X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removegroupscommand.h;h=c6e9d645c9f7fff26e2c23c634b6264a4614e01b;hp=daf2066feade74af3239e12f3a48a7b314de0a4c;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/removegroupscommand.h b/removegroupscommand.h
index daf2066..c6e9d64 100644
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -25,9 +25,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "remove.groups";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
-	string getDescription()		{ return "removes sequences from a list, fasta, name, group or taxonomy file from a given group or set of 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()); }	
@@ -35,18 +37,24 @@ public:
 	
 private:
 	set<string> names;
-	string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+	string accnosfile, fastafile, namefile, groupfile, countfile, 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 readCount();
 	int readList();
 	int readTax();
 	int fillNames();
+    int readDesign();
 	
 };