fixes while testing 1.33.0

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index 27d25c2f2c3d2739bb6cfecd85f7b059b4867442..7242342cdcdf455d2861f230fc65c039fd00bd6c 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -13,26 +13,38 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
-class GlobalData;
-
 class GetSAbundCommand : public Command {
 public:
+       GetSAbundCommand(string);
        GetSAbundCommand();
-       ~GetSAbundCommand();
-       int execute();
+       ~GetSAbundCommand() {}
+       
+       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:
-       GlobalData* globaldata;
-       string filename, format;
+       string filename, format, inputfile, listfile, rabundfile, outputDir, countfile;
        ofstream out;
-       ReadOTUFile* read;
-       OrderVector* order;
-       OrderVector* lastOrder;
-       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);
+
 };
 
 #endif