X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=splitabundcommand.h;h=9929b7967050308c2563561896fa615a6f371d12;hp=02d61f3dc3b7f343a9e0d9a73bb71e84fcdacbbd;hb=615301e57c25e241356a9c2380648d117709458d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/splitabundcommand.h b/splitabundcommand.h
index 02d61f3..9929b79 100644
--- a/splitabundcommand.h
+++ b/splitabundcommand.h
@@ -21,6 +21,8 @@ also allow an option where a user can give a group file with the list or names f
 #include "groupmap.h"
 #include "inputdata.h"
 #include "listvector.hpp"
+#include "sequence.hpp"
+#include "counttable.h"
 
 /***************************************************************************************/
 
@@ -30,37 +32,41 @@ public:
 	SplitAbundCommand(string);	
 	SplitAbundCommand();
 	~SplitAbundCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
-
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "split.abund";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Split.abund"; }
+	string getDescription()		{ return "split a list, name, group or fasta file based on abundance"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	int splitList(ListVector*);
 	int splitNames(); //namefile
 	int writeNames(); 
-	int writeList(ListVector*); 
+	int writeList(ListVector*, string, int); 
 	int writeAccnos(string); 
 	int parseGroup(string); 
 	int parseFasta(string); 
+    int parseCount(string);
+    int splitCount();
 	int readNamesFile(); //namefile
 	int createNameMap(ListVector*);
 	
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
-	ListVector* list;
-	GroupMap* groupMap;
-	InputData* input;
+    GroupMap groupMap;
+    CountTable ct;
 	
-	string outputDir, listfile, namefile, groupfile, label, groups, fastafile, inputFile;
+	string outputDir, listfile, namefile, groupfile, countfile, label, groups, fastafile, inputFile;
 	set<string> labels, rareNames, abundNames;
 	vector<string> Groups;
 	bool abort, allLines, accnos;
 	int cutoff;
-	//map<string, bool> wroteListFile;
 	map<string, string> nameMap;