changes while testing

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index cb9e270d170e0ab9dde910fdb7d24ef6c293828f..fd7a6b07fecf135262e310598a3936221cb98826 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -25,7 +25,9 @@ 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"; }
 
@@ -36,17 +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