X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupscommand.h;h=f67c36584a58a14556032ce2374bda17925c6aaa;hp=7c4c92fff02ae6f577ca92a736fb7b14711cb302;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=e3e0858c684c4608d679840024e5095ddc8e2719

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 7c4c92f..f67c365 100644
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -21,28 +21,40 @@ public:
 	GetGroupsCommand(string);	
 	GetGroupsCommand();
 	~GetGroupsCommand(){}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	
+	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()); }	
+	
 	
 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;
-	map<string, vector<string> > outputTypes;
 	GroupMap* groupMap;
 	
 	int readFasta();
 	int readName();
 	int readGroup();
-	void readAccnos();
+    int readCount();
 	int readList();
 	int readTax();
 	int fillNames();
+	int readShared();
+    int readDesign();
 	
 };