X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.h;h=24062bab3614fb3fc7ee803b3272c4242cdf68bd;hb=ecd4f324189cf1cb49a3eb49d5cff58562f27b7f;hp=955d94d5090b5fc6caf4ba2a937261a173a3eb91;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 955d94d..24062ba 100644
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -26,6 +26,8 @@ public:
 	string getCommandName()			{ return "remove.groups";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
 	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
+	string getDescription()		{ return "removes sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -33,18 +35,24 @@ public:
 	
 private:
 	set<string> names;
-	string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+	string accnosfile, fastafile, namefile, groupfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
 	bool abort;
 	vector<string> outputNames, Groups;
 	GroupMap* groupMap;
+	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
+	
 	
 	int readFasta();
+	int readShared();
 	int readName();
 	int readGroup();
 	void readAccnos();
 	int readList();
 	int readTax();
 	int fillNames();
+    int readDesign();
 	
 };