X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=splitgroupscommand.h;h=ec22b8fedaec8752dd1b9161c6476b0223fc157e;hp=c45c7ff6b386111ba34897c3e13ff213e832b79f;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/splitgroupscommand.h b/splitgroupscommand.h
index c45c7ff..ec22b8f 100644
--- a/splitgroupscommand.h
+++ b/splitgroupscommand.h
@@ -25,28 +25,30 @@ class SplitGroupCommand : public Command {
 public:
 	SplitGroupCommand(string);	
 	SplitGroupCommand();
-	~SplitGroupCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~SplitGroupCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "split.groups";				}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
+	string getDescription()		{ return "split a name or fasta file by group"; }
 
 	
-private:
-	int readNames(); 
-	int splitFasta(); 
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
+private:
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
-	map<string, vector<string> > nameMap;
-	map<string, vector<string> >::iterator itNames;
-	GroupMap* groupMap;
-	
-	string outputDir, namefile, groupfile, groups, fastafile;
+		
+	string outputDir, namefile, groupfile, countfile, groups, fastafile;
 	vector<string> Groups;
 	bool abort;
+    
+    int runNameGroup();
+    int runCount();
 };
 
 /***************************************************************************************/