X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupscommand.h;h=f67c36584a58a14556032ce2374bda17925c6aaa;hp=955de627ccb6f4952c6ed3a1444ee2b4d5397187;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 955de62..f67c365 100644
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -25,7 +25,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.groups";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.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(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -33,7 +38,10 @@ 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, countfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
 	bool abort;
 	vector<string> outputNames, Groups;
 	GroupMap* groupMap;
@@ -41,10 +49,12 @@ private:
 	int readFasta();
 	int readName();
 	int readGroup();
-	void readAccnos();
+    int readCount();
 	int readList();
 	int readTax();
 	int fillNames();
+	int readShared();
+    int readDesign();
 	
 };