X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.h;h=84abc85d46e0bc3fddd916a0095c4b45aa44dbd1;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=5ecc7ab13205d4f34d7c496a6b2cc3221615eafe;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/parselistscommand.h b/parselistscommand.h
index 5ecc7ab..84abc85 100644
--- a/parselistscommand.h
+++ b/parselistscommand.h
@@ -21,27 +21,32 @@ class ParseListCommand : public Command {
 public:
 	ParseListCommand(string);
 	ParseListCommand();	
-	~ParseListCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~ParseListCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "parse.list";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
+	string getDescription()		{ return "parses a list file by group"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	int parse(ListVector*);
 		
 	ListVector* list;
 	GroupMap* groupMap;
-	InputData* input;
+    CountTable ct;
 	
 	ofstream out;
-	string outputDir, listfile, groupfile, label;
+	string outputDir, listfile, groupfile, label, countfile;
 	set<string> labels;
 	bool abort, allLines;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	map<string, ofstream*> filehandles;
 	map<string, ofstream*>::iterator it3;