fixes while testing 1.33.0

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index d17574f57a8b33e3a0625ae056d604859736e036..7242342cdcdf455d2861f230fc65c039fd00bd6c 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -24,21 +24,26 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "get.sabund";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
        
+       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);
 
 };