X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.h;h=7b251eee11c2fa7ad5be7baa6cea4427c90265c7;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=b70050653fd5ded5a9b25b555efea08ae79b9565;hpb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;p=mothur.git

diff --git a/subsamplecommand.h b/subsamplecommand.h
index b700506..7b251ee 100644
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -11,11 +11,12 @@
  */
  
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "sharedrabundvector.h"
 #include "listvector.hpp"
 #include "rabundvector.hpp"
 #include "inputdata.h"
+#include "sequence.hpp"
+#include "counttable.h"
 
 
 class SubSampleCommand : public Command {
@@ -23,39 +24,43 @@ class SubSampleCommand : public Command {
 public:
 	SubSampleCommand(string);
 	SubSampleCommand();
-	~SubSampleCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~SubSampleCommand() {}
 	
-private:
-	GlobalData* globaldata;
+	vector<string> setParameters();
+	string getCommandName()			{ return "sub.sample";	}
+	string getCommandCategory()		{ return "Sequence Processing";		}
 	
-	bool abort, pickedGroups, allLines;
-	string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
+	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, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile, taxonomyfile;
 	set<string> labels; //holds labels to be used
 	string groups, label, outputDir;
 	vector<string> Groups, outputNames;
-	map<string, vector<string> > outputTypes;
 	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>&);
 	
 };