fixes while testing 1.33.0

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index b3b3e6f5d0381d2354d8113012b13251cdbec7e7..a916c854280c74d035968bfc84ec4ab88a4f70e6 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,14 +9,9 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readmatrix.hpp"
 
 /* The shared() command:
        The shared command can only be executed after a successful read.shared command.  
@@ -25,25 +20,44 @@
        There are no shared command parameters.  The shared command should be in the following format: shared(). */
 
 
-class GlobalData;
-
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
+       SharedCommand();
        ~SharedCommand();
-       int execute();  
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
+       string getDescription()         { return "make a shared file from a list and group file"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void printSharedData();
-       GlobalData* globaldata;
-       ReadMatrix* read;
-       SharedListVector* SharedList;
-       InputData* input;
-       Shared* shared;
-       map<string, SharedRAbundVector*>::iterator it;
-       ofstream out;
-       string filename;
+       void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+       int readOrderFile();
+       bool isValidGroup(string, vector<string>);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup();
+    int createSharedFromBiom();
+    string getTag(string&);
+    vector<string> readRows(string, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
+       
+       vector<string> Groups, outputNames, order;
+       set<string> labels;
+       string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
+       bool firsttime, pickedGroups, abort, allLines;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
 
 };