X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.h;h=7b251eee11c2fa7ad5be7baa6cea4427c90265c7;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=5656dab49e7ac7d58665369e58c1950c17b93542;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 5656dab..7b251ee 100644
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -16,6 +16,7 @@
 #include "rabundvector.hpp"
 #include "inputdata.h"
 #include "sequence.hpp"
+#include "counttable.h"
 
 
 class SubSampleCommand : public Command {
@@ -27,35 +28,39 @@ public:
 	
 	vector<string> setParameters();
 	string getCommandName()			{ return "sub.sample";	}
-	string getCommandCategory()		{ return "General";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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()); }	
 	
 private:	
 	bool abort, pickedGroups, allLines, persample;
-	string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
+	string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile, taxonomyfile;
 	set<string> labels; //holds labels to be used
 	string groups, label, outputDir;
 	vector<string> Groups, outputNames;
 	int size;
 	vector<string> names;
 	map<string, vector<string> > nameMap;
+    CountTable ct;
 	
-	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>&);
 	int getNames();
 	int readNames();
+    int getTax(set<string>&);
 	
 };