X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.h;h=7b251eee11c2fa7ad5be7baa6cea4427c90265c7;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=98085ee9d02cd163e8d9ed76022f5a0c2ee59fea;hpb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;p=mothur.git

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 98085ee..7b251ee 100644
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -11,42 +11,57 @@
  */
  
 #include "command.hpp"
-#include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
+#include "listvector.hpp"
+#include "rabundvector.hpp"
+#include "inputdata.h"
+#include "sequence.hpp"
+#include "counttable.h"
 
-class GlobalData;
 
 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;
-	ReadOTUFile* read;
-	InputData* input;
-	vector<SharedRAbundVector*> lookup;
-	ListVector* list;
-	RAbundVector* rabund;
-	SAbundVector* sabund;
+	vector<string> setParameters();
+	string getCommandName()			{ return "sub.sample";	}
+	string getCommandCategory()		{ return "Sequence Processing";		}
 	
-	bool abort, allLines, pickedGroups;
+	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 getSubSampleShared();
+	int getSubSampleList();
+	int getSubSampleRabund();
+	int getSubSampleSabund();
+	int getSubSampleFasta();
+	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>&);
 	
-	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-	int getSubSampleShared(vector<SharedRAbundVector*>&, ofstream&);
 };
 
 #endif