X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.h;h=224f4f07ea1c45d3e734d8f6406e8a17f40fd1fd;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=642107dafc9d567aa93270195740030d33698e52;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 642107d..224f4f0 100644
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -27,7 +27,7 @@ public:
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
-	string getDescription()		{ return "gets sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+	string getDescription()		{ return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
 
 	
 	int execute(); 
@@ -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, designfile, taxfile, outputDir, groups, sharedfile;
 	bool abort;
 	vector<string> outputNames, Groups;
 	GroupMap* groupMap;
@@ -48,6 +51,8 @@ private:
 	int readList();
 	int readTax();
 	int fillNames();
+	int readShared();
+    int readDesign();
 	
 };