changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 972f30e8e0e008111d14bc49670dc926a98d360f..c6d65037516c495f391ceb983273b1b9a20010e1 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,30 +9,38 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
 #include "inputdata.h"
-
-/* The read.otu command parameter options are listfile, sabundfile, rabundfile and orderfile.  
-The read.otu command should be in the following format: 
-read.otu(listfile=yourListFile, orderfile=yourOrderFile). The listfile, sabundfile or rabundfile are required, but only one may be used. */
-
-class GlobalData;
+#include "groupmap.h"
+#include "sharedcommand.h"
 
 class ReadOtuCommand : public Command {
 public:
+       ReadOtuCommand(string);
        ReadOtuCommand();
-       ~ReadOtuCommand();
-       int execute();
+       ~ReadOtuCommand() {}
+       
+       vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+       string getCommandName()                 { return "read.otu";    }
+       string getCommandCategory()             { return "Hidden";      }
+       string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }   
+       string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
+       string getDescription()         { return "read.otu"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
-       ReadMatrix* read;
        InputData* input;
-       string filename;
+       Command* shared;
+       GroupMap* groupMap;
+       string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+
 };
 
-#endif
\ No newline at end of file
+#endif