modified read.otu and shared command

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 972f30e8e0e008111d14bc49670dc926a98d360f..6ec35412c3c82206bef933787c820ca36e2158d2 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,30 +9,46 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "inputdata.h"
+#include "groupmap.h"
+#include "sharedcommand.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. */
+/* The read.otu must be run before you execute a collect.single, rarefaction.single, summary.single, 
+collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund 
+upon completion of the cluster command or you may use your own. The read.otu command parameter options are 
+listfile, rabundfile, sabundfile, groupfile and orderfile. The reaad.otu command can be used in two ways. 
+The first is to read a listfile, rabundfile or sabundfile and run the collect.single, rarefaction.single or summary.single. 
+For this use the read.otu command should be in the following format: read.otu(listfile=yourListFile, orderfile=yourOrderFile). 
+The listfile, rabundfile or sabundfile parameter is required, but you may only use one of them. 
+The second way to use the read.otu command is to read a listfile and a groupfile so you can use the collect.shared, 
+rarefaction.shared or summary.shared commands. In this case the read.otu command should be in the following format: 
+read.otu(listfile=yourListFile, groupfile=yourGroupFile). The listfile parameter and groupfile paramaters are required. 
+When using the command the second way read.otu command parses the .list file and separates it into groups. 
+It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. */
 
 class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-       ReadOtuCommand();
+       ReadOtuCommand(string);
        ~ReadOtuCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       //ReadOTUFile* read;
        InputData* input;
-       string filename;
+       Command* shared;
+       GroupMap* groupMap;
+       string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+
 };
 
-#endif
\ No newline at end of file
+#endif