changing command name classify.shared to classifyrf.shared

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 399f3d3966bf828ec32cd790dd0d7d14c7e08c25..39ef9a7a1ebc17f830103cf33d84520aca975f97 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "readotu.h"
 
 /* The shared() command:
        The shared command can only be executed after a successful read.shared command.  
@@ -21,31 +20,42 @@
        There are no shared command parameters.  The shared command should be in the following format: shared(). */
 
 
-class GlobalData;
-
 class SharedCommand : public Command {
        
 public:
        SharedCommand(string);  
+       SharedCommand();
        ~SharedCommand();
-       int execute();  
-       void help() {}
+       
+       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(vector<SharedRAbundVector*>);
-       int createMisMatchFile();
+       void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+       int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup(string);
+    int createSharedFromBiom(string);
+    string getTag(string&);
+    vector<string> readRows(string, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
-       SharedListVector* SharedList;
-       InputData* input;
-       GroupMap* groupMap;
-       vector<string> groups, outputNames;
-       ofstream out;
-       string filename, fileroot, outputDir;
-       bool firsttime, pickedGroups;
+       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;