X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getrabundcommand.h;h=fd7a6b07fecf135262e310598a3936221cb98826;hp=7e9363080e7bf7b794b3797c37df9527d8f84764;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 7e93630..fd7a6b0 100644
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.rabund";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
 	string getDescription()		{ return "creates a rabund file"; }
 
@@ -37,17 +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