X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.h;h=c746e144119dc4d4c0d45ef10872b1f7c9951129;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=6716903105f2fc25d018b77d977d6fa57875a148;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 6716903..c746e14 100644
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -28,8 +28,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "sub.sample";	}
 	string getCommandCategory()		{ return "General";		}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
-	
+	string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
+	string getDescription()		{ return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -43,13 +46,12 @@ private:
 	vector<string> names;
 	map<string, vector<string> > nameMap;
 	
-	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
 	int getSubSampleShared();
 	int getSubSampleList();
 	int getSubSampleRabund();
 	int getSubSampleSabund();
 	int getSubSampleFasta();
-	int processShared(vector<SharedRAbundVector*>&, ofstream&);
+	int processShared(vector<SharedRAbundVector*>&);
 	int processRabund(RAbundVector*&, ofstream&);
 	int processSabund(SAbundVector*&, ofstream&);
 	int processList(ListVector*&, ofstream&, set<string>&);