X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.h;h=80230b49b9872ab4633dbd2d4120826b3cc1ee82;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=642107dafc9d567aa93270195740030d33698e52;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 642107d..80230b4 100644
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -25,9 +25,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.groups";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	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 +37,10 @@ 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;
@@ -44,10 +48,11 @@ private:
 	int readFasta();
 	int readName();
 	int readGroup();
-	void readAccnos();
 	int readList();
 	int readTax();
 	int fillNames();
+	int readShared();
+    int readDesign();
 	
 };