:
 	int readList();
 	int readTax();
 	int fillNames();
+	int readShared();
 	
 };