X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=1100c3d30afc344119538e89e7c40a8dfa839578;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=861632ce7d6a8026c14b463387b9d8dbb320522d;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 861632c..1100c3d 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,6 +30,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "make.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
 	string getDescription()		{ return "make a shared file from a list and group file"; }
@@ -38,20 +39,22 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void printSharedData(vector<SharedRAbundVector*>);
-	int createMisMatchFile();
+	void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+	int createMisMatchFile(SharedListVector*, GroupMap*);
 	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
 	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-	int ListGroupSameSeqs();
+	int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup(string);
+    int createSharedFromBiom(string);
+    string getTag(string&);
+    vector<string> readRows(string, ifstream&, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, ifstream&, 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;
 	bool firsttime, pickedGroups, abort, allLines;
 	map<string, ofstream*> filehandles;
 	map<string, ofstream*>::iterator it3;