X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedcommand.h;h=a916c854280c74d035968bfc84ec4ab88a4f70e6;hp=f1e7c48cd71ee7ff1984e43cb7bb5676a3ee42a5;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/sharedcommand.h b/sharedcommand.h
index f1e7c48..a916c85 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,25 +30,31 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "make.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getHelpString();	
 	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
+	string getDescription()		{ return "make a shared file from a list and group file"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void printSharedData(vector<SharedRAbundVector*>);
-	int createMisMatchFile();
+	void printSharedData(vector<SharedRAbundVector*>, ofstream&);
 	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
 	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup();
+    int createSharedFromBiom();
+    string getTag(string&);
+    vector<string> readRows(string, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
 	
-	SharedListVector* SharedList;
-	InputData* input;
-	GroupMap* groupMap;
 	vector<string> Groups, outputNames, order;
 	set<string> labels;
-	ofstream out;
-	string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+	string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
 	bool firsttime, pickedGroups, abort, allLines;
 	map<string, ofstream*> filehandles;
 	map<string, ofstream*>::iterator it3;