X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.h;h=fd7a6b07fecf135262e310598a3936221cb98826;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=dd0cefc89457cb114596c988c35b6be59c650547;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getrabundcommand.h b/getrabundcommand.h
index dd0cefc..fd7a6b0 100644
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -25,7 +25,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.rabund";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+	string getDescription()		{ return "creates a rabund file"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -33,17 +38,16 @@ public:
 	
 private:
 	
-	string filename, listfile, sabundfile, inputfile, format, outputDir;
+	string filename, listfile, sabundfile, inputfile, format, outputDir, countfile;
 	ofstream out;
-	InputData* input;
-	RAbundVector* rabund;
 	vector<string> outputNames;
 
 	bool abort, allLines, sorted;
 	set<string> labels; //holds labels to be used
 	string label;
 
-	
+	int processList(ofstream& out);
+    int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
 };
 
 #endif