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[mothur.git] / sharedcommand.h

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+#ifndef SHAREDCOMMAND_H
+#define SHAREDCOMMAND_H
+/*
+ *  sharedcommand.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "sharedlistvector.h"
+#include "inputdata.h"
+
+/* The shared() command:
+       The shared command can only be executed after a successful read.shared command.  
+       The shared command parses a .list file and separates it into groups.  
+       It outputs a .shared file containing the OTU information for each group.  
+       There are no shared command parameters.  The shared command should be in the following format: shared(). */
+
+
+class SharedCommand : public Command {
+       
+public:
+       SharedCommand(string);  
+       SharedCommand();
+       ~SharedCommand();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       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*>, ofstream&);
+       int createMisMatchFile(SharedListVector*, GroupMap*);
+       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, ifstream&, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
+       
+       vector<string> Groups, outputNames, order;
+       set<string> labels;
+       string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
+       bool firsttime, pickedGroups, abort, allLines;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
+
+};
+
+#endif