X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mergegroupscommand.h;h=3e3d337ffa0309f5132d2d88cc3b4c0b81684869;hp=62839ec1a1dc80a3b77a7aad8666f35262f663b3;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=f598bd8389840cf030d61f5da7d0b2c3e37c06ba

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 62839ec..3e3d337 100644
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -14,33 +14,38 @@
 #include "inputdata.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 class MergeGroupsCommand : public Command {
 	
 public:
 	MergeGroupsCommand(string);
 	MergeGroupsCommand();
-	~MergeGroupsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~MergeGroupsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "merge.groups";	}
+	string getCommandCategory()		{ return "General";			}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
+	string getDescription()		{ return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	GroupMap* designMap;
 	vector<SharedRAbundVector*> lookup;
-	map<string, vector<string> > outputTypes;
 	
 	bool abort, allLines, pickedGroups;
 	set<string> labels; //holds labels to be used
-	string groups, label, outputDir, inputDir, designfile, sharedfile;
+	string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
 	vector<string> Groups, outputNames;
 		
 	int process(vector<SharedRAbundVector*>&, ofstream&);
+	int processSharedFile(GroupMap*&);
+	int processGroupFile(GroupMap*&);
 };
 
 #endif