X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getsabundcommand.h;h=7242342cdcdf455d2861f230fc65c039fd00bd6c;hp=da998f563ba4f9b5a1726f821a8e96dfbfa6209a;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/getsabundcommand.h b/getsabundcommand.h
index da998f5..7242342 100644
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -24,22 +24,26 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.sabund";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
-	
+	string getDescription()		{ return "creates a sabund file"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	string filename, format, inputfile, listfile, rabundfile, outputDir;
+	string filename, format, inputfile, listfile, rabundfile, outputDir, countfile;
 	ofstream out;
-	InputData* input;
-	SAbundVector* sabund;
 	vector<string> outputNames;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
 	string label;
+    
+    int processList(ofstream& out);
+    int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
 
 };