finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 972f30e8e0e008111d14bc49670dc926a98d360f..69741581b7caa06066b8900e1ba712cb23900d8c 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -15,10 +15,22 @@
 #include "command.hpp"
 #include "readmatrix.hpp"
 #include "inputdata.h"
+#include "groupmap.h"
+#include "sharedcommand.h"
+#include "parselistcommand.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;
 
@@ -32,6 +44,9 @@ private:
        GlobalData* globaldata;
        ReadMatrix* read;
        InputData* input;
+       Command* shared;
+       Command* parselist;
+       GroupMap* groupMap;
        string filename;
 };