X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=splitabundcommand.h;h=9929b7967050308c2563561896fa615a6f371d12;hp=8d2ab2e0503416a9e9e48fb49162a63e794c0191;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=cfe70bbc94980a0177af465d3464db754673bd56

diff --git a/splitabundcommand.h b/splitabundcommand.h
index 8d2ab2e..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"
 
 /***************************************************************************************/
 
@@ -28,24 +30,44 @@ class SplitAbundCommand : public Command {
 	
 public:
 	SplitAbundCommand(string);	
+	SplitAbundCommand();
 	~SplitAbundCommand();
-	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 split(ListVector*);
-	int split(); //namefile
+	int splitList(ListVector*);
+	int splitNames(); //namefile
+	int writeNames(); 
+	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;
-	ListVector* list;
-	GroupMap* groupMap;
-	InputData* input;
+    GroupMap groupMap;
+    CountTable ct;
 	
-	string outputDir, listfile, namefile, groupfile, label;
-	set<string> labels;
-	bool abort, allLines, accnos, wroteRareList, wroteAbundList;
+	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, string> nameMap;